8DUY | pdb_00008duy

Crystal structure of Cystathionine beta-lyase from Klebsiella pneumoniae

PDB DOI: https://doi.org/10.2210/pdb8DUY/pdb

Classification: LYASE
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-27 Released: 2022-08-10
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.195 (Depositor), 0.196 (DCC)
R-Value Work:
0.163 (Depositor), 0.163 (DCC)
R-Value Observed:
0.164 (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

Crystal Structure of Cystathionine beta-lyase from Klebsiella pneumoniae

Dranow, D.M., Abendroth, J.A., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 178.64 kDa
Atom Count: 14,023
Modeled Residue Count: 1,566
Deposited Residue Count: 1,612
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine beta-lyase	A, B, C, D	403	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: KPHS_45550 EC: 4.4.1.8 (PDB Primary Data), 4.4.1.13 (UniProt)
UniProt
Find proteins for A0A0H3GVN6 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GVN6 Go to UniProtKB: A0A0H3GVN6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3GVN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	G [auth A], L [auth C], O [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth A] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth C] Focus chain O [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	E [auth A] F [auth A] H [auth B] I [auth B] J [auth C] E [auth A], F [auth A], H [auth B], I [auth B], J [auth C], K [auth C], M [auth D], N [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B, C, D	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.195 (Depositor), 0.196 (DCC)
R-Value Work: 0.163 (Depositor), 0.163 (DCC)
R-Value Observed: 0.164 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.61	α = 90
b = 131.14	β = 99.93
c = 85.44	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PDB_EXTRACT	data extraction
XSCALE	data scaling
MoRDa	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-10

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-08-10
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection

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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.