4ML9 | pdb_00004ml9

Crystal Structure of Uncharacterized TIM Barrel Protein with the Conserved Phosphate Binding Site fromSebaldella termitidis

PDB DOI: https://doi.org/10.2210/pdb4ML9/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Sebaldella termitidis ATCC 33386
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2013-09-06 Released: 2013-09-18
Deposition Author(s): Kim, Y., Holowicki, J., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.176 (Depositor), 0.176 (DCC)
R-Value Work:
0.151 (Depositor), 0.151 (DCC)
R-Value Observed:
0.152 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Uncharacterized TIM Barrel Protein with the Conserved Phosphate Binding Site fromSebaldella termitidis

Kim, Y., Holowicki, J., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 63.33 kDa
Atom Count: 5,008
Modeled Residue Count: 551
Deposited Residue Count: 572
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	286	Sebaldella termitidis ATCC 33386	Mutation(s): 0 Gene Names: Sterm_2790
UniProt
Find proteins for D1AMR0 (Sebaldella termitidis (strain ATCC 33386 / NCTC 11300)) Explore D1AMR0 Go to UniProtKB: D1AMR0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D1AMR0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain V [auth B] MOL2 format, chain E [auth A] MOL2 format, chain V [auth B] mmCIF format, chain E [auth A] mmCIF format, chain V [auth B]	E [auth A], V [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain V [auth B] Interactions & Density Focus chain E [auth A] Focus chain V [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain T [auth B] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth B] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain T [auth B]	I [auth A], P [auth B], T [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth B] Focus chain T [auth B] Interactions & Density Focus chain I [auth A] Focus chain P [auth B] Focus chain T [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain W [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain W [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain U [auth B] mmCIF format, chain W [auth B]	D [auth A] F [auth A] G [auth A] H [auth A] J [auth A] D [auth A], F [auth A], G [auth A], H [auth A], J [auth A], K [auth A], L [auth A], O [auth B], Q [auth B], R [auth B], S [auth B], U [auth B], W [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth B] Focus chain W [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth B] Focus chain W [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	C [auth A], M [auth B], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [auth B] Focus chain N [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.176 (Depositor), 0.176 (DCC)
R-Value Work: 0.151 (Depositor), 0.151 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.475	α = 90
b = 127.475	β = 90
c = 91.013	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
DM	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-09-18

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-09-18
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary