SAXSdb — 4oqg

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

Ampicillin resistance protein

Escherichia coli

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 24–286	Fragment：TEM-1	2UL 3-[(2R)-2-{[(2R)-2-amino-2-phenylacetyl]amino}-2-(dihydroxyboranyl)ethyl]benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；6% PEG 8000, 100 mM MES buffer, 200mM Ca(OAc)2 and 50 M NaF, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.264
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 24–286	Fragment：TEM-1	2UL 3-[(2R)-2-{[(2R)-2-amino-2-phenylacetyl]amino}-2-(dihydroxyboranyl)ethyl]benzoic acid × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；6% PEG 8000, 100 mM MES buffer, 200mM Ca(OAc)2 and 50 M NaF, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.264
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 24–286	Fragment：TEM-1	2UL 3-[(2R)-2-{[(2R)-2-amino-2-phenylacetyl]amino}-2-(dihydroxyboranyl)ethyl]benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；6% PEG 8000, 100 mM MES buffer, 200mM Ca(OAc)2 and 50 M NaF, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.264
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 24–286	Fragment：TEM-1	2UL 3-[(2R)-2-{[(2R)-2-amino-2-phenylacetyl]amino}-2-(dihydroxyboranyl)ethyl]benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；6% PEG 8000, 100 mM MES buffer, 200mM Ca(OAc)2 and 50 M NaF, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.264
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 24–286	Fragment：TEM-1	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；6% PEG 8000, 100 mM MES buffer, 200mM Ca(OAc)2 and 50 M NaF, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.264
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 24–286	Fragment：TEM-1	2UL 3-[(2R)-2-{[(2R)-2-amino-2-phenylacetyl]amino}-2-(dihydroxyboranyl)ethyl]benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；6% PEG 8000, 100 mM MES buffer, 200mM Ca(OAc)2 and 50 M NaF, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.264

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 4OQG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3C7U Structural Insight into the Kinetics and Cp of interactions between TEM-1-Lactamase and BLIP Deposited 2008-02-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 24–286（263 aa）	Mutation：W150A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；298 K；15% PEG 8000, 0.1M Phosphate-Citrate, 0.1M NaCl, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.20 Å R-free 0.232
3C7U Structural Insight into the Kinetics and Cp of interactions between TEM-1-Lactamase and BLIP Deposited 2008-02-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 24–286（263 aa）	Mutation：W150A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；298 K；15% PEG 8000, 0.1M Phosphate-Citrate, 0.1M NaCl, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.20 Å R-free 0.232
3C7V Structural Insight into the Kinetics and Delta-Cp of interactions between TEM-1 Beta-Lactamase and BLIP Deposited 2008-02-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 24–286（263 aa）	Mutation：Y51A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；298 K；12% PEG 8000, 0.1M Phosphate-Citrate, 0.1M NaCl, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.07 Å R-free 0.238
3C7V Structural Insight into the Kinetics and Delta-Cp of interactions between TEM-1 Beta-Lactamase and BLIP Deposited 2008-02-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 24–286（263 aa）	Mutation：Y51A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；298 K；12% PEG 8000, 0.1M Phosphate-Citrate, 0.1M NaCl, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.07 Å R-free 0.238
3DTM Increased folding stability of TEM-1 beta-lactamase by in-vitro selection Deposited 2008-07-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–286（263 aa） Fragment：UNP residues 24-286	Mutation：P62S, V80I, E147G, M182T, L201P, I208M, A224V, I246V, L273R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；1.6-1.8 M Ammonium citrate, 5% PEG 400, 0.1M Tris buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.00 Å R-free 0.272
3TOI Tailoring Enzyme Stability and Exploiting Stability-Trait Linkage by Iterative Truncation and Optimization Deposited 2011-09-05	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 39–283（245 aa） Fragment：UNP residues 39-283	Mutation：I56V, R120G, M182T, T195S, I208M, A224V, R241H, T265M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.2 M imidazole maleate, 44% PEG600, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.90 Å R-free 0.237
3TOI Tailoring Enzyme Stability and Exploiting Stability-Trait Linkage by Iterative Truncation and Optimization Deposited 2011-09-05	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 39–283（245 aa） Fragment：UNP residues 39-283	Mutation：I56V, R120G, M182T, T195S, I208M, A224V, R241H, T265M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.2 M imidazole maleate, 44% PEG600, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.90 Å R-free 0.237

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q79DR3_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–263； UniProt 24–286 Author chain B； PDBConstruct 1–263； UniProt 24–286 Author chain C； PDBConstruct 1–263； UniProt 24–286 Author chain D； PDBConstruct 1–263； UniProt 24–286 Author chain E； PDBConstruct 1–263； UniProt 24–286 Author chain F； PDBConstruct 1–263； UniProt 24–286

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	4oqg
Deposition date deposition_date	2014-02-09
Structure title title	Crystal structure of TEM-1 beta-lactamase in complex with boron-based inhibitor EC25
Keywords keywords	Beta-lactamase, hydrolase-hydrolase inhibitor complex; hydrolase/hydrolase inhibitor
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	45.55 Å
Radius of gyration Rg (electron density) rg_electron	45.52 Å
Forward intensity I(0) i0	466746000.00
Molecular weight molecular_weight	175430.0 kDa
Excluded volume excluded_volume	218860 Å³
Envelope volume envelope_volume	303420 Å³
Hydration-shell volume shell_volume	57498 Å³
Envelope diameter envelope_diameter	151.5 Å
Shell Rg shell_rg	48.21 Å
Envelope Rg envelope_rg	44.25 Å
Shape Rg shape_rg	45.53 Å
Total Rg total_rg	45.60 Å
Total atoms total_atoms	12306
Residues n_residues	1578
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	154.4 Å
Rg (real space) rg_real	45.65 Å
Rg uncertainty (real space) rg_real_error	1.57 Å
I(0) (real space) i0_real	4.6670e+08
I(0) uncertainty (real space) i0_real_error	9.4060e+06
Rg (reciprocal space) rg_reciprocal	45.55 Å
I(0) (reciprocal space) i0_reciprocal	466700000.0000
Solution quality estimate total_estimate	0.5850
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	52.9 Å
Skewness Skewness skewness	0.313
Kurtosis Kurtosis kurtosis	-0.521
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21600000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 0.010; Positv: 1.000; Valcen: 0.933; Smooth: 0.000

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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	Ampicillin resistance protein
Molecular weight formula_weight	28984.1 kDa
EC 编号 ec_number	3.5.2.6
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	12393

HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	3-[(2R)-2-{[(2R)-2-amino-2-phenylacetyl]amino}-2-(dihydroxyboranyl)ethyl]benzoic acid
Molecular weight formula_weight	342.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	71

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4oqga_
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

Domain ID domain_id	d4oqgb_
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

Domain ID domain_id	d4oqgc_
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

Domain ID domain_id	d4oqgd_
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

Domain ID domain_id	d4oqge_
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

Domain ID domain_id	d4oqgf_
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 (6 domains)

Domain ID domain_id	4oqgA00
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

Domain ID domain_id	4oqgB00
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

Domain ID domain_id	4oqgC00
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

Domain ID domain_id	4oqgD00
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

Domain ID domain_id	4oqgE00
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

Domain ID domain_id	4oqgF00
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 (1)

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Unit-cell length a length_a	81.690 Å
Unit-cell length b length_b	81.690 Å
Unit-cell length c length_c	497.920 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	48

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	45.810 Å
R factor r_factor	0.2060
R_work r_work	0.2030
R_free r_free	0.2640

fit	/app/data/saxs_computation/oq/4oqg/4oqg.fit
pddf	/app/data/pr_computation/oq/4oqg/4oqg.pr.out
profile	/app/data/saxs_computation/oq/4oqg/4oqg.dat

Crystal structure of TEM-1 beta-lactamase in complex with boron-based inhibitor EC25

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

Ampicillin resistance protein

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