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- PDB-5iqk: Rm3 metallo-beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 5iqk
TitleRm3 metallo-beta-lactamase
Componentsbeta-lactamase Rm3
KeywordsHYDROLASE / lactamase / metallo / metagenomic / antibiotic resistance
Function / homology
Function and homology information


Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSalimraj, R. / Spencer, J.
Funding support United Kingdom, United States, 4items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1100135 United Kingdom
Natural Environment Research CouncilNE/E004482/1 United Kingdom
European Regional Development Fund500020 United Kingdom
R01AI100560 United States
CitationJournal: Antimicrob.Agents Chemother. / Year: 2016
Title: Structural and Biochemical Characterization of Rm3, a Subclass B3 Metallo-beta-Lactamase Identified from a Functional Metagenomic Study.
Authors: Salimraj, R. / Zhang, L. / Hinchliffe, P. / Wellington, E.M. / Brem, J. / Schofield, C.J. / Gaze, W.H. / Spencer, J.
History
DepositionMar 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta-lactamase Rm3
B: beta-lactamase Rm3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4139
Polymers57,9552
Non-polymers4587
Water5,441302
1
A: beta-lactamase Rm3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2395
Polymers28,9781
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase Rm3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1744
Polymers28,9781
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.880, 74.450, 77.460
Angle α, β, γ (deg.)90.00, 99.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein beta-lactamase Rm3


Mass: 28977.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pLHZRM3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ArcticExpress / References: UniProt: A0A059Q5E8*PLUS, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 14% w/v PEG 8000, 0.1 M Tris, 0.15 M LiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 23, 2013
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→53.321 Å / Num. obs: 50630 / % possible obs: 97.6 % / Redundancy: 2.4 % / Biso Wilson estimate: 19.22 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.1
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.1 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QDT

2qdt


Resolution: 1.75→53.321 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.47
RfactorNum. reflection% reflection
Rfree0.2294 2574 5.09 %
Rwork0.2028 --
obs0.2042 50593 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→53.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4051 0 7 302 4360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074158
X-RAY DIFFRACTIONf_angle_d1.095665
X-RAY DIFFRACTIONf_dihedral_angle_d12.6321494
X-RAY DIFFRACTIONf_chiral_restr0.046618
X-RAY DIFFRACTIONf_plane_restr0.006756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.78370.32181180.31152662X-RAY DIFFRACTION97
1.7837-1.82010.31141460.27942667X-RAY DIFFRACTION97
1.8201-1.85970.27281390.26232653X-RAY DIFFRACTION98
1.8597-1.90290.33971490.25552676X-RAY DIFFRACTION98
1.9029-1.95050.31491500.24062606X-RAY DIFFRACTION97
1.9505-2.00330.25351390.2422662X-RAY DIFFRACTION97
2.0033-2.06220.25321460.24122621X-RAY DIFFRACTION97
2.0622-2.12880.24261580.22622641X-RAY DIFFRACTION97
2.1288-2.20490.25331450.21672679X-RAY DIFFRACTION98
2.2049-2.29320.23581480.21752680X-RAY DIFFRACTION98
2.2932-2.39750.26211150.21652663X-RAY DIFFRACTION97
2.3975-2.52390.24881580.21342645X-RAY DIFFRACTION98
2.5239-2.6820.22251320.20682700X-RAY DIFFRACTION97
2.682-2.88910.25731310.21062693X-RAY DIFFRACTION99
2.8891-3.17980.24291510.21392686X-RAY DIFFRACTION98
3.1798-3.63990.21061600.20122662X-RAY DIFFRACTION98
3.6399-4.58550.17811470.16362713X-RAY DIFFRACTION98
4.5855-53.34550.17431420.14062710X-RAY DIFFRACTION97

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