SAXSdb — 9whk

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Anti-bacteriophage protein A/HamA C-terminal domain-containing protein

Klebsiella pneumoniae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	DNA polymerase theta (Helicase domain only) × 2 （A0A486PCQ5） ;DNA (5'-D(PAPAPAPAPAPAPAPAPA)-3') ; × 1 ;DNA (5'-D(PAPAPAPAPAPAPA)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A486PDC8_KLEPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–528； UniProt 1–528 Author chain D； PDBConstruct 1–528； UniProt 1–528

DNA polymerase theta (Helicase domain only)

Klebsiella pneumoniae

UniProt A0A486PCQ5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	Anti-bacteriophage protein A/HamA C-terminal domain-containing protein × 2 （A0A486PDC8） ;DNA (5'-D(PAPAPAPAPAPAPAPAPA)-3') ; × 1 ;DNA (5'-D(PAPAPAPAPAPAPA)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A486PCQ5_KLEPN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–853； UniProt 1–853 Author chain E； PDBConstruct 1–853； UniProt 1–853

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9whk
Deposition date deposition_date	2025-08-27
Structure title title	Structure of Klebsiella pneumoniae trypsin-HamAB bound with DNA, dimer
Keywords keywords	ATPase, Helicase, DNA BINDING PROTEIN/DNA, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9whk__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9whk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9whk__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	47.53 Å
Rg (electron density)	47.17 Å
Total Rg	47.42 Å
Atom count	18888
Residues	2286
Excluded volume	337250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9whk__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Anti-bacteriophage protein A/HamA C-terminal domain-containing protein
Molecular weight formula_weight	59614.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	18888

MSIDIADKLGVKISYNNKNSSGFICHGDDYSYVLTAKHSICKSSPNDCKFKHKKCDTCVFSGVAKNKVSICKPDTDTFPLCKVKDVLLSPKKDVAILVLNKKSHIDLKTKELPSTKIINTANYNSSHKFVSCGYPAINEHQSVQPLHYNNFSLFRNEKICLQIINDTLTALEDPKNGLSGNSGAGIILNSSSCVGLLGLYTDTGDYGICYGDIVDFSINELLTSSGYVPLEMEEDLSNNFKALIQSDFMECFVRMECDLNLDKNRIVNLYRLCLDGKKYNYVKIGERLIDCIPSFSLSRKQLMRCRERNAFGKATLSAIRNFLKIERKTKISEMLLQGFLESYLHAPKLYSFDEINNAGFHGAHVKFNKNRNVELIHSAAFISNSLSDGVSYAIDVILKAFPELRSLDGLLGNTFLETNFTEDECQILASLLIPGESSYSQGYEDRLAIFIGYNHKIEESLIYENASRFPSLLEQKIILNVQQALEYRKEEINKLSIVNATIDCFFVPFDDVNKFNDEFIESLKNEED

Source Source

Source organism organism	Klebsiella pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	573
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA polymerase theta (Helicase domain only)
Molecular weight formula_weight	99035.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MKKIDSFIIEKIFNSAYFKKLYKKIIKAYSALTIESENHFNISNTELRDIFRFIDLLANSSNQNARMCAYHWISLLEPFSDKWGKFSLISSLVYSKLGLYALDFNDHALPFSQRLENEAKKSAQTFSNTYIFTDAQFDIYTDMLKSPYYSFSGPTSLGKSFILKRYIEEIIQNSTSNIVILVPTRALISQFSLEIKNELHELIENFNYKIVTHGSLASKSDAVIIKHIFILTPERLLNLFSQGKVVSIDYLFVDEAHKLSNNDDSDVRSLTEYNAIDSALFNNPNMKIVFSSPNIENPEVFLNLFGREKIYASRIIESPVSQNLYLIDFHKKEIKYFSNSECIDIESGSLYTLNKKSDFIYNIGSRHGSNMIYCSSRAKAVDSALEFYQIRLSENIVLSPLLIDSIKKISNYIHPEYYLAMFLMKRIAYHHGQLPQAIRNIVEELFRKGDIDFIFCTPTLVEGVNMPTRNIFINCDDKIRLIADAKKNPNKTLAFWNLAGRAGRYCKELSGNIFCLQDESNRWDNTDIFLEKTAHLTTTIDARIESKSGLREIERYLSDTETDIYKRNQAIEYLANIMAVDTIRFKNNLKDSFVLRKFYDIHREELLSLAKLKANDILDIPIDIINSYKSLNFKIQRKVFDYVSVSPVNKKLPSLDYANILSVLELFYDLYRWGETETKYVKSKGQLTYFATLMNQWTNDYSINRIINENIDIKRTIVIERGQQPIPFDKNDINHVNKVIDDILYNIERILSFFFEKYFNHYYKCLAAILGEDNAGHNWATFLEYGSKNPLCISLQTLGISRHAANIIASSKELRKYLKFNEDSYEIISVNKQGLLNSLQKDSVEYGEVKIFL

Source Source

Source organism organism	Klebsiella pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	573
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PAPAPAPAPAPAPAPAP*A)-3') ;
Molecular weight formula_weight	2773.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

AAAAAAAAA

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(PAPAPAPAPAPAP*A)-3') ;
Molecular weight formula_weight	2147.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

AAAAAAA

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	3.22 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	88815

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Anti-bacteriophage protein A/HamA C-terminal domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase theta (Helicase domain only)

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9whk__assembly_1__model_1

9whk__assembly_1__model_1 | I(q)

9whk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

7. Citations (1)

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Anti-bacteriophage protein A/HamA C-terminal domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA polymerase theta (Helicase domain only)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9whk__assembly_1__model_1

9whk__assembly_1__model_1 | I(q)

9whk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

7. Citations (1)