9WTC | pdb_00009wtc

Crystal structure of a selenate-soaked multiheme cytochrome c selenoprotein mutant (MccSep U325A)

PDB DOI: https://doi.org/10.2210/pdb9WTC/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Geobacter sulfurreducens PCA
Expression System: Geobacter sulfurreducens PCA
Mutation(s): No

Deposited: 2025-09-16 Released: 2026-07-22
Deposition Author(s): Mihara, H., Yoshizawa, T., Izu, Y., Inoue, M., Aono, R., Zhang, W., Shibamoto, N., Tobe, R., Kurihara, T., Matsumura, H.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.214 (Depositor), 0.211 (DCC)
R-Value Work:
0.168 (Depositor), 0.166 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Multiheme selenoenzyme essential for elemental sulfur respiration

Mihara, H., Yoshizawa, T., Izu, Y., Inoue, M., Aono, R., Zhang, W., Shibamoto, N., Tobe, R., Kurihara, T., Matsumura, H.

To be published.

Macromolecule Content

Total Structure Weight: 214.55 kDa
Atom Count: 15,244
Modeled Residue Count: 1,688
Deposited Residue Count: 1,800
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c,Multiheme cytochrome c selenoprotein (MccSep)	A, B, C, D	450	Geobacter sulfurreducens PCA	Mutation(s): 0 Gene Names: GSU2937, GSU2936
UniProt
Find proteins for Q748R4 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q748R4 Go to UniProtKB: Q748R4
Find proteins for Q748R5 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q748R5 Go to UniProtKB: Q748R5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q748R5 Q748R4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC (Subject of Investigation/LOI) Query on HEC Download:Ideal Coordinates CCD File SDF format, chain DB [auth D] SDF format, chain E [auth A] SDF format, chain EB [auth D] SDF format, chain F [auth A] SDF format, chain FB [auth D] SDF format, chain G [auth A] SDF format, chain GB [auth D] SDF format, chain H [auth A] SDF format, chain HB [auth D] SDF format, chain I [auth A] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain E [auth A] MOL2 format, chain EB [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FB [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain I [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain E [auth A] mmCIF format, chain EB [auth D] mmCIF format, chain F [auth A] mmCIF format, chain FB [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HB [auth D] mmCIF format, chain I [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	DB [auth D] E [auth A] EB [auth D] F [auth A] FB [auth D] DB [auth D], E [auth A], EB [auth D], F [auth A], FB [auth D], G [auth A], GB [auth D], H [auth A], HB [auth D], I [auth A], MA [auth C], NA [auth C], OA [auth C], PA [auth C], QA [auth C], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain DB [auth D] Focus chain E [auth A] Focus chain EB [auth D] Focus chain F [auth A] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HB [auth D] Focus chain I [auth A] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain DB [auth D] Focus chain E [auth A] Focus chain EB [auth D] Focus chain F [auth A] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HB [auth D] Focus chain I [auth A] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain Y [auth B]	Y [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain Y [auth B] Interactions & Density Focus chain Y [auth B]
SE4 (Subject of Investigation/LOI) Query on SE4 Download:Ideal Coordinates CCD File SDF format, chain IB [auth D] SDF format, chain J [auth A] SDF format, chain RA [auth C] SDF format, chain X [auth B] MOL2 format, chain IB [auth D] MOL2 format, chain J [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain X [auth B] mmCIF format, chain IB [auth D] mmCIF format, chain J [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain X [auth B]	IB [auth D], J [auth A], RA [auth C], X [auth B]	SELENATE ION O₄ Se QYHFIVBSNOWOCQ-UHFFFAOYSA-L		Interactions Focus chain IB [auth D] Focus chain J [auth A] Focus chain RA [auth C] Focus chain X [auth B] Interactions & Density Focus chain IB [auth D] Focus chain J [auth A] Focus chain RA [auth C] Focus chain X [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth C] SDF format, chain BA [auth B] SDF format, chain BB [auth D] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain JB [auth D] SDF format, chain K [auth A] SDF format, chain KB [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain LB [auth D] SDF format, chain M [auth A] SDF format, chain MB [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OB [auth D] SDF format, chain P [auth A] SDF format, chain PB [auth D] SDF format, chain Q [auth A] SDF format, chain QB [auth D] SDF format, chain R [auth A] SDF format, chain RB [auth D] SDF format, chain SA [auth C] SDF format, chain SB [auth D] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain Z [auth B] SDF format, chain ZA [auth C] SDF format, chain YA [auth C] SDF format, chain UA [auth C] SDF format, chain TA [auth C] SDF format, chain NB [auth D] SDF format, chain KA [auth B] SDF format, chain CB [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain LB [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RB [auth D] MOL2 format, chain SA [auth C] MOL2 format, chain SB [auth D] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain NB [auth D] MOL2 format, chain KA [auth B] MOL2 format, chain CB [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KB [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain LB [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MB [auth D] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OB [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PB [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain QB [auth D] mmCIF format, chain R [auth A] mmCIF format, chain RB [auth D] mmCIF format, chain SA [auth C] mmCIF format, chain SB [auth D] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain NB [auth D] mmCIF format, chain KA [auth B] mmCIF format, chain CB [auth D]	AA [auth B] AB [auth C] BA [auth B] BB [auth D] CA [auth B] AA [auth B], AB [auth C], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], JB [auth D], K [auth A], KA [auth B], KB [auth D], L [auth A], LA [auth C], LB [auth D], M [auth A], MB [auth D], N [auth A], NB [auth D], O [auth A], OB [auth D], P [auth A], PB [auth D], Q [auth A], QB [auth D], R [auth A], RB [auth D], SA [auth C], SB [auth D], TA [auth C], UA [auth C], VA [auth C], WA [auth C], XA [auth C], YA [auth C], Z [auth B], ZA [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LA [auth C] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MB [auth D] Focus chain N [auth A] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RB [auth D] Focus chain SA [auth C] Focus chain SB [auth D] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LA [auth C] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MB [auth D] Focus chain N [auth A] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RB [auth D] Focus chain SA [auth C] Focus chain SB [auth D] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A, B, C, D	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.214 (Depositor), 0.211 (DCC)
R-Value Work: 0.168 (Depositor), 0.166 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.39	α = 90
b = 123.62	β = 91.6
c = 116.64	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	24K01994
Japan Society for the Promotion of Science (JSPS)	Japan	23K18033
Japan Society for the Promotion of Science (JSPS)	Japan	25H02292