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

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Basic information

Entry
Database: PDB / ID: 4pvt
TitleCrystal Structure of VIM-2 metallo-beta-lactamase in complex with ML302F
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / alpha-beta/beta-alpha / 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 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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

Downloads & links

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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)52,62315
Polymers51,3872
Non-polymers1,23613
Water6,233346
1
A: 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
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3578
Polymers25,6931
Non-polymers6647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.391, 78.909, 67.742
Angle α, β, γ (deg.)90.000, 130.320, 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 , 5 types, 359 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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.03 Å3/Da / Density % sol: 39.41 % / Mosaicity: 0.753 ° / Mosaicity esd: 0.01 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1mM TCEP, 1mM ML302F, 50mM HEPES pH 7.5, 100mM NaCl, 0.1mM ZnCl2, 0.1M magnesium formate, 23% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 1, 2013 / Details: Osmic HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 27747 / Num. obs: 27185 / % possible obs: 98 % / Observed criterion σ(F): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 17.32 Å2 / Rmerge(I) obs: 0.175 / Χ2: 1.337 / Net I/σ(I): 6.848
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2-2.073.40.5212.526611.40496.4
2.07-2.153.60.4283.126721.32996.9
2.15-2.253.60.4373.127001.41596.9
2.25-2.373.60.3893.526721.41297.6
2.37-2.523.60.3423.827171.37797.8
2.52-2.713.60.2924.527111.44998.2
2.71-2.993.50.245.127231.38498.4
2.99-3.423.70.1448.327541.28699
3.42-4.313.70.10710.327801.15699.5
4.31-503.60.09510.827951.19198.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å24.93 Å
Translation2 Å24.93 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.5phasing
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: 4PVO

4pvo


Resolution: 2→24.93 Å / Isotropic thermal model: isotropic
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 2010 7.4 %random
Rwork0.1658 ---
all-27185 --
obs-27168 99.9 %-
Displacement parametersBiso max: 62.9 Å2 / Biso mean: 21.7411 Å2 / Biso min: 6.48 Å2
Refinement stepCycle: LAST / Resolution: 2→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3445 0 54 346 3845
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.0098
X-RAY DIFFRACTIONf_angle_deg1.209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2.0018-2.05180.25811340.2156X-RAY DIFFRACTION189294.7
4.8138-24.92810.22751510.1733X-RAY DIFFRACTION202599.4
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.2392-1.5468-2.7932.61381.19724.3833-0.4681-1.1181-0.86650.70330.40790.51480.54920.15860.0930.24880.053-0.01620.31540.11950.3964-14.78740.674868.2778
23.570.7141-5.10362.0214-0.52947.40680.0109-0.0945-0.41230.101-0.0824-0.07090.1920.29410.12370.2160.007-0.04820.12590.01250.1995-13.01734.746762.3015
31.930.22670.43691.73960.65091.67070.0027-0.02820.0637-0.06810.0126-0.0747-0.08350.0458-0.0160.1048-0.0140.02570.09930.0040.1014-16.797213.937153.677
43.3221-2.82331.72544.4093-1.23560.9153-0.1026-0.33-0.41770.45820.28050.4022-0.0364-0.4868-0.08690.15690.0140.02980.230.02870.1966-27.8353-1.117253.2336
52.9165-0.05550.09141.05970.22121.72270.04080.2786-0.1438-0.1663-0.0262-0.18320.07760.17840.03520.2162-0.01540.02390.1603-0.01110.1716-18.21620.14245.1348
65.75770.69950.26192.44150.03021.9724-0.08040.0971-0.28780.0085-0.03690.07810.2519-0.16470.07720.184-0.00160.0050.1093-0.01910.1324-26.8229-6.321646.6707
72.8847-0.0872-1.26572.14330.74627.0806-0.2496-0.1380.66160.0870.025-0.3562-0.68110.91860.13060.2305-0.058-0.06280.22330.02710.3678-27.9592-7.234581.0862
81.4332-0.46170.31381.9436-0.42931.3388-0.01420.02180.00710.0374-0.0069-0.0492-0.00050.05360.02020.0949-0.00080.00760.11820.00540.0888-39.6991-15.056477.3914
96.9144-0.88023.3814.6812-2.36312.7147-0.29250.24710.08660.0664-0.1602-0.1416-0.17370.16840.46560.08120.01430.00160.08820.02280.186-46.79771.362669.1523
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 30:42 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 43:63 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 64:222 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 223:238 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 239:279 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 280:296 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 30:63 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 64:279 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 280:296 )

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