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1hxd

CRYSTAL STRUCTURE OF E. COLI BIOTIN REPRESSOR WITH BOUND BIOTIN

Method: X-RAY DIFFRACTION Dmax: 117.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

BIRA BIFUNCTIONAL PROTEIN

Escherichia coli

UniProt P06709

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–321 Not recorded BTN BIOTIN × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–321 Not recorded BTN BIOTIN × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å

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 1HXD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BIA THE E. COLI BIOTIN HOLOENZYME SYNTHETASE(SLASH)BIO REPRESSOR CRYSTAL STRUCTURE DELINEATES THE BIOTIN AND DNA-BINDING DOMAINS Deposited 1992-07-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–321（321 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1BIB THE E. COLI BIOTIN HOLOENZYME SYNTHETASE(SLASH)BIO REPRESSOR CRYSTAL STRUCTURE DELINEATES THE BIOTIN AND DNA-BINDING DOMAINS Deposited 1992-07-06 Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–321（321 aa）
Not recorded BTN BIOTIN × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å
2EWN Ecoli Biotin Repressor with co-repressor analog Deposited 2005-11-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–321（321 aa）
Chain B 1–321（321 aa）
Not recorded BTX ((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL 5-((3AS,4S,6AR)-2-OXO-HEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL)PENTYL HYDROGEN PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；20% PEG 4K, 100mM Tris-HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.264
4WF2 Structure of E. coli BirA G142A bound to biotinol-5'-AMP Deposited 2014-09-11 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–321（321 aa）
Mutation：G142A BTX ((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL 5-((3AS,4S,6AR)-2-OXO-HEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL)PENTYL HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M TrisHCl, pH 8.0 and 12.5% (w/v) PEG 8K (Hampton) at 20 deg C
Resolution 2.31 Å R-free 0.218

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BIRA_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–321； UniProt 1–321 Author chain B； PDBConstruct 1–321； UniProt 1–321

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 1hxd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1hxd
Deposition date deposition_date2001-01-12
Structure title titleCRYSTAL STRUCTURE OF E. COLI BIOTIN REPRESSOR WITH BOUND BIOTIN
Keywords keywordsLigase, Repressor, BIOTIN, DNA-Binding; LIGASE
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_guinier36.39 Å
Radius of gyration Rg (electron density) rg_electron36.22 Å
Forward intensity I(0) i065768100.00
Molecular weight molecular_weight67363.0 kDa
Excluded volume excluded_volume85474 ų
Envelope volume envelope_volume116570 ų
Hydration-shell volume shell_volume27709 ų
Envelope diameter envelope_diameter121.4 Å
Shell Rg shell_rg41.66 Å
Envelope Rg envelope_rg34.72 Å
Shape Rg shape_rg36.20 Å
Total Rg total_rg36.68 Å
Total atoms total_atoms4744
Residues n_residues610
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 dmax117.4 Å
Rg (real space) rg_real36.60 Å
Rg uncertainty (real space) rg_real_error1.25 Å
I(0) (real space) i0_real6.5770e+07
I(0) uncertainty (real space) i0_real_error1.1080e+06
Rg (reciprocal space) rg_reciprocal36.48 Å
I(0) (reciprocal space) i0_reciprocal65760000.0000
Solution quality estimate total_estimate0.8111
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.3 Å
Skewness Skewness skewness0.256
Kurtosis Kurtosis kurtosis-0.921
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7437000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.714; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.577; Smooth: 0.822
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1hxda1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.1 — Biotin repressor-like
Domain ID domain_idd1hxda2
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.1 — C-terminal domain of transcriptional repressors
Family Family familyb.34.1.1 — Biotin repressor (BirA)
Domain ID domain_idd1hxda3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.2 — Biotin holoenzyme synthetase
Domain ID domain_idd1hxdb1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.1 — Biotin repressor-like
Domain ID domain_idd1hxdb2
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.1 — C-terminal domain of transcriptional repressors
Family Family familyb.34.1.1 — Biotin repressor (BirA)
Domain ID domain_idd1hxdb3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.2 — Biotin holoenzyme synthetase

CATH v4.4 (6 domains)

Domain ID domain_id1hxdA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id1hxdA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id1hxdA03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily100 —
Domain ID domain_id1hxdB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id1hxdB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id1hxdB03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily100 —
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8. Citations (3)

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9. Files and Curves (10)