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- PDB-4pvo: Crystal Structure of VIM-2 metallo-beta-lactamase in complex with... -

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Basic information

Entry
Database: PDB / ID: 4pvo
TitleCrystal Structure of VIM-2 metallo-beta-lactamase in complex with ML302 and ML302F
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / alpha-beta/beta-alpha fold / beta-lactamase / HYDROLASE-HYDROLASE INHIBITOR complex
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
FORMIC ACID / Chem-S3C / Chem-SVB / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 Å
AuthorsAik, W.S. / Brem, J. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Nat.Chem. / Year: 2014
Title: Rhodanine hydrolysis leads to potent thioenolate mediated metallo-beta-lactamase inhibition.
Authors: Brem, J. / van Berkel, S.S. / Aik, W. / Rydzik, A.M. / Avison, M.B. / Pettinati, I. / Umland, K.D. / Kawamura, A. / Spencer, J. / Claridge, T.D. / McDonough, M.A. / Schofield, C.J.
History
DepositionMar 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Nov 8, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase class B VIM-2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,08916
Polymers51,3872
Non-polymers1,70214
Water9,656536
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8239
Polymers25,6931
Non-polymers1,1308
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2657
Polymers25,6931
Non-polymers5726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.570, 79.239, 67.967
Angle α, β, γ (deg.)90.000, 131.570, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase class B VIM-2 / Class B beta-lactamase / Metallo beta-lactamase / Metallo-beta-lactamase / Metallo-beta-lactamase ...Class B beta-lactamase / Metallo beta-lactamase / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-2 / Mettalo-beta-lactamase VIM-2 / VIM-2 / VIM-2 class B metallo b-lactamase / VIM-2 protein / VIM-2 type metallo-beta-lactamase


Mass: 25693.488 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla-VIM-2, blasVIM-2, blaVIM-2, blaVIM2, VIM-2 / Plasmid: pOPIN-F VIM-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K2N0

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Non-polymers , 6 types, 550 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-S3C / (2Z)-2-sulfanyl-3-(2,3,6-trichlorophenyl)prop-2-enoic acid


Mass: 283.559 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H5Cl3O2S
#4: Chemical ChemComp-SVB / N-(4-methylpiperazin-1-yl)-2-[(5Z)-4-oxo-2-thioxo-5-(2,3,6-trichlorobenzylidene)-1,3-thiazolidin-3-yl]acetamide


Mass: 479.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17Cl3N4O2S2
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / 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: 2.05 Å3/Da / Density % sol: 39.99 % / Mosaicity: 0.2 ° / Mosaicity esd: 0.004 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1mM TCEP, 2.5mM ML302, 50mM HEPES pH 7.5, 100mM NaCl, 0.1mM ZnCl2, 0.1M magnesium formate, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.8344 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2013 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8344 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. all: 68860 / Num. obs: 68140 / % possible obs: 98.954 % / Observed criterion σ(F): -3 / Redundancy: 5 % / Biso Wilson estimate: 10.65 Å2 / Rmerge(I) obs: 0.136 / Χ2: 1.202 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.48-1.534.10.5682.464321.14993.9
1.53-1.594.40.5322.866711.15197.2
1.59-1.674.60.5143.267881.19798.9
1.67-1.755.10.4334.568331.19899.9
1.75-1.865.10.3335.768891.2399.9
1.86-2.015.30.2428.268631.166100
2.01-2.215.30.17410.668641.186100
2.21-2.535.40.13713.169061.211100
2.53-3.195.20.10116.868971.24100
3.19-505.20.07123.469971.26999.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4-1496)refinement
PDB_EXTRACT3.14data extraction
GDAdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1KO3

1ko3


Resolution: 1.48→39.1 Å / Isotropic thermal model: isotropic
RfactorNum. reflection% reflectionSelection details
Rfree0.1646 2002 2.94 %random
Rwork0.1408 ---
all-68138 --
obs-68092 99.9 %-
Displacement parametersBiso max: 70.96 Å2 / Biso mean: 17.7609 Å2 / Biso min: 5.05 Å2
Refinement stepCycle: LAST / Resolution: 1.48→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3465 0 70 536 4071
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.013
X-RAY DIFFRACTIONf_angle_deg1.518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.4808-1.51790.25951350.2153X-RAY DIFFRACTION450992.1
3.5682-39.1310.14591410.1331X-RAY DIFFRACTION500999.8

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