SAXSdb — 1blc

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

BETA-LACTAMASE

Staphylococcus aureus

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 25–281	Not recorded	SO4 SULFATE ION × 2 CEM N-(1-CARBOXY-2-HYDROXY-4-OXO-BUTYL)-N-(3-OXO-CISPROPENYL)AMINE × 2 TEM N-(2-HYDROXY-4-OXO-BUTYL)-N-(3-OXO-TRANSPROPENYL)AMINE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.20 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 1BLC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ALQ CIRCULARLY PERMUTED BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 Deposited 1997-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–244（220 aa）	Mutation：;CIRCULARLY PERMUTED WITH AN EIGHT RESIDUE LINKER INSERTED TO JOIN THE ORIGINAL N- AND C-TERMINI, AND A NEW N-TERMINUS AT RESIDUE 254 ;	SO4 SULFATE ION × 1 CO3 CARBONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；PROTEIN WAS CRYSTALLIZED FROM 70% SATURATED AMMONIUM SULFATE SOLUTION, 0.3M KCL, 100MM NAHCO3 AT PH8.0, 0.5% V/V PEG600	Resolution 1.80 Å R-free 0.256
1BLH STRUCTURE OF A PHOSPHONATE-INHIBITED BETA-LACTAMASE. AN ANALOG OF THE TETRAHEDRAL TRANSITION STATE(SLASH)INTERMEDIATE OF BETA-LACTAM HYDROLYSIS Deposited 1993-09-30	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–281（257 aa）	Not recorded	FOS [[N-(BENZYLOXYCARBONYL)AMINO]METHYL]PHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1BLP STRUCTURAL BASIS FOR THE INACTIVATION OF THE P54 MUTANT OF BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 Deposited 1993-09-23	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–281（257 aa）	Mutation：D170N	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1DJA STRUCTURE OF BETA-LACTAMASE PRECURSOR, K73H MUTANT, AT 298K Deposited 1996-08-13	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–281（257 aa）	Mutation：A30M, K73H	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1DJB STRUCTURE OF BETA-LACTAMASE PRECURSOR, S70A MUTANT, AT 298K Deposited 1996-08-13	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–281（257 aa）	Mutation：S70A	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1DJC STRUCTURE OF BETA-LACTAMASE PRECURSOR, S70A MUTANT, AT 120K Deposited 1996-08-13	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–281（257 aa）	Mutation：S70A	SO4 SULFATE ION × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1GHI STRUCTURE OF BETA-LACTAMASE GLU166ASP:ASN170GLN MUTANT Deposited 2000-12-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–281（257 aa）	Mutation：E166D, N170Q	CO3 CARBONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.00	Resolution 2.30 Å R-free 0.263
1GHM Structures of the acyl-enzyme complex of the staphylococcus aureus beta-lactamase mutant GLU166ASP:ASN170GLN with degraded cephaloridine Deposited 2000-12-19	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–281（257 aa）	Mutation：E166D, N170Q	SO4 SULFATE ION × 5 CO3 CARBONATE ION × 1 CED 5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.00	Resolution 1.86 Å R-free 0.241
1GHP STRUCTURES OF THE ACYL-ENZYME COMPLEX OF THE STAPHYLOCOCCUS AUREUS BETA-LACTAMASE MUTANT GLU166ASP:ASN170GLN WITH DEGRADED BENZYLPENICILLIN Deposited 2000-12-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–281（257 aa）	Mutation：E166D, N170Q	SO4 SULFATE ION × 4 PNM OPEN FORM - PENICILLIN G × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.00	Resolution 1.76 Å R-free 0.264
1KGE STRUCTURE OF BETA-LACTAMASE ASN 170 MET MUTANT Deposited 1996-10-17	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–281（257 aa）	Mutation：N170M	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1KGF STRUCTURE OF BETA-LACTAMASE ASN 170 GLN MUTANT Deposited 1996-10-17	Different mutation/modification Different oligomeric state Different ligand/ion	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–281（257 aa）	Mutation：N170Q	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1KGG STRUCTURE OF BETA-LACTAMASE GLU166GLN:ASN170ASP MUTANT Deposited 1999-05-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–281（258 aa）	Mutation：E166Q,N170D	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.30 Å R-free 0.263
1OME CRYSTAL STRUCTURE OF THE OMEGA LOOP DELETION MUTANT (RESIDUES 163-178 DELETED) OF BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 Deposited 1998-02-09	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 25–281（257 aa） Chain B 25–281（257 aa）	Mutation：DELETION OF AN OMEGA LOOP (RESIDUES 163 - 178) Mutation：DELETION OF AN OMEGA LOOP (RESIDUES 163 - 178)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；68% SATURATED AMMONIUM SULFATE, 0.5% PEG 1000, 0.3M KCL, 0.1M SODIUM BICARBONATE PH 8.0	Resolution 2.30 Å R-free 0.298
1PIO AN ENGINEERED STAPHYLOCOCCUS AUREUS PC1 BETA-LACTAMASE THAT HYDROLYSES THIRD GENERATION CEPHALOSPORINS Deposited 1995-10-11	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 25–281（257 aa） Chain B 25–281（257 aa）	Mutation：INS(MET 30), A238S, DEL(I239) Mutation：INS(MET 30), A238S, DEL(I239)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.80 Å R-free 0.189
3BLM REFINED CRYSTAL STRUCTURE OF BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 AT 2.0 Deposited 1990-12-03	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–281（257 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BLAC_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–257； UniProt 25–281

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	1blc
Deposition date deposition_date	1993-09-27
Structure title title	INHIBITION OF BETA-LACTAMASE BY CLAVULANATE: TRAPPED INTERMEDIATES IN CRYOCRYSTALLOGRAPHIC STUDIES
Keywords keywords	HYDROLASE(ACTING IN CYCLIC AMIDES); HYDROLASE(ACTING IN CYCLIC AMIDES)
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	18.60 Å
Radius of gyration Rg (electron density) rg_electron	17.61 Å
Forward intensity I(0) i0	14000900.00
Molecular weight molecular_weight	29107.0 kDa
Excluded volume excluded_volume	36954 Å³
Envelope volume envelope_volume	40366 Å³
Hydration-shell volume shell_volume	18892 Å³
Envelope diameter envelope_diameter	59.0 Å
Shell Rg shell_rg	24.11 Å
Envelope Rg envelope_rg	17.93 Å
Shape Rg shape_rg	17.59 Å
Total Rg total_rg	18.67 Å
Total atoms total_atoms	2048
Residues n_residues	257
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	58.8 Å
Rg (real space) rg_real	18.50 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	1.4000e+07
I(0) uncertainty (real space) i0_real_error	1.6480e+05
Rg (reciprocal space) rg_reciprocal	18.52 Å
I(0) (reciprocal space) i0_reciprocal	14000000.0000
Solution quality estimate total_estimate	0.8135
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.207
Kurtosis Kurtosis kurtosis	-0.332
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3764000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	BETA-LACTAMASE
Molecular weight formula_weight	28843.2 kDa
EC 编号 ec_number	3.5.2.6
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	2384

KELNDLEKKYNAHIGVYALDTKSGKEVKFNSDKRFAYASTSKAINSAILLEQVPYNKLNKKVHINKDDIVAYSPILEKYVGKDITLKALIEASMTYSDNTANNKIIKEIGGIKKVKQRLKELGDKVTNPVRYEIELNYYSPKSKKDTSTPAAFGKTLNKLIANGKLSKENKKFLLDLMLNNKSGDTLIKDGVPKDYKVADKSGQAITYASRNDVAFVYPKGQSEPIVLVIFTNKDNKSDKPNDKLISETAKSVMKEF

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	N-(1-CARBOXY-2-HYDROXY-4-OXO-BUTYL)-N-(3-OXO-CISPROPENYL)AMINE
Molecular weight formula_weight	201.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	N-(2-HYDROXY-4-OXO-BUTYL)-N-(3-OXO-TRANSPROPENYL)AMINE
Molecular weight formula_weight	157.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	324

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1blca_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

CATH v4.4 (1 domains)

Domain ID domain_id	1blcA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

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8. Citations (7)

Inhibition of beta-lactamase by clavulanate. Trapped intermediates in cryocrystallographic studies.

J.Mol.Biol. (1992)

PMID: 1569569 · DOI: 10.1016/0022-2836(92)90472-V PRIMARY

Refined Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.0 Angstroms Resolution

J.Mol.Biol. (1991)

Structural Basis for the Inactivation of the P54 Mutant of Beta-Lactamase from Staphylococcus Aureus Pc1

Biochemistry (1991)

Penicillin-Binding and Degrading Enzymes

Curr.Opin.Struct.Biol. (1991)

;Bacterial Resistance to Beta-Lactam Antibiotics. Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.5 Angstroms Resolution ;

Science (1987)

The Crystal Structure of Beta-Lactamase from Staphylococcus Aureus at 0.5Nm Resolution

J.Biochem.(Tokyo) (1985)

;Structure of a Phosphonate-Inhibited Beta-Lactamase: An Analog of the Tetrahedral Transition State(Slash)Intermediate of Beta-Lactam Hydrolysis ;

To be Published

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Unit-cell length a length_a	54.100 Å
Unit-cell length b length_b	88.000 Å
Unit-cell length c length_c	141.300 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1790
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/bl/1blc/1blc.fit
pddf	/app/data/pr_computation/bl/1blc/1blc.pr.out
profile	/app/data/saxs_computation/bl/1blc/1blc.dat

INHIBITION OF BETA-LACTAMASE BY CLAVULANATE: TRAPPED INTERMEDIATES IN CRYOCRYSTALLOGRAPHIC STUDIES

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

BETA-LACTAMASE

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