5E31 | pdb_00005e31

2.3 Angstrom Crystal Structure of the Monomeric Form of Penicillin Binding Protein 2 Prime from Enterococcus faecium.

PDB DOI: https://doi.org/10.2210/pdb5E31/pdb

Classification: PENICILLIN-BINDING PROTEIN
Organism(s): Enterococcus faecium DO
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-10-01 Released: 2015-10-14
Deposition Author(s): Minasov, G., Wawrzak, Z., Shuvalova, L., Dubrovska, I., Flores, K., Filippova, E., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.244 (Depositor), 0.250 (DCC)
R-Value Work:
0.197 (Depositor), 0.205 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

2.3 Angstrom Crystal Structure of the Monomeric Form of Penicillin Binding Protein 2 Prime from Enterococcus faecium.

Minasov, G., Wawrzak, Z., Shuvalova, L., Dubrovska, I., Flores, K., Filippova, E., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 70.76 kDa
Atom Count: 5,187
Modeled Residue Count: 641
Deposited Residue Count: 644
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin binding protein 2 prime	A	644	Enterococcus faecium DO	Mutation(s): 0 Gene Names: pbp5, HMPREF0351_11456
UniProt
Find proteins for Q3XZN6 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)) Explore Q3XZN6 Go to UniProtKB: Q3XZN6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3XZN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.244 (Depositor), 0.250 (DCC)
R-Value Work: 0.197 (Depositor), 0.205 (DCC)
R-Value Observed: 0.199 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.44	α = 90
b = 64.34	β = 90
c = 182.786	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
BLU-MAX	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection
Version 1.3: 2024-10-30
Changes: Structure summary

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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.