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- PDB-1tdg: Complex of S130G SHV-1 beta-lactamase with tazobactam -

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Basic information

Entry
Database: PDB / ID: 1tdg
TitleComplex of S130G SHV-1 beta-lactamase with tazobactam
ComponentsBeta-lactamase SHV-1
KeywordsHYDROLASE / S130G SHV-1 class A beta-lactamase / penicillinase / beta-lactam hydrolase / detergent binding / inhibitor complex / tazobactam / aldehyde / cymal-6
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
CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE / MALONALDEHYDE / TAZOBACTAM INTERMEDIATE / Beta-lactamase SHV-1 / Beta-lactamase SHV-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSun, T. / Bethel, C.R. / Bonomo, R.A. / Knox, J.R.
CitationJournal: Biochemistry / Year: 2004
Title: Inhibitor-resistant class A beta-lactamases: consequences of the Ser130-to-Gly mutation seen in Apo and tazobactam structures of the SHV-1 variant
Authors: Sun, T. / Bethel, C.R. / Bonomo, R.A. / Knox, J.R.
History
DepositionMay 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / 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.pdbx_ptnr2_label_alt_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN Apparent short contacts between the 2 intermediates, TBE and MDD, arise because the ...HETEROGEN Apparent short contacts between the 2 intermediates, TBE and MDD, arise because the crystal structure contains a composite of 2 complexes, one a breakdown product of the other.

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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)30,5057
Polymers28,8771
Non-polymers1,6286
Water7,134396
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.834, 55.255, 83.571
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 / PIT-2


Mass: 28876.994 Da / Num. of mol.: 1 / Mutation: S130G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla / Plasmid: pBC SK / Species (production host): Escherichia coli
Production host: Escherichia coli str. K-12 substr. DH10B (bacteria)
Strain (production host): DH10B
References: UniProt: P14557, UniProt: P0AD64*PLUS, beta-lactamase

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Non-polymers , 6 types, 402 molecules

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


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


Mass: 302.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N4O5S
#4: Chemical ChemComp-MDD / MALONALDEHYDE / Malondialdehyde


Mass: 72.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O2
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 1.99 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% PEG 6000, 50 mM HEPES, 0.56 mM Cymal-6 detergent, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jul 1, 2003 / Details: double-mirror Franks focusing
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→28 Å / Num. all: 22043 / Num. obs: 20318 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 14.8
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3624 / Rsym value: 0.138 / % possible all: 79.1

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Processing

Software
NameClassification
FRAMBOdata collection
X-GENdata reduction
EPMRphasing
CNSrefinement
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SHV

1shv


Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Atoms having alternate conformations are only listed once in the above list of the number of atoms used in the refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.176 964 -random
Rwork0.14 ---
all0.141 22020 --
obs0.141 20094 91.3 %-
Displacement parametersBiso mean: 10.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 86 396 2504
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.8-1.910.20361510.1753X-RAY DIFFRACTION276979
1.91-2.060.19731450.1487X-RAY DIFFRACTION314789
2.06-2.270.1871430.1462X-RAY DIFFRACTION330992
2.27-2.60.18081660.1336X-RAY DIFFRACTION343395
2.6-3.270.17531760.1368X-RAY DIFFRACTION360898
3.27-200.15111830.1291X-RAY DIFFRACTION3828100

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