3FRM | pdb_00003frm

The crystal structure of a functionally unknown conserved protein from Staphylococcus epidermidis ATCC 12228.

PDB DOI: https://doi.org/10.2210/pdb3FRM/pdb

Classification: structural genomics, unknown function
Organism(s): Staphylococcus epidermidis ATCC 12228
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-08 Released: 2009-01-27
Deposition Author(s): Tan, K., Sather, A., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.263 (Depositor), 0.273 (DCC)
R-Value Work:
0.197 (Depositor), 0.207 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of a functionally unknown conserved protein from Staphylococcus epidermidis ATCC 12228.

Tan, K., Sather, A., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 180.28 kDa
Atom Count: 12,801
Modeled Residue Count: 1,515
Deposited Residue Count: 1,524
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized conserved protein	A, B, C, D, E A, B, C, D, E, F	254	Staphylococcus epidermidis ATCC 12228	Mutation(s): 0 Gene Names: SE_1855, Staphylococcus epidermidis
UniProt
Find proteins for A0A0H2VHN1 (Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)) Explore A0A0H2VHN1 Go to UniProtKB: A0A0H2VHN1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2VHN1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain T [auth E] SDF format, chain V [auth F] SDF format, chain W [auth F] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F] MOL2 format, chain W [auth F] mmCIF format, chain T [auth E] mmCIF format, chain V [auth F] mmCIF format, chain W [auth F]	T [auth E], V [auth F], W [auth F]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F] Interactions & Density Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain S [auth E] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth E] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A] J [auth B] K [auth B] M [auth C] N [auth C] H [auth A], J [auth B], K [auth B], M [auth C], N [auth C], P [auth D], R [auth E], S [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth E] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth E]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain U [auth F] SDF format, chain Q [auth E] SDF format, chain O [auth D] SDF format, chain L [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain U [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain U [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C]	G [auth A] I [auth B] L [auth C] O [auth D] Q [auth E] G [auth A], I [auth B], L [auth C], O [auth D], Q [auth E], U [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain U [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain U [auth F]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.263 (Depositor), 0.273 (DCC)
R-Value Work: 0.197 (Depositor), 0.207 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.711	α = 90
b = 126.549	β = 94.52
c = 112.807	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-01-27

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-01-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary