2FRV | pdb_00002frv

CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE

PDB DOI: https://doi.org/10.2210/pdb2FRV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Megalodesulfovibrio gigas
Mutation(s): No

Deposited: 1997-06-10 Released: 1998-06-17
Deposition Author(s): Volbeda, A., Frey, M., Fontecilla-Camps, J.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free:
0.219 (Depositor)
R-Value Work:
0.201 (Depositor)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structure of the [Nife] Hydrogenase Active Site: Evidence for Biologically Uncommon Fe Ligands

Volbeda, A., Garcin, E., Piras, C., De Lacey, A.L., Fernandez, V.M., Hatchikian, E.C., Frey, M., Fontecilla-Camps, J.C.

(1996) J Am Chem Soc 118: 12989

Macromolecule Content

Total Structure Weight: 534.94 kDa
Atom Count: 38,040
Modeled Residue Count: 4,746
Deposited Residue Count: 4,800
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIPLASMIC HYDROGENASE	A [auth S] C [auth A] E [auth C] G [auth E] I [auth G] A [auth S], C [auth A], E [auth C], G [auth E], I [auth G], K [auth I]	264	Megalodesulfovibrio gigas	Mutation(s): 0 EC: 1.18.99.1 (PDB Primary Data), 1.12.2.1 (UniProt)
UniProt
Find proteins for P12943 (Megalodesulfovibrio gigas) Explore P12943 Go to UniProtKB: P12943
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12943
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIPLASMIC HYDROGENASE	B [auth L] D [auth B] F [auth D] H [auth F] J [auth H] B [auth L], D [auth B], F [auth D], H [auth F], J [auth H], L [auth J]	536	Megalodesulfovibrio gigas	Mutation(s): 0 EC: 1.18.99.1 (PDB Primary Data), 1.12.2.1 (UniProt)
UniProt
Find proteins for P12944 (Megalodesulfovibrio gigas) Explore P12944 Go to UniProtKB: P12944
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12944
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain JA [auth E] SDF format, chain O [auth S] SDF format, chain T [auth A] SDF format, chain XA [auth I] SDF format, chain VA [auth I] SDF format, chain V [auth A] SDF format, chain QA [auth G] SDF format, chain OA [auth G] SDF format, chain M [auth S] SDF format, chain HA [auth E] SDF format, chain CA [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain JA [auth E] MOL2 format, chain O [auth S] MOL2 format, chain T [auth A] MOL2 format, chain XA [auth I] MOL2 format, chain VA [auth I] MOL2 format, chain V [auth A] MOL2 format, chain QA [auth G] MOL2 format, chain OA [auth G] MOL2 format, chain M [auth S] MOL2 format, chain HA [auth E] MOL2 format, chain CA [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain JA [auth E] mmCIF format, chain O [auth S] mmCIF format, chain T [auth A] mmCIF format, chain XA [auth I] mmCIF format, chain VA [auth I] mmCIF format, chain V [auth A] mmCIF format, chain QA [auth G] mmCIF format, chain OA [auth G] mmCIF format, chain M [auth S] mmCIF format, chain HA [auth E] mmCIF format, chain CA [auth C]	AA [auth C] CA [auth C] HA [auth E] JA [auth E] M [auth S] AA [auth C], CA [auth C], HA [auth E], JA [auth E], M [auth S], O [auth S], OA [auth G], QA [auth G], T [auth A], V [auth A], VA [auth I], XA [auth I]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain CA [auth C] Focus chain HA [auth E] Focus chain JA [auth E] Focus chain M [auth S] Focus chain O [auth S] Focus chain OA [auth G] Focus chain QA [auth G] Focus chain T [auth A] Focus chain V [auth A] Focus chain VA [auth I] Focus chain XA [auth I]
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain IA [auth E] SDF format, chain N [auth S] SDF format, chain WA [auth I] SDF format, chain U [auth A] SDF format, chain PA [auth G] SDF format, chain BA [auth C] MOL2 format, chain IA [auth E] MOL2 format, chain N [auth S] MOL2 format, chain WA [auth I] MOL2 format, chain U [auth A] MOL2 format, chain PA [auth G] MOL2 format, chain BA [auth C] mmCIF format, chain IA [auth E] mmCIF format, chain N [auth S] mmCIF format, chain WA [auth I] mmCIF format, chain U [auth A] mmCIF format, chain PA [auth G] mmCIF format, chain BA [auth C]	BA [auth C] IA [auth E] N [auth S] PA [auth G] U [auth A] BA [auth C], IA [auth E], N [auth S], PA [auth G], U [auth A], WA [auth I]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain IA [auth E] Focus chain N [auth S] Focus chain PA [auth G] Focus chain U [auth A] Focus chain WA [auth I]
FCO Query on FCO Download:Ideal Coordinates CCD File SDF format, chain MA [auth F] SDF format, chain TA [auth H] SDF format, chain Y [auth B] SDF format, chain R [auth L] SDF format, chain FA [auth D] SDF format, chain AB [auth J] MOL2 format, chain MA [auth F] MOL2 format, chain TA [auth H] MOL2 format, chain Y [auth B] MOL2 format, chain R [auth L] MOL2 format, chain FA [auth D] MOL2 format, chain AB [auth J] mmCIF format, chain MA [auth F] mmCIF format, chain TA [auth H] mmCIF format, chain Y [auth B] mmCIF format, chain R [auth L] mmCIF format, chain FA [auth D] mmCIF format, chain AB [auth J]	AB [auth J] FA [auth D] MA [auth F] R [auth L] TA [auth H] AB [auth J], FA [auth D], MA [auth F], R [auth L], TA [auth H], Y [auth B]	CARBONMONOXIDE-(DICYANO) IRON C₃ Fe N₂ O VBQUCMTXYFMTTE-UHFFFAOYSA-N		Interactions Focus chain AB [auth J] Focus chain FA [auth D] Focus chain MA [auth F] Focus chain R [auth L] Focus chain TA [auth H] Focus chain Y [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain P [auth L] SDF format, chain W [auth B] SDF format, chain YA [auth J] SDF format, chain RA [auth H] SDF format, chain KA [auth F] MOL2 format, chain DA [auth D] MOL2 format, chain P [auth L] MOL2 format, chain W [auth B] MOL2 format, chain YA [auth J] MOL2 format, chain RA [auth H] MOL2 format, chain KA [auth F] mmCIF format, chain DA [auth D] mmCIF format, chain P [auth L] mmCIF format, chain W [auth B] mmCIF format, chain YA [auth J] mmCIF format, chain RA [auth H] mmCIF format, chain KA [auth F]	DA [auth D] KA [auth F] P [auth L] RA [auth H] W [auth B] DA [auth D], KA [auth F], P [auth L], RA [auth H], W [auth B], YA [auth J]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain KA [auth F] Focus chain P [auth L] Focus chain RA [auth H] Focus chain W [auth B] Focus chain YA [auth J]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain ZA [auth J] SDF format, chain X [auth B] SDF format, chain SA [auth H] SDF format, chain Q [auth L] SDF format, chain LA [auth F] SDF format, chain EA [auth D] MOL2 format, chain ZA [auth J] MOL2 format, chain X [auth B] MOL2 format, chain SA [auth H] MOL2 format, chain Q [auth L] MOL2 format, chain LA [auth F] MOL2 format, chain EA [auth D] mmCIF format, chain ZA [auth J] mmCIF format, chain X [auth B] mmCIF format, chain SA [auth H] mmCIF format, chain Q [auth L] mmCIF format, chain LA [auth F] mmCIF format, chain EA [auth D]	EA [auth D] LA [auth F] Q [auth L] SA [auth H] X [auth B] EA [auth D], LA [auth F], Q [auth L], SA [auth H], X [auth B], ZA [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain LA [auth F] Focus chain Q [auth L] Focus chain SA [auth H] Focus chain X [auth B] Focus chain ZA [auth J]
O Query on O Download:Ideal Coordinates CCD File SDF format, chain BB [auth J] SDF format, chain NA [auth F] SDF format, chain UA [auth H] SDF format, chain Z [auth B] SDF format, chain S [auth L] SDF format, chain GA [auth D] MOL2 format, chain BB [auth J] MOL2 format, chain NA [auth F] MOL2 format, chain UA [auth H] MOL2 format, chain Z [auth B] MOL2 format, chain S [auth L] MOL2 format, chain GA [auth D] mmCIF format, chain BB [auth J] mmCIF format, chain NA [auth F] mmCIF format, chain UA [auth H] mmCIF format, chain Z [auth B] mmCIF format, chain S [auth L] mmCIF format, chain GA [auth D]	BB [auth J] GA [auth D] NA [auth F] S [auth L] UA [auth H] BB [auth J], GA [auth D], NA [auth F], S [auth L], UA [auth H], Z [auth B]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain BB [auth J] Focus chain GA [auth D] Focus chain NA [auth F] Focus chain S [auth L] Focus chain UA [auth H] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.219 (Depositor)
R-Value Work: 0.201 (Depositor)
R-Value Observed: 0.202 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.78	α = 90.03
b = 113.16	β = 90.02
c = 133.91	γ = 119.99

Software Package:

Software Name	Purpose
MOSFLM	data reduction
CCP4	data reduction
AMoRE	phasing
PROLSQ	refinement
CCP4	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 1998-06-17

Deposition Author(s):

Volbeda, A.

Frey, M.

Fontecilla-Camps, J.C.

Revision History (Full details and data files)

Version 1.0: 1998-06-17
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-09
Changes: Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-20
Changes: Data collection, Structure summary
Version 1.5: 2026-08-12
Type: Remediation
Reason: Metalloprotein remediation
Changes: Data collection, Derived calculations, Structure summary