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- PDB-6mfi: MIM-2 Metallo-Beta-Lactamase -

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Basic information

Entry
Database: PDB / ID: 6mfi
TitleMIM-2 Metallo-Beta-Lactamase
ComponentsMetallo-beta-lactamase
KeywordsHYDROLASE / Metallohydrolase / B3
Function / homologyMetallo-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 / Beta-lactamase-like protein
Function and homology information
Biological speciesSimiduia agarivorans
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.839 Å
AuthorsSelleck, C. / Guddat, L. / Schenk, G. / Monteiro Pedroso, M.
Funding support Australia, Ireland, United States, 6items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1084778 Australia
Australian Research Council (ARC)FT120100694 Australia
Australian Research Council (ARC)FT120100421 Australia
Other privateSFI-PIYRA Ireland
National Science Foundation (NSF, United States)CHE1303852 United States
National Science Foundation (NSF, United States)CHE0820965 United States
CitationJournal: Chemistry / Year: 2017
Title: characterization of the B3 MBLs MIM-1 and MIM-2 from environmental microorganisms.
Authors: Selleck, C. / Clayton, D. / Gahan, L.R. / Mitic, N. / McGeary, R.P. / Pedroso, M.M. / Guddat, L.W. / Schenk, G. / Monteiro Pedroso, M.
History
DepositionSep 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4883
Polymers31,3571
Non-polymers1312
Water8,899494
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.672, 69.527, 76.541
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-830-

HOH

21A-926-

HOH

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Components

#1: Protein Metallo-beta-lactamase


Mass: 31357.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simiduia agarivorans (strain DSM 21679 / JCM 13881 / BCRC 17597 / SA1) (bacteria)
Strain: DSM 21679 / JCM 13881 / BCRC 17597 / SA1 / Gene: M5M_14960 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: K4KM71
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 323 K / Method: vapor diffusion, hanging drop
Details: 0.1 mM DS56E8 (a detergent), 0.1 M sodium citrate, pH 5.5, and 22% w/v PEG-3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.7107 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 13, 2016
RadiationMonochromator: MX2 Beamline / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7107 Å / Relative weight: 1
ReflectionResolution: 1.839→42.83 Å / Num. obs: 24468 / % possible obs: 99.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.06 / Net I/σ(I): 7.5
Reflection shellResolution: 1.8393→1.905 Å / Num. unique obs: 24436 / % possible all: 99.23

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PHENIXphasing
Blu-Icedata collection
XDSdata scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SML

1sml


Resolution: 1.839→42.826 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.68
RfactorNum. reflection% reflection
Rfree0.309 2000 8.18 %
Rwork0.2602 --
obs0.2641 24436 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.839→42.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 2 494 2463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022044
X-RAY DIFFRACTIONf_angle_d0.5682798
X-RAY DIFFRACTIONf_dihedral_angle_d7.2082022
X-RAY DIFFRACTIONf_chiral_restr0.038316
X-RAY DIFFRACTIONf_plane_restr0.004368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8393-1.88520.39961260.34891417X-RAY DIFFRACTION89
1.8852-1.93620.34161400.31671572X-RAY DIFFRACTION100
1.9362-1.99320.31731430.29381599X-RAY DIFFRACTION100
1.9932-2.05750.33061420.28451602X-RAY DIFFRACTION100
2.0575-2.13110.29651410.2921565X-RAY DIFFRACTION100
2.1311-2.21640.34481420.28011608X-RAY DIFFRACTION100
2.2164-2.31720.32771440.27771598X-RAY DIFFRACTION100
2.3172-2.43940.31761410.27321597X-RAY DIFFRACTION100
2.4394-2.59220.34591430.27591607X-RAY DIFFRACTION100
2.5922-2.79230.32591450.27541617X-RAY DIFFRACTION100
2.7923-3.07330.29981440.24271613X-RAY DIFFRACTION100
3.0733-3.51780.26891460.21841637X-RAY DIFFRACTION100
3.5178-4.43130.25321470.2071657X-RAY DIFFRACTION100
4.4313-42.83810.32821560.27011747X-RAY DIFFRACTION100
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)
10.20110.28990.282.5377-0.7391.2294-0.07360.1881-0.0756-0.10860.0226-0.19130.15450.42390.08920.12680.01020.03080.2012-0.04410.204273.509979.066620.5433
21.44480.53990.29820.66870.35411.3836-0.1599-0.04570.0525-0.11170.021-0.0913-0.05410.04210.12870.07040.00220.00290.0696-0.00010.196663.937188.263529.552
33.42130.868-0.49981.69850.24340.802-0.30850.3745-0.6606-0.16020.05370.21010.2788-0.19470.10940.1229-0.05550.08030.2404-0.06020.289745.51780.60628.2245
41.27940.6825-0.09171.02280.34271.3256-0.19350.15630.2129-0.2661-0.03870.0668-0.1666-0.31140.09710.08790.0143-0.0360.1248-0.04130.170352.026291.791525.3952
52.285-0.7247-0.79764.0579-0.33323.738-0.01240.06060.6037-0.35290.0326-0.2513-0.44170.3595-0.05420.2338-0.075-0.05040.16630.02940.260261.378296.000917.0216
62.52090.8270.97861.97610.53580.9438-0.22940.17970.0752-0.3501-0.19860.3231-0.0159-0.46470.1060.2113-0.06450.01040.3781-0.11670.199149.071483.207212.5824
71.54790.40582.25692.44020.53983.3041-0.14490.4752-0.0474-0.2364-0.1143-0.0162-0.00590.0612-0.00910.2328-0.00110.02880.2855-0.13430.135460.84282.55717.8049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 139 )
3X-RAY DIFFRACTION3chain 'A' and (resid 140 through 158 )
4X-RAY DIFFRACTION4chain 'A' and (resid 159 through 198 )
5X-RAY DIFFRACTION5chain 'A' and (resid 199 through 217 )
6X-RAY DIFFRACTION6chain 'A' and (resid 218 through 259 )
7X-RAY DIFFRACTION7chain 'A' and (resid 260 through 300 )

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