SAXSdb — 1y54

▼

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

Beta-lactamase

Enterobacter cloacae

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 21–381	Not recorded	FDT (7R)-6-FORMYL-7-(1-METHYL-1H-1,2,3-TRIAZOL-4-YL)-4,7-DIHYDRO-1,4-THIAZEPINE-3-CARBOXYLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；PEG 6000 30%, bicine 100mM, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.292

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 1Y54	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BLS CRYSTALLOGRAPHIC STRUCTURE OF A PHOSPHONATE DERIVATIVE OF THE ENTEROBACTER CLOACAE P99 CEPHALOSPORINASE: MECHANISTIC INTERPRETATION OF A BETA-LACTAMASE TRANSITION STATE ANALOG Deposited 1993-12-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–381（361 aa）	Not recorded	IPP (P-IODOPHENYLACETYLAMINO)METHYLPHOSPHINIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1BLS CRYSTALLOGRAPHIC STRUCTURE OF A PHOSPHONATE DERIVATIVE OF THE ENTEROBACTER CLOACAE P99 CEPHALOSPORINASE: MECHANISTIC INTERPRETATION OF A BETA-LACTAMASE TRANSITION STATE ANALOG Deposited 1993-12-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 21–381（361 aa）	Not recorded	IPP (P-IODOPHENYLACETYLAMINO)METHYLPHOSPHINIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1GCE STRUCTURE OF THE BETA-LACTAMASE OF ENTEROBACTER CLOACAE GC1 Deposited 1999-05-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–381（361 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5；298 K；VAPOR DIFFUSION, WITH 6.7 OR 8.0 MG/ML PROTEIN IN 5-7.5% PEG8000, 20-25MM POTASSIUM PHOSPHATE (MONOBASIC), OVER 12.5 OR 15% PEG8000, 50MM POTASSIUM PHOSPHATE (MONOBASIC) RESERVOIR AT ROOM TEMPERATURE., temperature 298K	Resolution 1.80 Å R-free 0.232
1RGZ Enterobacter cloacae GC1 Class C beta-Lactamase Complexed with Transition-State Analog of Cefotaxime Deposited 2003-11-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–384（363 aa）	Not recorded	PTX {[(2E)-2-(2-AMINO-1,3-THIAZOL-4-YL)-2-(METHOXYIMINO)ETHANOYL]AMINO}METHYLPHOSPHONIC ACID × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；296 K；PEG 8000, HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 1.37 Å R-free 0.195
1XX2 Refinement of P99 beta-lactamase from Enterobacter cloacae Deposited 2004-11-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–381（361 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；PEG 8000, SODIUM CACODYLATE, MgCl2, NaN3, pH 6.5 - 8.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.88 Å R-free 0.214
1XX2 Refinement of P99 beta-lactamase from Enterobacter cloacae Deposited 2004-11-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 21–381（361 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；PEG 8000, SODIUM CACODYLATE, MgCl2, NaN3, pH 6.5 - 8.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.88 Å R-free 0.214
2Q9M 4-Substituted Trinems as Broad Spectrum-Lactamase Inhibitors: Structure-based Design, Synthesis and Biological Activity Deposited 2007-06-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–380（359 aa）	Not recorded	LK7 (1R,4S,7AS)-1-(1-FORMYLPROP-1-EN-1-YL)-4-METHOXY-2,4,5,6,7,7A-HEXAHYDRO-1H-ISOINDOLE-3-CARBOXYLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.05M Cacodylate, 30% PEG8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.05 Å R-free 0.245
2Q9N 4-Substituted Trinems as Broad Spectrum-Lactamase Inhibitors: Structure-based Design, Synthesis and Biological Activity Deposited 2007-06-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–380（359 aa）	Not recorded	LK5 (1S,4R,7AR)-4-BUTOXY-1-[(1R)-1-FORMYLPROPYL]-2,4,5,6,7,7A-HEXAHYDRO-1H-ISOINDOLE-3-CARBOXYLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；292 K；0.1M sodium acetate 0.2M ammonium acetate 22% PEG4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.20 Å R-free 0.315
3S4X Crystal structure of the Asn152Gly mutant of P99 beta-lactamase Deposited 2011-05-20	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 21–381（361 aa）	Mutation：I16V, A88P, N152G, A299V	SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.15 M ammonium sulfate, 30% polyethylene glycol (PEG) 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.95 Å R-free 0.234
3S4X Crystal structure of the Asn152Gly mutant of P99 beta-lactamase Deposited 2011-05-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 21–381（361 aa）	Mutation：I16V, A88P, N152G, A299V	SO4 SULFATE ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.15 M ammonium sulfate, 30% polyethylene glycol (PEG) 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.95 Å R-free 0.234
4XUX Structure of ampC bound to RPX-7009 at 1.75 A Deposited 2015-01-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–381（361 aa） Fragment：UNP residues 21-381	Not recorded	4D6 Vaborbactam × 1 EDO 1,2-ETHANEDIOL × 2 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；30mg/ml AmpC, 30% PEG3000, 0.1M TRIS, PH 7.0, 0.2M NACL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K	Resolution 1.75 Å R-free 0.186
5HAI P99 beta-lactamase mutant - S64G Deposited 2015-12-30	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 21–381（361 aa） Fragment：UNP residues 21-381	Mutation：S64G	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；0.1M SPG buffer (succinic acid, sodium dihydrogen phosphate, and glycine) and 25% PEG 1500	Resolution 2.74 Å R-free 0.243
5XHR Crystal structure of P99 beta-lactamase in complex with a penicillin derivative MPC-1 Deposited 2017-04-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–381（361 aa） Fragment：UNP residues 21-381	Not recorded	PXH (2~{R},4~{S})-5,5-dimethyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-5-thiophen-2-yl-pentan-2-yl]-1,3-thiazolidine-4-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Bis-Tris pH 6.5, 25% PEG3350	Resolution 1.80 Å R-free 0.233
7TI1 Structure of AmpC bound to RPX-7063 at 2.0A Deposited 2022-01-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–381（381 aa）	Not recorded	ZXQ {(3R,7S)-2-hydroxy-3-[2-(thiophen-2-yl)acetamido]-2,3,4,7-tetrahydro-1,2-oxaborepin-7-yl}acetic acid × 1 EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；30% PEG3000, 0.1M Tris pH 7.0, 0.2M NaCl	Resolution 2.00 Å R-free 0.214

11 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AMPC_ENTCL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–361； UniProt 21–381

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1y54
Deposition date deposition_date	2004-12-02
Structure title title	Crystal structure of the native class C beta-lactamase from Enterobacter cloacae 908R complexed with BRL42715
Keywords keywords	class C beta-lactamase, Hydrolase; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	20.68 Å
Radius of gyration Rg (electron density) rg_electron	19.64 Å
Forward intensity I(0) i0	25200200.00
Molecular weight molecular_weight	39344.0 kDa
Excluded volume excluded_volume	49606 Å³
Envelope volume envelope_volume	55382 Å³
Hydration-shell volume shell_volume	23015 Å³
Envelope diameter envelope_diameter	72.4 Å
Shell Rg shell_rg	26.72 Å
Envelope Rg envelope_rg	19.90 Å
Shape Rg shape_rg	19.63 Å
Total Rg total_rg	20.59 Å
Total atoms total_atoms	2775
Residues n_residues	359
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

▼

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

Maximum dimension Dmax dmax	67.2 Å
Rg (real space) rg_real	20.57 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	2.5200e+07
I(0) uncertainty (real space) i0_real_error	3.3680e+05
Rg (reciprocal space) rg_reciprocal	20.59 Å
I(0) (reciprocal space) i0_reciprocal	25200000.0000
Solution quality estimate total_estimate	0.8032
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.3 Å
Skewness Skewness skewness	0.211
Kurtosis Kurtosis kurtosis	-0.315
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8207000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.814; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Beta-lactamase
Molecular weight formula_weight	39309.8 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	2916

TPVSEKQLAEVVANTITPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLVRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ

来源 Source

来源生物 organism	Enterobacter cloacae
NCBI Class编号 ncbi_taxonomy_id	550
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(7R)-6-FORMYL-7-(1-METHYL-1H-1,2,3-TRIAZOL-4-YL)-4,7-DIHYDRO-1,4-THIAZEPINE-3-CARBOXYLIC ACID
Molecular weight formula_weight	266.3 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	141

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1y54a_
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	1y54A00
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	44.365 Å
Unit-cell length b length_b	82.221 Å
Unit-cell length c length_c	96.156 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2270
R_work r_work	0.2268
R_free r_free	0.2919

fit	/app/data/saxs_computation/y5/1y54/1y54.fit
pddf	/app/data/pr_computation/y5/1y54/1y54.pr.out
profile	/app/data/saxs_computation/y5/1y54/1y54.dat

Crystal structure of the native class C beta-lactamase from Enterobacter cloacae 908R complexed with BRL42715

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