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- PDB-5f82: Apo GES-5 C69G mutant -

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Basic information

Entry
Database: PDB / ID: 5f82
TitleApo GES-5 C69G mutant
ComponentsBeta-lactamase
KeywordsHYDROLASE / carbapenemase / 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, 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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.96 Å
AuthorsSmith, C.A. / Vakulenko, S.B.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Role of the Conserved Disulfide Bridge in Class A Carbapenemases.
Authors: Smith, C.A. / Nossoni, Z. / Toth, M. / Stewart, N.K. / Frase, H. / Vakulenko, S.B.
History
DepositionDec 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Oct 26, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_detector.type / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0685
Polymers62,3532
Non-polymers7153
Water16,844935
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6533
Polymers31,1761
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4152
Polymers31,1761
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.711, 80.939, 71.052
Angle α, β, γ (deg.)90.00, 101.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase / GES-5


Mass: 31176.375 Da / Num. of mol.: 2 / Mutation: C69G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaGES-5 / Production host: Escherichia coli (E. coli) / References: UniProt: A0EL75, beta-lactamase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 935 / 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: 1.93 Å3/Da / Density % sol: 36.3 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M D,L-malic acid, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9495 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 27, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9495 Å / Relative weight: 1
ReflectionResolution: 0.96→37.2 Å / Num. obs: 280826 / % possible obs: 97.6 % / Redundancy: 3.5 % / Net I/σ(I): 13.6
Reflection shellResolution: 0.96→0.98 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.2 / % possible all: 73.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.96→37.192 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.67 / Phase error: 10.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1339 14245 5.07 %RANDOM
Rwork0.1179 ---
obs0.1187 281215 97.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.96→37.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4043 0 45 935 5023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084438
X-RAY DIFFRACTIONf_angle_d1.3996059
X-RAY DIFFRACTIONf_dihedral_angle_d14.5881715
X-RAY DIFFRACTIONf_chiral_restr0.077690
X-RAY DIFFRACTIONf_plane_restr0.007791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.96-0.97090.24463300.23936345X-RAY DIFFRACTION70
0.9709-0.98230.22893530.21397096X-RAY DIFFRACTION78
0.9823-0.99430.20824450.19738516X-RAY DIFFRACTION94
0.9943-1.00690.19754670.17699073X-RAY DIFFRACTION100
1.0069-1.02020.17475060.16229052X-RAY DIFFRACTION100
1.0202-1.03410.16434870.15119050X-RAY DIFFRACTION100
1.0341-1.04890.16574780.13839019X-RAY DIFFRACTION100
1.0489-1.06460.14354840.13239087X-RAY DIFFRACTION100
1.0646-1.08120.14614550.12329040X-RAY DIFFRACTION100
1.0812-1.09890.13465100.12099075X-RAY DIFFRACTION100
1.0989-1.11790.12964880.11139033X-RAY DIFFRACTION100
1.1179-1.13820.11614580.10769079X-RAY DIFFRACTION100
1.1382-1.16010.1184930.10219089X-RAY DIFFRACTION100
1.1601-1.18380.12924840.10089072X-RAY DIFFRACTION100
1.1838-1.20950.10724930.09989015X-RAY DIFFRACTION100
1.2095-1.23770.1135120.10159029X-RAY DIFFRACTION100
1.2377-1.26860.1215250.10169017X-RAY DIFFRACTION100
1.2686-1.30290.12024670.10199061X-RAY DIFFRACTION100
1.3029-1.34130.11245010.10189038X-RAY DIFFRACTION99
1.3413-1.38450.11324710.10119095X-RAY DIFFRACTION100
1.3845-1.4340.11164630.10059051X-RAY DIFFRACTION100
1.434-1.49140.11935110.09899053X-RAY DIFFRACTION100
1.4914-1.55930.11565220.09929051X-RAY DIFFRACTION100
1.5593-1.64150.11534540.10219160X-RAY DIFFRACTION100
1.6415-1.74440.13134850.10899045X-RAY DIFFRACTION100
1.7444-1.87910.12984590.11679151X-RAY DIFFRACTION100
1.8791-2.06820.13265080.11729085X-RAY DIFFRACTION100
2.0682-2.36740.12324540.11269166X-RAY DIFFRACTION100
2.3674-2.98250.1384850.12149112X-RAY DIFFRACTION100
2.9825-37.21950.14934970.12929215X-RAY DIFFRACTION99

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