4LR4 | pdb_00004lr4

Crystal structure of a putative secreted protein (EUBREC_3654) from Eubacterium rectale at 2.43 A resolution

PDB DOI: https://doi.org/10.2210/pdb4LR4/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Agathobacter rectalis ATCC 33656
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-07-19 Released: 2013-09-18
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free:
0.216 (Depositor), 0.230 (DCC)
R-Value Work:
0.186 (Depositor), 0.200 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a hypothetical protein (EUBREC_3654) from Eubacterium rectale at 2.43 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 167.71 kDa
Atom Count: 11,652
Modeled Residue Count: 1,381
Deposited Residue Count: 1,480
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein	A, B, C, D	370	Agathobacter rectalis ATCC 33656	Mutation(s): 0 Gene Names: EUBREC_3654, RER070207000171
UniProt
Find proteins for C4ZEB7 (Agathobacter rectalis (strain ATCC 33656 / DSM 3377 / JCM 17463 / KCTC 5835 / VPI 0990)) Explore C4ZEB7 Go to UniProtKB: C4ZEB7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C4ZEB7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain Q [auth B] SDF format, chain I [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain I [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain I [auth A]	AA [auth C] HA [auth D] I [auth A] IA [auth D] J [auth A] AA [auth C], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], Q [auth B], Y [auth C], Z [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth C] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain Q [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain Q [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain GA [auth D] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain S [auth C] SDF format, chain N [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain FA [auth D] SDF format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain E [auth A]	E [auth A] EA [auth D] F [auth A] FA [auth D] G [auth A] E [auth A], EA [auth D], F [auth A], FA [auth D], G [auth A], GA [auth D], H [auth A], M [auth B], N [auth B], O [auth B], P [auth B], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain NA [auth D] SDF format, chain R [auth B] SDF format, chain MA [auth D] SDF format, chain LA [auth D] SDF format, chain L [auth A] SDF format, chain KA [auth D] SDF format, chain DA [auth C] SDF format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain NA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain MA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain NA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain MA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain DA [auth C] mmCIF format, chain BA [auth C]	BA [auth C] CA [auth C] DA [auth C] KA [auth D] L [auth A] BA [auth C], CA [auth C], DA [auth C], KA [auth D], L [auth A], LA [auth D], MA [auth D], NA [auth D], R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain R [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain R [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free: 0.216 (Depositor), 0.230 (DCC)
R-Value Work: 0.186 (Depositor), 0.200 (DCC)
R-Value Observed: 0.188 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34LR4

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.016	α = 90
b = 106.733	β = 92.45
c = 115.078	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement