SAXSdb — 1ghm

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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	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

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 1GHM	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 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）	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
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 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）	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 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：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 experimental conditions 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 experimental conditions 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 experimental conditions 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 ligand/ion 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
1GHP STRUCTURES OF THE ACYL-ENZYME COMPLEX OF THE STAPHYLOCOCCUS AUREUS BETA-LACTAMASE MUTANT GLU166ASP:ASN170GLN WITH DEGRADED BENZYLPENICILLIN Deposited 2000-12-21	Different ligand/ion 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 experimental conditions 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 experimental conditions 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 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）	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 2–258； 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	1ghm
Deposition date deposition_date	2000-12-19
Structure title title	Structures of the acyl-enzyme complex of the staphylococcus aureus beta-lactamase mutant GLU166ASP:ASN170GLN with degraded cephaloridine
Keywords keywords	HYDROLASE, ANTIBIOTIC RESISTANCE, BETA-LACTAM HYDROLYSIS, BENZYLPENICILLIN, CEPHALORIDINE; HYDROLASE
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	18.64 Å
Radius of gyration Rg (electron density) rg_electron	17.62 Å
Forward intensity I(0) i0	15214700.00
Molecular weight molecular_weight	29690.0 kDa
Excluded volume excluded_volume	37382 Å³
Envelope volume envelope_volume	41431 Å³
Hydration-shell volume shell_volume	19237 Å³
Envelope diameter envelope_diameter	61.3 Å
Shell Rg shell_rg	24.29 Å
Envelope Rg envelope_rg	18.01 Å
Shape Rg shape_rg	17.59 Å
Total Rg total_rg	18.69 Å
Total atoms total_atoms	2080
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	59.6 Å
Rg (real space) rg_real	18.54 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	1.5210e+07
I(0) uncertainty (real space) i0_real_error	1.7540e+05
Rg (reciprocal space) rg_reciprocal	18.55 Å
I(0) (reciprocal space) i0_reciprocal	15210000.0000
Solution quality estimate total_estimate	0.8882
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.7 Å
Skewness Skewness skewness	0.198
Kurtosis Kurtosis kurtosis	-0.333
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4094000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.990

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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	28974.4 kDa
EC 编号 ec_number	3.5.2.6
Mutation mutation	E166D, N170Q
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	2406

MKELNDLEKKYNAHIGVYALDTKSGKEVKFNSDKRFAYASTSKAINSAILLEQVPYNKLNKKVHINKDDIVAYSPILEKYVGKDITLKALIEASMTYSDNTANNKIIKEIGGIKKVKQRLKELGDKVTNPVRYDIELQYYSPKSKKDTSTPAAFGKTLNKLIANGKLSKENKKFLLDLMLNNKSGDTLIKDGVPKDYKVADKSGQAITYASRNDVAFVYPKGQSEPIVLVIFTNKDNKSDKPNDKLISETAKSVMKEF

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

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	5

Entity 3 Entity 3 non-polymer

Description description	CARBONATE ION
Molecular weight formula_weight	60.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID
Molecular weight formula_weight	340.4 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	326

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ghma_
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	1ghmA00
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 (4)

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Unit-cell length a length_a	53.500 Å
Unit-cell length b length_b	90.800 Å
Unit-cell length c length_c	140.200 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	1.860 Å
Low-resolution limit resolution_low	21.800 Å
R factor r_factor	0.1880
R_work r_work	0.1880
R_free r_free	0.2410

fit	/app/data/saxs_computation/gh/1ghm/1ghm.fit
pddf	/app/data/pr_computation/gh/1ghm/1ghm.pr.out
profile	/app/data/saxs_computation/gh/1ghm/1ghm.dat

Structures of the acyl-enzyme complex of the staphylococcus aureus beta-lactamase mutant GLU166ASP:ASN170GLN with degraded cephaloridine

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