6ORI | pdb_00006ori

Enterococcal surface protein, partial N-terminal region

PDB DOI: https://doi.org/10.2210/pdb6ORI/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Enterococcus faecalis
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-04-30 Released: 2020-05-13
Deposition Author(s): Spiegelman, L., Zhang, L., Tezcan, A., Ghosh, P.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.174 (Depositor), 0.173 (DCC)
R-Value Work:
0.152 (Depositor), 0.153 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Enterococcal surface protein, partial N-terminal region (CASP target)

Spiegelman, L., Zhang, L., Tezcan, A., Ghosh, P.

To be published.

Macromolecule Content

Total Structure Weight: 46.42 kDa
Atom Count: 3,612
Modeled Residue Count: 381
Deposited Residue Count: 411
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EF0056	A	411	Enterococcus faecalis	Mutation(s): 0 Gene Names: ef0056, esp
UniProt
Find proteins for Q9Z4N7 (Enterococcus faecalis) Explore Q9Z4N7 Go to UniProtKB: Q9Z4N7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Z4N7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.174 (Depositor), 0.173 (DCC)
R-Value Work: 0.152 (Depositor), 0.153 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.85	α = 107.36
b = 49.96	β = 111.42
c = 51.2399	γ = 90.43

Software Package:

Software Name	Purpose
PHENIX	refinement
ELVES	data processing
MOSFLM	data reduction
Aimless	data scaling
PHENIX	model building
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-05-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DMR-1602537
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	5T32GM007240

Revision History (Full details and data files)

Version 1.0: 2020-05-13
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references
Version 1.2: 2024-04-03
Changes: Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.