SAXSdb — 4wf2

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

Bifunctional ligase/repressor BirA

Escherichia coli

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	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

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 4WF2	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 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）	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 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）	Not recorded	BTN BIOTIN × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1HXD CRYSTAL STRUCTURE OF E. COLI BIOTIN REPRESSOR WITH BOUND BIOTIN Deposited 2001-01-12	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）	Not recorded	BTN BIOTIN × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1HXD CRYSTAL STRUCTURE OF E. COLI BIOTIN REPRESSOR WITH BOUND BIOTIN Deposited 2001-01-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–321（321 aa）	Not recorded	BTN BIOTIN × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 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

4 other PDB entries and 5 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

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	4wf2
Deposition date deposition_date	2014-09-11
Structure title title	Structure of E. coli BirA G142A bound to biotinol-5'-AMP
Keywords keywords	;biotin protein ligase, biotin repressor, G142A mutant, complex with biotinol-5'-AMP, LIGASE ;; LIGASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.05 Å
Radius of gyration Rg (electron density) rg_electron	21.22 Å
Forward intensity I(0) i0	19152400.00
Molecular weight molecular_weight	33938.0 kDa
Excluded volume excluded_volume	42939 Å³
Envelope volume envelope_volume	50576 Å³
Hydration-shell volume shell_volume	20761 Å³
Envelope diameter envelope_diameter	81.3 Å
Shell Rg shell_rg	27.27 Å
Envelope Rg envelope_rg	21.68 Å
Shape Rg shape_rg	21.23 Å
Total Rg total_rg	22.03 Å
Total atoms total_atoms	4834
Residues n_residues	304
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	77.4 Å
Rg (real space) rg_real	22.13 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	1.9150e+07
I(0) uncertainty (real space) i0_real_error	2.9270e+05
Rg (reciprocal space) rg_reciprocal	22.12 Å
I(0) (reciprocal space) i0_reciprocal	19150000.0000
Solution quality estimate total_estimate	0.5669
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.3 Å
Skewness Skewness skewness	0.510
Kurtosis Kurtosis kurtosis	-0.015
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4502000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.682; Stabil: 0.997; Sysdev: 0.145; Positv: 1.000; Valcen: 0.894; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Bifunctional ligase/repressor BirA
Molecular weight formula_weight	36194.8 kDa
EC 编号 ec_number	6.3.4.15
Mutation mutation	G142A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4990

MKDNTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPGKGYSLPEPIQLLNAKQILGQLDGGSVAVLPVIDSTNQYLLDRIGELKSGDACIAEYQQAGRGRRGRKWFSPFGANLYLSMFWRLEQAPAAAIGLSLVIGIVMAEVLRKLGADKVRVKWPNDLYLQDRKLAGILVELTGKTGDAAQIVIGAGINMAMRRVEESVVNQGWITLQEAGINLDRNTLAAMLIRELRAALELFEQEGLAPYLSRWEKLDNFINRPVKLIIGDKEIFGISRGIDKQGALLLEQDGIIKPWMGGEISLRSAEKHHHHHH

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;((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 ;
Molecular weight formula_weight	559.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	135

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4wf2a1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.0 — automated matches

Domain ID domain_id	d4wf2a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.2 — Biotin holoenzyme synthetase

Domain ID domain_id	d4wf2a3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	4wf2A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	4wf2A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	4wf2A03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

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8. Citations (1)

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Unit-cell length a length_a	46.239 Å
Unit-cell length b length_b	46.239 Å
Unit-cell length c length_c	157.107 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	4

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.310 Å
Low-resolution limit resolution_low	39.850 Å
R factor r_factor	0.1744
R_work r_work	0.1721
R_free r_free	0.2183

fit	/app/data/saxs_computation/wf/4wf2/4wf2.fit
pddf	/app/data/pr_computation/wf/4wf2/4wf2.pr.out
profile	/app/data/saxs_computation/wf/4wf2/4wf2.dat

Structure of E. coli BirA G142A bound to biotinol-5'-AMP

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

Bifunctional ligase/repressor BirA

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction