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- PDB-5zgf: Crystal structure of NDM-1 Q123G mutant -

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Basic information

Entry
Database: PDB / ID: 5zgf
TitleCrystal structure of NDM-1 Q123G mutant
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / NDM-1 / metallo-beta-lactamase / antibiotic resistent / conformational change
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HYDROXIDE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsZhang, H. / Hao, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31670753 China
CitationJournal: Antimicrob. Agents Chemother. / Year: 2018
Title: Active-Site Conformational Fluctuations Promote the Enzymatic Activity of NDM-1.
Authors: Zhang, H. / Ma, G. / Zhu, Y. / Zeng, L. / Ahmad, A. / Wang, C. / Pang, B. / Fang, H. / Zhao, L. / Hao, Q.
History
DepositionMar 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7094
Polymers25,5611
Non-polymers1483
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-84 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.745, 59.282, 41.815
Angle α, β, γ (deg.)90.000, 94.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta- ...B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase type II / New Delhi metallo-beta-lactamase-1 / NDM-1


Mass: 25560.744 Da / Num. of mol.: 1 / Mutation: Q123G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Plasmid: pRHisMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C7C422, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 1.92 Å3/Da / Density % sol: 35.94 % / Mosaicity: 0.748 ° / Mosaicity esd: 0.009 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Sodium succinate pH7.5, 30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 6, 2018
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 59277 / % possible obs: 98.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.015 / Rrim(I) all: 0.04 / Χ2: 0.881 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.2-1.244.90.54455930.8550.2580.6050.89193.3
1.24-1.2960.48560040.9010.2120.530.87999.9
1.29-1.356.10.36859010.940.1590.4020.8998.7
1.35-1.426.50.26159680.9660.110.2840.87699
1.42-1.516.50.17159930.9840.0720.1860.89499.8
1.51-1.636.30.11258340.990.0480.1220.90397.4
1.63-1.796.70.07160320.9960.0290.0770.90199.9
1.79-2.056.50.04358850.9980.0180.0470.95397.9
2.05-2.596.90.0360250.9990.0120.0330.92199.6
2.59-506.60.02260420.9990.0090.0230.70698.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6X

3q6x
PDB Unreleased entry


Resolution: 1.2→41.66 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.22 / SU ML: 0.029 / SU R Cruickshank DPI: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.045
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1761 2879 5.3 %RANDOM
Rwork0.1519 ---
obs0.1532 51695 90.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 67.61 Å2 / Biso mean: 22.184 Å2 / Biso min: 12.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20.01 Å2
2---0.08 Å20 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.2→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 3 343 2042
Biso mean--18.91 34.52 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191774
X-RAY DIFFRACTIONr_bond_other_d0.0020.021612
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9292424
X-RAY DIFFRACTIONr_angle_other_deg0.96333741
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4855240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08524.54577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92515267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.926158
X-RAY DIFFRACTIONr_chiral_restr0.090.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02358
LS refinement shellResolution: 1.201→1.232 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 75 -
Rwork0.197 1332 -
all-1407 -
obs--31.58 %
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)
11.1896-0.2767-0.07411.5533-0.05290.49690.00580.024-0.02320.0069-0.02990.0278-0.0075-0.01350.02420.00080.00310.00020.0146-0.00040.0231-7.8541.668-20.969
22.5799-0.751-0.37511.6912-0.23482.1151-0.1922-0.3558-0.05520.26970.1291-0.02370.08660.070.0630.07170.0332-0.0070.0945-0.00170.0176-2.4111.018-6.891
31.82410.46470.05670.66290.37813.3999-0.1679-0.4474-0.14430.17260.10660.02820.13670.12410.06130.15370.10560.05020.20920.05440.0451-6.622-2.745-0.718
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 175
2X-RAY DIFFRACTION2A176 - 241
3X-RAY DIFFRACTION3A242 - 270

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