SAXSdb — 2bmi

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

PROTEIN (CLASS B BETA-LACTAMASE)

Bacteroides fragilis

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 18–249 Chain B； UniProt 18–249	Not recorded	ZN ZINC ION × 4 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 9；FORM II CRYSTAL IN ACTA CRYST(1997) D53 485-487, pH 9.0	Resolution 2.00 Å R-free 0.262

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 2BMI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A7T METALLO-BETA-LACTAMASE WITH MES Deposited 1998-03-17	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 18–249（232 aa） Chain B 18–249（232 aa）	Mutation：A171T, D208N Mutation：A171T, D208N	ZN ZINC ION × 4 NA SODIUM ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 100 MM POTASSIUM ACETATE, 100 MM MES, PH 6.1	Resolution 1.85 Å
1A8T METALLO-BETA-LACTAMASE IN COMPLEX WITH L-159,061 Deposited 1998-03-23	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 18–249（232 aa）	Mutation：A171T, D208N	ZN ZINC ION × 2 061 2-BUTYL-6-HYDROXY-3-[2'-(1H-TETRAZOL-5-YL)-BIPHENYL-4-YLMETHYL]-3H-QUINAZOLIN-4-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.6；PROTEIN WAS CRYSTALLIZED FROM 28% PEG 4000, 100 MM SODIUM CHLORIDE, 100 MM SODIUM CACODYLATE BUFFER, PH 6.6	Resolution 2.55 Å R-free 0.319
1A8T METALLO-BETA-LACTAMASE IN COMPLEX WITH L-159,061 Deposited 1998-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 18–249（232 aa）	Mutation：A171T, D208N	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.6；PROTEIN WAS CRYSTALLIZED FROM 28% PEG 4000, 100 MM SODIUM CHLORIDE, 100 MM SODIUM CACODYLATE BUFFER, PH 6.6	Resolution 2.55 Å R-free 0.319
1HLK METALLO-BETA-LACTAMASE FROM BACTEROIDES FRAGILIS IN COMPLEX WITH A TRICYCLIC INHIBITOR Deposited 2000-12-01	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 21–247（227 aa）	Not recorded	ZN ZINC ION × 2 NA SODIUM ION × 1 113 7,8-DIHYDROXY-1-METHOXY-3-METHYL-10-OXO-4,10-DIHYDRO-1H,3H-PYRANO[4,3-B]CHROMENE-9-CARBOXYLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；294 K；20mM HEPES, pH 7.5, 32% PEG 1000, 01M MES, 10 uM ZnCl2, pH 6.0, VAPOR DIFFUSION, SITTING DROP at 294K	Resolution 2.50 Å R-free 0.228
1HLK METALLO-BETA-LACTAMASE FROM BACTEROIDES FRAGILIS IN COMPLEX WITH A TRICYCLIC INHIBITOR Deposited 2000-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 21–247（227 aa）	Not recorded	ZN ZINC ION × 2 NA SODIUM ION × 1 113 7,8-DIHYDROXY-1-METHOXY-3-METHYL-10-OXO-4,10-DIHYDRO-1H,3H-PYRANO[4,3-B]CHROMENE-9-CARBOXYLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；294 K；20mM HEPES, pH 7.5, 32% PEG 1000, 01M MES, 10 uM ZnCl2, pH 6.0, VAPOR DIFFUSION, SITTING DROP at 294K	Resolution 2.50 Å R-free 0.228
1KR3 Crystal Structure of the Metallo beta-Lactamase from Bacteroides fragilis (CfiA) in Complex with the Tricyclic Inhibitor SB-236050. Deposited 2002-01-08	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 18–249（232 aa）	Not recorded	ZN ZINC ION × 2 NA SODIUM ION × 1 113 7,8-DIHYDROXY-1-METHOXY-3-METHYL-10-OXO-4,10-DIHYDRO-1H,3H-PYRANO[4,3-B]CHROMENE-9-CARBOXYLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；32% PEG1000, 0.1M MES, 10microM ZnCl2, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.50 Å R-free 0.222
1KR3 Crystal Structure of the Metallo beta-Lactamase from Bacteroides fragilis (CfiA) in Complex with the Tricyclic Inhibitor SB-236050. Deposited 2002-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 18–249（232 aa）	Not recorded	ZN ZINC ION × 2 NA SODIUM ION × 1 113 7,8-DIHYDROXY-1-METHOXY-3-METHYL-10-OXO-4,10-DIHYDRO-1H,3H-PYRANO[4,3-B]CHROMENE-9-CARBOXYLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；32% PEG1000, 0.1M MES, 10microM ZnCl2, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.50 Å R-free 0.222
1ZNB METALLO-BETA-LACTAMASE Deposited 1996-06-06	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 18–249（232 aa）	Not recorded	ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.85 Å R-free 0.241
1ZNB METALLO-BETA-LACTAMASE Deposited 1996-06-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 18–249（232 aa）	Not recorded	ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.85 Å R-free 0.241
2ZNB METALLO-BETA-LACTAMASE (CADMIUM-BOUND FORM) Deposited 1997-10-14	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 18–249（232 aa）	Not recorded	CD CADMIUM ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；26-28%POLYETHYLENE GLYCOL 4000, 0.1M HEPES, PH 7.0, 0.3M NACL, 10UM CDCL2, AT ROOM TEMPERATURE	Resolution 2.15 Å R-free 0.259
2ZNB METALLO-BETA-LACTAMASE (CADMIUM-BOUND FORM) Deposited 1997-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 18–249（232 aa）	Not recorded	CD CADMIUM ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；26-28%POLYETHYLENE GLYCOL 4000, 0.1M HEPES, PH 7.0, 0.3M NACL, 10UM CDCL2, AT ROOM TEMPERATURE	Resolution 2.15 Å R-free 0.259
3ZNB METALLO-BETA-LACTAMASE (ZN, HG-BOUND FORM) Deposited 1997-10-15	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 18–249（232 aa）	Not recorded	ZN ZINC ION × 1 HG MERCURY (II) ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；27-29% POLYETHYLENE GLYCOL 2000, 0.1M HEPES, PH 7.0, 10UM ZNCL2, 0.3M NACL, AT ROOM TEMPERATURE. THE CRYSTALS WERE SOAKED OVERNIGHT AT ROOM TEMPERATURE IN 10MM K2HGI4 + 20MM KI.	Resolution 2.70 Å R-free 0.268
3ZNB METALLO-BETA-LACTAMASE (ZN, HG-BOUND FORM) Deposited 1997-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 18–249（232 aa）	Not recorded	ZN ZINC ION × 1 HG MERCURY (II) ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；27-29% POLYETHYLENE GLYCOL 2000, 0.1M HEPES, PH 7.0, 10UM ZNCL2, 0.3M NACL, AT ROOM TEMPERATURE. THE CRYSTALS WERE SOAKED OVERNIGHT AT ROOM TEMPERATURE IN 10MM K2HGI4 + 20MM KI.	Resolution 2.70 Å R-free 0.268
4ZNB METALLO-BETA-LACTAMASE (C181S MUTANT) Deposited 1998-10-20	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 18–249（232 aa）	Mutation：C181S	ZN ZINC ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.65 Å R-free 0.250
4ZNB METALLO-BETA-LACTAMASE (C181S MUTANT) Deposited 1998-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 18–249（232 aa）	Mutation：C181S	ZN ZINC ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.65 Å R-free 0.250

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

View Construct and Data Evidence

UniProt name	BLAB_BACFR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–232； UniProt 18–249 Author chain B； PDBConstruct 1–232； UniProt 18–249

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	2bmi
Deposition date deposition_date	1998-09-17
Structure title title	METALLO-BETA-LACTAMASE
Keywords keywords	BETA-LACTAMASE, METALLO BETA-LACTAMASE, ZINC, HYDROLASE; 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	25.05 Å
Radius of gyration Rg (electron density) rg_electron	24.05 Å
Forward intensity I(0) i0	42506000.00
Molecular weight molecular_weight	50185.0 kDa
Excluded volume excluded_volume	62603 Å³
Envelope volume envelope_volume	73284 Å³
Hydration-shell volume shell_volume	25609 Å³
Envelope diameter envelope_diameter	87.3 Å
Shell Rg shell_rg	30.89 Å
Envelope Rg envelope_rg	24.50 Å
Shape Rg shape_rg	24.06 Å
Total Rg total_rg	24.81 Å
Total atoms total_atoms	3516
Residues n_residues	458
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	82.0 Å
Rg (real space) rg_real	25.08 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	4.2510e+07
I(0) uncertainty (real space) i0_real_error	6.4760e+05
Rg (reciprocal space) rg_reciprocal	25.07 Å
I(0) (reciprocal space) i0_reciprocal	42510000.0000
Solution quality estimate total_estimate	0.8874
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.0 Å
Skewness Skewness skewness	0.371
Kurtosis Kurtosis kurtosis	-0.440
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13470000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PROTEIN (CLASS B BETA-LACTAMASE)
Molecular weight formula_weight	25358.6 kDa
EC 编号 ec_number	3.5.2.6
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3935

AQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP

来源 Source

来源生物 organism	Bacteroides fragilis
NCBI Class编号 ncbi_taxonomy_id	817
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	419

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2bmia_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.1 — Zn metallo-beta-lactamase

Domain ID domain_id	d2bmib_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.1 — Zn metallo-beta-lactamase

CATH v4.4 (2 domains)

Domain ID domain_id	2bmiA00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	2bmiB00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

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8. Citations (2)

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Unit-cell length a length_a	47.256 Å
Unit-cell length b length_b	94.920 Å
Unit-cell length c length_c	111.420 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.2620

fit	/app/data/saxs_computation/bm/2bmi/2bmi.fit
pddf	/app/data/pr_computation/bm/2bmi/2bmi.pr.out
profile	/app/data/saxs_computation/bm/2bmi/2bmi.dat

METALLO-BETA-LACTAMASE

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

PROTEIN (CLASS B 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