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- PDB-2ynu: Apo GIM-1 with 2Mol. Crystal structures of Pseudomonas aeruginosa... -

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Basic information

Entry
Database: PDB / ID: 2ynu
TitleApo GIM-1 with 2Mol. Crystal structures of Pseudomonas aeruginosa GIM-1: active site plasticity in metallo-beta-lactamases
ComponentsGIM-1 PROTEIN
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / RESIDUE DETERMINANTS / LOOP DYNAMICS
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsBorra, P.S. / Samuelsen, O. / Spencer, J. / Lorentzen, M.S. / Leiros, H.-K.S.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2013
Title: Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active-Site Plasticity in Metallo-Beta-Lactamases.
Authors: Borra, P.S. / Samuelsen, O. / Spencer, J. / Walsh, T.R. / Lorentzen, M.S. / Leiros, H.-K.S.
History
DepositionOct 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GIM-1 PROTEIN
B: GIM-1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)51,2402
Polymers51,2402
Non-polymers00
Water3,207178
1
A: GIM-1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)25,6201
Polymers25,6201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GIM-1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)25,6201
Polymers25,6201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.788, 135.385, 40.509
Angle α, β, γ (deg.)90.00, 90.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GIM-1 PROTEIN / METALLO-BETA-LACTAMASE GIM-1


Mass: 25619.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR PLYSS PRARE / References: UniProt: Q704V1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-18 IN THE GENE SEQUENCE ARE REMOVED AND A HIS TAG AND TEV CLEAVE SITE WAS INTRODUCED. A ...RESIDUES 1-18 IN THE GENE SEQUENCE ARE REMOVED AND A HIS TAG AND TEV CLEAVE SITE WAS INTRODUCED. A SERINE FROM THE TEV SITE IS THEN THE FIRST RESIDUE FOLLOWED BY GLN19 IN THE GENE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.91 % / Description: NONE
Crystal growDetails: 0.1M TRIS PH 7.1, 21% POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000 (PEG MME 2K), 4% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 2.06→45 Å / Num. obs: 25067 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.1
Reflection shellResolution: 2.06→2.17 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→19.712 Å / SU ML: 0.3 / σ(F): 1.36 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 1268 5.07 %
Rwork0.1852 --
obs0.1878 25008 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→19.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 0 178 3499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153507
X-RAY DIFFRACTIONf_angle_d1.5194781
X-RAY DIFFRACTIONf_dihedral_angle_d15.4651275
X-RAY DIFFRACTIONf_chiral_restr0.085533
X-RAY DIFFRACTIONf_plane_restr0.008609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.14240.33781410.27462717X-RAY DIFFRACTION99
2.1424-2.23980.30491610.2572608X-RAY DIFFRACTION98
2.2398-2.35770.30721500.23712642X-RAY DIFFRACTION98
2.3577-2.50510.25951480.22872639X-RAY DIFFRACTION98
2.5051-2.69810.32361380.21432642X-RAY DIFFRACTION97
2.6981-2.96880.29211180.21632666X-RAY DIFFRACTION97
2.9688-3.39650.24181340.19332624X-RAY DIFFRACTION97
3.3965-4.2720.22631290.16462618X-RAY DIFFRACTION95
4.272-19.71330.18111490.15132584X-RAY DIFFRACTION94

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