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- PDB-3hre: X-ray crystallographic structure of CTX-M-9 S70G -

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Basic information

Entry
Database: PDB / ID: 3hre
TitleX-ray crystallographic structure of CTX-M-9 S70G
ComponentsCTX-M-9 extended-spectrum beta-lactamase
KeywordsHYDROLASE / beta-lactamase / BLSE / CTX-M-9 / Antibiotic resistance
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
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsDelmas, J. / Leyssene, D. / Dubois, D. / Vazeille, E. / Robin, F. / Bonnet, R.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural insights into substrate recognition and product expulsion in CTX-M enzymes.
Authors: Delmas, J. / Leyssene, D. / Dubois, D. / Birck, C. / Vazeille, E. / Robin, F. / Bonnet, R.
History
DepositionJun 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2013Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CTX-M-9 extended-spectrum beta-lactamase
B: CTX-M-9 extended-spectrum beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1705
Polymers55,8852
Non-polymers2853
Water16,790932
1
A: CTX-M-9 extended-spectrum beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1323
Polymers27,9421
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CTX-M-9 extended-spectrum beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0372
Polymers27,9421
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.069, 106.291, 47.543
Angle α, β, γ (deg.)90.000, 102.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CTX-M-9 extended-spectrum beta-lactamase / Beta-lactamase / Beta-lactamase CTX-M-9a / Betalactamase CTX-M-9 / CTX-M-9 beta-lactamase


Mass: 27942.467 Da / Num. of mol.: 2 / Fragment: UNP residues 29-291 / Mutation: S70G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M-9, blaCTX-M-9a, blaCTX-M-9b / Plasmid: pET9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE03) / References: UniProt: Q9L5C8, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 932 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE NUMBERS 58, 239, 253 ARE SIMPLY SKIPPED.

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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: 38.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: potassium phosphate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2008 / Details: Single Silicon (111) monochromator
RadiationMonochromator: Single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 82496 / Num. obs: 78452 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 22.43
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.43 / Num. unique all: 7779 / % possible all: 91

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
DNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P74

2p74


Resolution: 1.45→42.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.184 3724 5 %RANDOM
Rwork0.154 ---
obs0.156 74760 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 298.1 Å2 / Biso mean: 10.506 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.131 Å
Refinement stepCycle: LAST / Resolution: 1.45→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 15 932 4847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224152
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.975683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5095570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80524.525179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51315708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8071535
X-RAY DIFFRACTIONr_chiral_restr0.10.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023151
X-RAY DIFFRACTIONr_nbd_refined0.2440.22270
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2771
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.2114
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.2123
X-RAY DIFFRACTIONr_mcbond_it0.5221.52679
X-RAY DIFFRACTIONr_mcangle_it0.93224321
X-RAY DIFFRACTIONr_scbond_it1.48331473
X-RAY DIFFRACTIONr_scangle_it2.4044.51334
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 258 -
Rwork0.166 4992 -
all-5250 -
obs--92.51 %

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