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- PDB-1vm1: STRUCTURE OF SHV-1 BETA-LACTAMASE INHIBITED BY TAZOBACTAM -

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Basic information

Entry
Database: PDB / ID: 1vm1
TitleSTRUCTURE OF SHV-1 BETA-LACTAMASE INHIBITED BY TAZOBACTAM
ComponentsBETA-LACTAMASE SHV-1
KeywordsHYDROLASE / Beta-LACTAMASE / BETA-LACTAM HYDROLASE / PENICILLINASE / DETERGENT Binding / Inhibitor design
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACRYLIC ACID / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE / TAZOBACTAM / TAZOBACTAM INTERMEDIATE / Beta-lactamase SHV-1 / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsKuzin, A.P. / Nukaga, M. / Nukaga, Y. / Hujer, A. / Bonomo, R.A. / Knox, J.R.
Citation
Journal: Biochemistry / Year: 2001
Title: Inhibition of the SHV-1 beta-lactamase by sulfones: crystallographic observation of two reaction intermediates with tazobactam.
Authors: Kuzin, A.P. / Nukaga, M. / Nukaga, Y. / Hujer, A. / Bonomo, R.A. / Knox, J.R.
#1: Journal: Biochemistry / Year: 1999
Title: Structure of the SHV-1 Beta-Lactamase
Authors: Kuzin, A.P. / Nukaga, M. / Nukaga, Y. / Hujer, A.M. / Bonomo, R.A. / Knox, J.R.
History
DepositionAug 27, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionSep 7, 2004ID: 1G56
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE SHV-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5996
Polymers28,9071
Non-polymers1,6925
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.200, 56.100, 82.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein BETA-LACTAMASE SHV-1


Mass: 28907.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: BLA / Plasmid: PBCSK / Species (production host): Escherichia coli
Production host: Escherichia coli str. K-12 substr. DH10B (bacteria)
Strain (production host): DH10B
References: UniProt: Q9F643, UniProt: P0AD64*PLUS, beta-lactamase

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Non-polymers , 5 types, 180 molecules

#2: Chemical ChemComp-MA4 / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE


Mass: 508.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H44O11 / Details: Synthesized by Wyeth-Ayerst
#3: Chemical ChemComp-TBE / TAZOBACTAM INTERMEDIATE


Mass: 302.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N4O5S / Details: From Hampton Research, made by Analabs.
#4: Chemical ChemComp-AKR / ACRYLIC ACID / Acrylic acid


Mass: 72.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O2
#5: Chemical ChemComp-TAZ / TAZOBACTAM / Tazobactam


Mass: 300.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4O5S / Comment: antibiotic*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% PEG-6000, 50 mM HEPES, 0.56 mM Cymal-6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.54 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Feb 1, 1999 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.541
ReflectionResolution: 2.02→50 Å / Num. all: 14540 / Num. obs: 13813 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.077 / Net I/σ(I): 12.1
Reflection shellResolution: 2.02→2.14 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1843 / Rsym value: 0.26 / % possible all: 72

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SHV

1shv


Resolution: 2.02→50 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 727 5 %RANDOM
Rwork0.171 ---
all0.177 14540 --
obs0.177 13813 95 %-
Displacement parametersBiso mean: 15.2 Å2
Refine analyzeLuzzati coordinate error free: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.02→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 87 175 2285
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_deg2.3
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs
2.02-2.1330.273746.70.1467521459
2.133-2.2450.251870.1361690
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARALLHDG.PROTOPALLHDG.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARM.MA1TOPH.MA1

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