5UH0 | pdb_00005uh0

1.95 Angstrom Resolution Crystal Structure of Fragment (35-274) of Membrane-bound Lytic Murein Transglycosylase F from Yersinia pestis.

PDB DOI: https://doi.org/10.2210/pdb5UH0/pdb

Classification: HYDROLASE,OXIDOREDUCTASE
Organism(s): Yersinia pestis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-01-10 Released: 2017-01-25
Deposition Author(s): Minasov, G., Shuvalova, L., Flores, K., Kiryukhina, O., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.267 (Depositor), 0.269 (DCC)
R-Value Work:
0.213 (Depositor)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

1.95 Angstrom Resolution Crystal Structure of Fragment (35-274) of Membrane-bound Lytic Murein Transglycosylase F from Yersinia pestis.

Minasov, G., Shuvalova, L., Flores, K., Kiryukhina, O., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 54.93 kDa
Atom Count: 4,024
Modeled Residue Count: 461
Deposited Residue Count: 486
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane-bound lytic murein transglycosylase F	A, B	243	Yersinia pestis	Mutation(s): 0 Gene Names: mltF, YPO2922, y1308, YP_2535 EC: 4.2.2
UniProt
Find proteins for Q74SQ6 (Yersinia pestis) Explore Q74SQ6 Go to UniProtKB: Q74SQ6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q74SQ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [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: 1.95 Å
R-Value Free: 0.267 (Depositor), 0.269 (DCC)
R-Value Work: 0.213 (Depositor)
R-Value Observed: 0.216 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.086	α = 90
b = 66.507	β = 90
c = 96.427	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-01-25

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2017-01-25
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection, Database references
Version 1.3: 2024-10-23
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.