SAXSdb — 1bul

▼

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

NMC-A BETA-LACTAMASE

OrganismNot specified

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 28–292	Not recorded	AP3 2-(1-CARBOXY-2-HYDROXY-2-METHYL-PROPYL)-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；20% (W/V)PEG 1500, 0.200 M MES PH 5.25, 6% (V/V) N-PROPANOL, pH 7.5	Resolution 1.89 Å R-free 0.257

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 1BUL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BUE NMC-A CARBAPENEMASE FROM ENTEROBACTER CLOACAE Deposited 1998-09-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–292（265 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.25；INITIAL PROTEIN CONCENTRATION WAS 2.0 G/L EQUILIBRATED AGAINST 0.200 M MES PH 5.25, 20% (W/V)PEG 1500, 6% (V/V) N-PROPANOL AT 295K.	Resolution 1.64 Å R-free 0.214

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BLAN_ENTCL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–265； UniProt 28–292

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	1bul
Deposition date deposition_date	1998-09-04
Structure title title	6ALPHA-(HYDROXYPROPYL)PENICILLANATE ACYLATED ON NMC-A BETA-LACTAMASE FROM ENTEROBACTER CLOACAE
Keywords keywords	HYDROLASE, ANTIBIOTIC RESISTANCE, CLASS A CARBAPENEMASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	19.28 Å
Radius of gyration Rg (electron density) rg_electron	18.09 Å
Forward intensity I(0) i0	16590700.00
Molecular weight molecular_weight	29857.0 kDa
Excluded volume excluded_volume	37010 Å³
Envelope volume envelope_volume	41383 Å³
Hydration-shell volume shell_volume	18970 Å³
Envelope diameter envelope_diameter	68.6 Å
Shell Rg shell_rg	24.69 Å
Envelope Rg envelope_rg	18.61 Å
Shape Rg shape_rg	18.05 Å
Total Rg total_rg	19.11 Å
Total atoms total_atoms	2096
Residues n_residues	265
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	65.9 Å
Rg (real space) rg_real	19.22 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	1.6590e+07
I(0) uncertainty (real space) i0_real_error	2.1520e+05
Rg (reciprocal space) rg_reciprocal	19.23 Å
I(0) (reciprocal space) i0_reciprocal	16590000.0000
Solution quality estimate total_estimate	0.6397
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.316
Kurtosis Kurtosis kurtosis	-0.166
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4287000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.753; Stabil: 1.000; Sysdev: 0.356; Positv: 1.000; Valcen: 0.987; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	NMC-A BETA-LACTAMASE
Molecular weight formula_weight	29137.6 kDa
EC 编号 ec_number	3.5.2.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2292

NTKGIDEIKNLETDFNGRIGVYALDTGSGKSFSYRANERFPLCSSFKGFLAAAVLKGSQDNRLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDEDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILSEHEKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASRIAIDNLK

Entity 2 Entity 2 non-polymer

Description description	2-(1-CARBOXY-2-HYDROXY-2-METHYL-PROPYL)-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID
Molecular weight formula_weight	277.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	191

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bula_
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	1bulA00
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	77.550 Å
Unit-cell length b length_b	52.460 Å
Unit-cell length c length_c	67.220 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	1.890 Å
Low-resolution limit resolution_low	18.600 Å
R factor r_factor	0.2090
R_work r_work	0.2090
R_free r_free	0.2570

fit	/app/data/saxs_computation/bu/1bul/1bul.fit
pddf	/app/data/pr_computation/bu/1bul/1bul.pr.out
profile	/app/data/saxs_computation/bu/1bul/1bul.dat

6ALPHA-(HYDROXYPROPYL)PENICILLANATE ACYLATED ON NMC-A BETA-LACTAMASE FROM ENTEROBACTER CLOACAE

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

NMC-A 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