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1woc

Crystal structure of PriB

Method: X-RAY DIFFRACTION Dmax: 77.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Primosomal replication protein n

Escherichia coli

UniProt P07013

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–103 Chain B； UniProt 1–103 Chain C； UniProt 1–103 Chain D； UniProt 1–103 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；25%(v/v) MPD, 50mM Magnesium Chloride, 100mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.00 Å R-free 0.276
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–103 Chain D； UniProt 1–103 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；25%(v/v) MPD, 50mM Magnesium Chloride, 100mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.00 Å R-free 0.276
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–103 Chain C； UniProt 1–103 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；25%(v/v) MPD, 50mM Magnesium Chloride, 100mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.00 Å R-free 0.276

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1WOC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1TXY E. coli PriB Deposited 2004-07-06 Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–103（103 aa）
Chain B 1–103（103 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 8000, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.285
1V1Q Crystal structure of PriB- a primosomal DNA replication protein of Escherichia coli Deposited 2004-04-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–104（104 aa）
Chain B 1–104（104 aa）
Mutation：YES Mutation：YES CYS CYSTEINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.7；pH 5.70
Resolution 2.10 Å R-free 0.263
2CCZ Crystal structure of E. coli primosomol protein PriB bound to ssDNA Deposited 2006-01-19 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain A 1–103（103 aa）
Chain B 1–103（103 aa）
Mutation：YES Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.50
Resolution 2.70 Å R-free 0.284
2PNH Escherichia coli PriB E39A variant Deposited 2007-04-24 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–104（104 aa）
Chain B 1–104（104 aa）
Mutation：E39A Mutation：E39A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；8% polyethylene glycol 8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.25 Å R-free 0.276
8FAK DNA replication fork binding triggers structural changes in the PriA DNA helicase that regulate the PriA-PriB replication restart pathway in E. coli Deposited 2022-11-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain A 1–104（104 aa）
Chain B 1–104（104 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
9ZBT Visualization of PriA/PriB/DnaT complexes reveals mechanisms governing structure-specific assembly of the DNA replication restart primosome Deposited 2025-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: heptameric
Chain A 1–104（104 aa）
Chain B 1–104（104 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；50 mM Tris-HCl, pH 8, 2 mM dithiothreitol, 5 mM ethylenediaminetetraacetic acid, 75 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
9ZBU Visualization of PriA/PriB/DnaT complexes reveals mechanisms governing structure-specific assembly of the DNA replication restart primosome Deposited 2025-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: tridecameric
Chain A 2–100（99 aa）
Chain B 2–100（99 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；50 mM Tris-HCl, pH 8, 2 mM dithiothreitol, 5 mM ethylenediaminetetraacetic acid, 75 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PRIB_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–103； UniProt 1–103 Author chain B； PDBConstruct 1–103； UniProt 1–103 Author chain C； PDBConstruct 1–103； UniProt 1–103 Author chain D； PDBConstruct 1–103； UniProt 1–103

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1woc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1woc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1woc
Deposition date deposition_date2004-08-13
Structure title titleCrystal structure of PriB
Keywords keywordsOligonucleotide Binding fold, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.52 Å
Radius of gyration Rg (electron density) rg_electron24.63 Å
Forward intensity I(0) i036227900.00
Molecular weight molecular_weight44192.0 kDa
Excluded volume excluded_volume54606 ų
Envelope volume envelope_volume73058 ų
Hydration-shell volume shell_volume25104 ų
Envelope diameter envelope_diameter78.1 Å
Shell Rg shell_rg31.23 Å
Envelope Rg envelope_rg24.56 Å
Shape Rg shape_rg24.66 Å
Total Rg total_rg25.35 Å
Total atoms total_atoms3068
Residues n_residues389
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax77.2 Å
Rg (real space) rg_real25.40 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real3.6230e+07
I(0) uncertainty (real space) i0_real_error4.8690e+05
Rg (reciprocal space) rg_reciprocal25.44 Å
I(0) (reciprocal space) i0_reciprocal36230000.0000
Solution quality estimate total_estimate0.9162
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.9 Å
Skewness Skewness skewness0.096
Kurtosis Kurtosis kurtosis-0.627
Angular range angular_range— – 0.3100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4571000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.974; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.986
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1woca_
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.3 — Single strand DNA-binding domain, SSB
Domain ID domain_idd1wocb_
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.3 — Single strand DNA-binding domain, SSB
Domain ID domain_idd1wocc_
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.3 — Single strand DNA-binding domain, SSB
Domain ID domain_idd1wocd_
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.3 — Single strand DNA-binding domain, SSB

CATH v4.4 (4 domains)

Domain ID domain_id1wocA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id1wocB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id1wocC00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id1wocD00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
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8. Citations (1)

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9. Files and Curves (10)