1ZMA | pdb_00001zma

Crystal Structure of the Bacterocin Transport Accessory Protein from Streptococcus pneumoniae

PDB DOI: https://doi.org/10.2210/pdb1ZMA/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Streptococcus pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2005-05-10 Released: 2005-06-21
Deposition Author(s): Kim, Y., Hatzos, C., Abdullah, J., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.167 (Depositor), 0.171 (DCC)
R-Value Work:
0.127 (Depositor), 0.134 (DCC)
R-Value Observed:
0.131 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1ZMA

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

Literature

The Crystal Structure of the Bacterocin Transport Accessory Protein from Streptococcus pneumoniae

Kim, Y., Hatzos, C., Abdullah, J., Collart, F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 13.29 kDa
Atom Count: 1,348
Modeled Residue Count: 118
Deposited Residue Count: 118
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
bacterocin transport accessory protein	A	118	Streptococcus pneumoniae	Mutation(s): 2
UniProt
Find proteins for Q8DP51 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DP51 Go to UniProtKB: Q8DP51
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DP51
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT Query on FMT 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]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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: 1.25 Å
R-Value Free: 0.167 (Depositor), 0.171 (DCC)
R-Value Work: 0.127 (Depositor), 0.134 (DCC)
R-Value Observed: 0.131 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.006	α = 90
b = 69.658	β = 112.27
c = 29.621	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-06-21

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2005-06-21
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.