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- PDB-5a87: Crystal structure of the metallo-beta-lactamase VIM-5 -

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Basic information

Entry
Database: PDB / ID: 5a87
TitleCrystal structure of the metallo-beta-lactamase VIM-5
ComponentsMETALLO-BETA-LACTAMASE VIM-5
KeywordsHYDROLASE / METALLO-BETA-LACTAMASE / ANTIBIOTIC RESITANCE
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 VIM-5 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBrem, J. / Duzgun, A.O. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2015
Title: Comparison of Verona Integron-Borne Metallo-beta-Lactamase (VIM) Variants Reveals Differences in Stability and Inhibition Profiles.
Authors: Makena, A. / Duzgun, A.O. / Brem, J. / McDonough, M.A. / Rydzik, A.M. / Abboud, M.I. / Saral, A. / Cicek, A.C. / Sandalli, C. / Schofield, C.J.
History
DepositionJul 13, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_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_conn.ptnr2_label_seq_id / _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: METALLO-BETA-LACTAMASE VIM-5
B: METALLO-BETA-LACTAMASE VIM-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,91911
Polymers52,2242
Non-polymers6959
Water7,350408
1
A: METALLO-BETA-LACTAMASE VIM-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5847
Polymers26,1121
Non-polymers4736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: METALLO-BETA-LACTAMASE VIM-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3354
Polymers26,1121
Non-polymers2233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.270, 78.960, 64.030
Angle α, β, γ (deg.)90.00, 104.82, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9998, -0.0162, -0.01), (-0.0162, -0.9999, -0.0002), (-0.01, 0.0004, -1)
Vector: 0.4279, -24.6432, 30.0623)

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Components

#1: Protein METALLO-BETA-LACTAMASE VIM-5 / VIM-5 / BETA-LACTAMASE VIM-5


Mass: 26111.984 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 21-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Plasmid: PET28-BLAVIM-5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q4ZE97, UniProt: Q8GKX2*PLUS, beta-lactamase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.15 Å3/Da / Density % sol: 42.7 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M TRIS (PH 8.5), 25% PEG 3350, 0.2 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91741
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2015 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 1.5→39.9 Å / Num. obs: 61767 / % possible obs: 97.4 % / Observed criterion σ(I): 9.7 / Redundancy: 7.1 % / Biso Wilson estimate: 14.86 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.7
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.2 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBP ENTRY 2WRS

2wrs


Resolution: 1.5→39.9 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 18.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1915 2019 3.3 %
Rwork0.154 --
obs0.1552 61764 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 29 408 3861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083565
X-RAY DIFFRACTIONf_angle_d1.1664894
X-RAY DIFFRACTIONf_dihedral_angle_d12.7761242
X-RAY DIFFRACTIONf_chiral_restr0.043569
X-RAY DIFFRACTIONf_plane_restr0.006645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.29491340.26554249X-RAY DIFFRACTION97
1.5375-1.57910.27731440.24854211X-RAY DIFFRACTION97
1.5791-1.62560.25321610.23874232X-RAY DIFFRACTION98
1.6256-1.6780.26761260.23074296X-RAY DIFFRACTION97
1.678-1.7380.22371460.20634256X-RAY DIFFRACTION98
1.738-1.80760.22211420.17914290X-RAY DIFFRACTION98
1.8076-1.88990.1911460.15394281X-RAY DIFFRACTION98
1.8899-1.98950.16091520.15124273X-RAY DIFFRACTION98
1.9895-2.11410.18611320.143960X-RAY DIFFRACTION91
2.1141-2.27740.17491520.13814361X-RAY DIFFRACTION99
2.2774-2.50650.16561440.13354340X-RAY DIFFRACTION99
2.5065-2.86910.18821450.13874381X-RAY DIFFRACTION99
2.8691-3.61440.17611440.1294331X-RAY DIFFRACTION98
3.6144-39.91120.1831510.14264284X-RAY DIFFRACTION96
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)
12.08020.3078-0.03113.14770.87054.57060.03720.0375-0.0785-0.005-0.00530.04790.0657-0.17260.00210.0588-0.0017-0.00210.08930.00590.08161.2895-4.993328.7459
22.1267-0.6840.0450.90970.06040.74790.00060.00720.1669-0.0167-0.0238-0.0499-0.04950.02140.03670.1152-0.0201-0.00140.0964-0.00550.105311.17584.704330.5512
33.66310.1849-1.50122.6254-0.2472.0691-0.02340.0784-0.1607-0.05990.0506-0.00950.06110.0024-0.01930.09880.0038-0.0250.10220.020.113314.5069-9.142130.7753
44.588-0.0055-0.29721.5098-0.76084.33130.0168-0.3771-0.22350.1414-0.0167-0.05340.02540.181-0.00510.1170.0007-0.01870.0350.00150.104518.0267-11.564135.3285
58.4462-1.962-4.19797.89371.7682.4387-0.02140.1982-0.2442-0.27970.009-0.40440.12050.10890.03640.12540.0017-0.0220.119-0.0120.162820.8994-17.965728.4049
62.3375-0.1626-0.06573.35771.38964.33950.01910.09890.0746-0.0396-0.03540.0854-0.1584-0.28840.03170.0788-0.00590.00060.16-0.01790.09880.8498-18.95620.9655
76.59280.31850.64411.12330.68042.18170.0166-0.0236-0.07870.0536-0.10430.11020.0715-0.22690.11330.1409-0.02170.0040.1019-0.0130.10432.0742-27.92720.9516
83.38551.18610.04832.48770.46651.77250.0484-0.0052-0.26350.1517-0.0431-0.09240.25540.06620.00420.1380.0252-0.00510.12-0.01640.118115.1399-30.6373-1.5456
94.4658-0.50180.90543.47080.85591.5642-0.0332-0.08680.15670.11690.0391-0.0194-0.10950.0318-0.00580.10650.00010.03020.11940.02550.092913.85-15.6578-0.8955
104.9551-0.81110.40591.9412-0.54.48860.03250.27510.3734-0.2253-0.0163-0.1632-0.15440.16520.00020.1442-0.01670.01430.0590.00710.115217.1548-13.1489-5.2842
119.60631.53346.20736.01441.39344.4318-0.16450.11110.4126-0.04130.0563-0.6358-0.40560.43020.14340.1678-0.03220.03020.1668-0.01710.213820.2132-6.88361.3274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 32 THROUGH 88 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 89 THROUGH 183 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 184 THROUGH 215 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 216 THROUGH 245 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 246 THROUGH 261 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 28 THROUGH 88 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 89 THROUGH 122 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 123 THROUGH 183 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 184 THROUGH 215 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 216 THROUGH 245 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 246 THROUGH 261 )

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