SAXSdb — 1kr3

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

beta-Lactamase, type II

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 18–249	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 18–249	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

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 1KR3	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 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 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 mutation/modification 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 mutation/modification 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 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 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
1ZNB METALLO-BETA-LACTAMASE Deposited 1996-06-06	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 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
2BMI METALLO-BETA-LACTAMASE Deposited 1998-09-17	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 18–249（232 aa） Chain B 18–249（232 aa）	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
2ZNB METALLO-BETA-LACTAMASE (CADMIUM-BOUND FORM) Deposited 1997-10-14	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 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 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 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 mutation/modification 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 mutation/modification 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 14 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	1kr3
Deposition date deposition_date	2002-01-08
Structure title title	Crystal Structure of the Metallo beta-Lactamase from Bacteroides fragilis (CfiA) in Complex with the Tricyclic Inhibitor SB-236050.
Keywords keywords	beta sandwich, protein-inhibitor complex, metallo, beta-lactamase, 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	26.27 Å
Radius of gyration Rg (electron density) rg_electron	25.49 Å
Forward intensity I(0) i0	42682200.00
Molecular weight molecular_weight	50460.0 kDa
Excluded volume excluded_volume	62929 Å³
Envelope volume envelope_volume	75809 Å³
Hydration-shell volume shell_volume	25307 Å³
Envelope diameter envelope_diameter	82.8 Å
Shell Rg shell_rg	32.26 Å
Envelope Rg envelope_rg	25.34 Å
Shape Rg shape_rg	25.50 Å
Total Rg total_rg	26.21 Å
Total atoms total_atoms	3536
Residues n_residues	454
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	80.8 Å
Rg (real space) rg_real	26.32 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	4.2680e+07
I(0) uncertainty (real space) i0_real_error	5.4890e+05
Rg (reciprocal space) rg_reciprocal	26.30 Å
I(0) (reciprocal space) i0_reciprocal	42680000.0000
Solution quality estimate total_estimate	0.8969
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.329
Kurtosis Kurtosis kurtosis	-0.640
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17130000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.914

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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, type II
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	3576

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

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 non-polymer

Description description	7,8-DIHYDROXY-1-METHOXY-3-METHYL-10-OXO-4,10-DIHYDRO-1H,3H-PYRANO[4,3-B]CHROMENE-9-CARBOXYLIC ACID
Molecular weight formula_weight	322.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	40

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1kr3a_
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	d1kr3b_
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	1kr3A00
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	1kr3B00
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 (1)

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Unit-cell length a length_a	41.800 Å
Unit-cell length b length_b	44.200 Å
Unit-cell length c length_c	58.500 Å
Unit-cell angle α angle_alpha	92.80 °
Unit-cell angle β angle_beta	95.30 °
Unit-cell angle γ angle_gamma	98.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	29.070 Å
R factor r_factor	0.1520
R_work r_work	0.1520
R_free r_free	0.2220

fit	/app/data/saxs_computation/kr/1kr3/1kr3.fit
pddf	/app/data/pr_computation/kr/1kr3/1kr3.pr.out
profile	/app/data/saxs_computation/kr/1kr3/1kr3.dat

Crystal Structure of the Metallo beta-Lactamase from Bacteroides fragilis (CfiA) in Complex with the Tricyclic Inhibitor SB-236050.

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

beta-Lactamase, type II

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