SAXSdb — 1blh

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 25–281	Not recorded	FOS [[N-(BENZYLOXYCARBONYL)AMINO]METHYL]PHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.30 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 1BLH	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 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
1BLC INHIBITION OF BETA-LACTAMASE BY CLAVULANATE: TRAPPED INTERMEDIATES IN CRYOCRYSTALLOGRAPHIC STUDIES Deposited 1993-09-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–281（257 aa）	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 conditions	Resolution 2.20 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 ligand/ion	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 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 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 oligomeric state 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 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 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 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 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 ligand/ion Different structure-quality metrics	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 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 oligomeric state 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 oligomeric state 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 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	1blh
Deposition date deposition_date	1993-09-30
Structure title title	STRUCTURE OF A PHOSPHONATE-INHIBITED BETA-LACTAMASE. AN ANALOG OF THE TETRAHEDRAL TRANSITION STATE(SLASH)INTERMEDIATE OF BETA-LACTAM HYDROLYSIS
Keywords keywords	HYDROLASE(BETA-LACTAMASE); HYDROLASE(BETA-LACTAMASE)
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	18.51 Å
Radius of gyration Rg (electron density) rg_electron	17.52 Å
Forward intensity I(0) i0	13561600.00
Molecular weight molecular_weight	28590.0 kDa
Excluded volume excluded_volume	36255 Å³
Envelope volume envelope_volume	39858 Å³
Hydration-shell volume shell_volume	18758 Å³
Envelope diameter envelope_diameter	60.9 Å
Shell Rg shell_rg	24.11 Å
Envelope Rg envelope_rg	17.81 Å
Shape Rg shape_rg	17.51 Å
Total Rg total_rg	18.55 Å
Total atoms total_atoms	2014
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	67.5 Å
Rg (real space) rg_real	18.41 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	1.3560e+07
I(0) uncertainty (real space) i0_real_error	1.8750e+05
Rg (reciprocal space) rg_reciprocal	18.43 Å
I(0) (reciprocal space) i0_reciprocal	13560000.0000
Solution quality estimate total_estimate	0.7542
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.215
Kurtosis Kurtosis kurtosis	-0.308
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4052000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.606; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; 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	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	2209

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	[[N-(BENZYLOXYCARBONYL)AMINO]METHYL]PHOSPHATE
Molecular weight formula_weight	245.2 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	195

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1blha_
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	1blhA00
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)

;Structure of a phosphonate-inhibited beta-lactamase. An analog of the tetrahedral transition state/intermediate of beta-lactam hydrolysis. ;

J.Mol.Biol. (1993)

PMID: 8230196 · DOI: 10.1006/jmbi.1993.1571 PRIMARY

Inhibition of Beta-Lactamase by Clavulanate. Trapped Intermediates in Cryocrystallographic Studies

J.Mol.Biol. (1992)

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

Biochem.J. (1985)

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Unit-cell length a length_a	53.960 Å
Unit-cell length b length_b	94.200 Å
Unit-cell length c length_c	138.930 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	2.300 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1660
R_work r_work	—
R_free r_free	—

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

STRUCTURE OF A PHOSPHONATE-INHIBITED BETA-LACTAMASE. AN ANALOG OF THE TETRAHEDRAL TRANSITION STATE(SLASH)INTERMEDIATE OF BETA-LACTAM HYDROLYSIS

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