4KJM | pdb_00004kjm

Crystal structure of the Staphylococcus aureus protein (NP_646141.1, domain 3912-4037) similar to streptococcal adhesins emb and ebhA/ebhB

PDB DOI: https://doi.org/10.2210/pdb4KJM/pdb
Entry: 4KJM supersedes: 1XVH

Classification: CELL ADHESION
Organism(s): Staphylococcus aureus subsp. aureus MW2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-05-03 Released: 2013-05-29
Deposition Author(s): Cymborowski, M., Shabalin, I.G., Joachimiak, G., Chruszcz, M., Gornicki, P., Zhang, R., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.230 (Depositor), 0.235 (DCC)
R-Value Work:
0.185 (Depositor), 0.194 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the Staphylococcus aureus protein (NP_646141.1, domain 3912-4037) similar to streptococcal adhesins emb and ebhA/ebhB

Cymborowski, M., Shabalin, I.G., Joachimiak, G., Chruszcz, M., Gornicki, P., Zhang, R., Joachimiak, A., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 28.66 kDa
Atom Count: 2,099
Modeled Residue Count: 240
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular matrix-binding protein ebh	A, B	129	Staphylococcus aureus subsp. aureus MW2	Mutation(s): 0 Gene Names: 1003436, ebh
UniProt
Find proteins for Q8NWQ6 (Staphylococcus aureus (strain MW2)) Explore Q8NWQ6 Go to UniProtKB: Q8NWQ6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NWQ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [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 V [auth B] SDF format, chain Y [auth B] SDF format, chain T [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [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 V [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain T [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain P [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 V [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain T [auth B]	AA [auth B] E [auth A] F [auth A] G [auth A] H [auth A] AA [auth B], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], Y [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Y [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain O [auth B] SDF format, chain W [auth B] SDF format, chain Z [auth B] MOL2 format, chain D [auth A] MOL2 format, chain O [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain D [auth A] mmCIF format, chain O [auth B] mmCIF format, chain W [auth B] mmCIF format, chain Z [auth B]	D [auth A], O [auth B], W [auth B], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain O [auth B] Focus chain W [auth B] Focus chain Z [auth B] Interactions & Density Focus chain D [auth A] Focus chain O [auth B] Focus chain W [auth B] Focus chain Z [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain X [auth B] MOL2 format, chain C [auth A] MOL2 format, chain X [auth B] mmCIF format, chain C [auth A] mmCIF format, chain X [auth B]	C [auth A], X [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain X [auth B] Interactions & Density Focus chain C [auth A] Focus chain X [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: 2.00 Å
R-Value Free: 0.230 (Depositor), 0.235 (DCC)
R-Value Work: 0.185 (Depositor), 0.194 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.783	α = 90
b = 59.23	β = 90
c = 88.186	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXD	phasing
MLPHARE	phasing
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling
RESOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-05-29

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

This entry supersedes: 1XVH

Revision History (Full details and data files)

Version 1.0: 2013-05-29
Type: Initial release
Version 1.1: 2013-11-27
Changes: Structure summary
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-11-20
Changes: Data collection, Refinement description, Structure summary
Version 1.4: 2025-10-22
Changes: Structure summary