9WH1 | pdb_00009wh1

Structure of Klebsiella pneumoniae trypsin-HamAB bound with DNA, monomer

PDB DOI: https://doi.org/10.2210/pdb9WH1/pdb
EM Map EMD-65964: EMDB EMDataResource

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-08-25 Released: 2026-06-03
Deposition Author(s): Huang, P.P., Chen, M.R., Xiao, Y.B.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.23 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9WH1

This is version 1.0 of the entry. See complete history.

Literature

Structure of Klebsiella pneumoniae HamAB monomer bound with DNA

Huang, P.P., Chen, M.R.

To be published.

Macromolecule Content

Total Structure Weight: 161.42 kDa
Atom Count: 9,465
Modeled Residue Count: 1,144
Deposited Residue Count: 1,390
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-bacteriophage protein A/HamA C-terminal domain-containing protein	A	528	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: SAMEA4873653_00088
UniProt
Find proteins for A0A486PDC8 (Klebsiella pneumoniae) Explore A0A486PDC8 Go to UniProtKB: A0A486PDC8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A486PDC8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase theta (Helicase domain only)	B	853	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: B6I68_29715, SAMEA4873653_00087
UniProt
Find proteins for A0A486PCQ5 (Klebsiella pneumoniae) Explore A0A486PCQ5 Go to UniProtKB: A0A486PCQ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A486PCQ5
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 3
DNA (5'-D(PAPAPAPAPAPAPAPAP*A)-3')	C	9	Klebsiella pneumoniae
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.23 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-03

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2026-06-03
Type: Initial release

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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.