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- PDB-5zgi: Crystal structure of NDM-1 at pH6.5 (Succinate) with 1 molecule p... -

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Basic information

Entry
Database: PDB / ID: 5zgi
TitleCrystal structure of NDM-1 at pH6.5 (Succinate) with 1 molecule per asymmetric unit
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / NDM-1 / metallo-beta-lactamase / antibiotic resistent / conformational change / ANTIBIOTIC
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 / SUCCINIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 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 9, 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)26,0848
Polymers25,6321
Non-polymers4527
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-52 kcal/mol
Surface area9640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.445, 59.805, 42.132
Angle α, β, γ (deg.)90.000, 97.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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: 25631.820 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 346 molecules

#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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.02 Å3/Da / Density % sol: 39.07 % / Mosaicity: 0.189 ° / Mosaicity esd: 0.002 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M sodium succinate pH6.5, 40% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 0.98→50 Å / Num. obs: 109068 / % possible obs: 93.5 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.095 / Χ2: 1.004 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
0.98-1.026.10.2986090.741174.1
1.02-1.067.90.238107320.798192.3
1.06-1.18.20.182107790.974192.9
1.1-1.168.10.149109200.975194
1.16-1.238.20.131110451.02194.8
1.23-1.338.30.119111341.103195.6
1.33-1.468.20.113112621.103196.7
1.46-1.688.20.112113951.046197.6
1.68-2.117.80.09114991.075198.2
2.11-506.70.081116931.071198.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6X

3q6x
PDB Unreleased entry


Resolution: 0.98→41.75 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.406 / SU ML: 0.011 / SU R Cruickshank DPI: 0.0197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.02
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1352 5462 5 %RANDOM
Rwork0.1196 ---
obs0.1204 103572 93.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.43 Å2 / Biso mean: 9.824 Å2 / Biso min: 4.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.09 Å2
2---0.24 Å20 Å2
3---0.28 Å2
Refinement stepCycle: final / Resolution: 0.98→41.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 31 339 2067
Biso mean--17.58 23.25 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.021900
X-RAY DIFFRACTIONr_bond_other_d0.0010.021258
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.9422597
X-RAY DIFFRACTIONr_angle_other_deg0.863.0013093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2195260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.72124.69983
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81815302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.767159
X-RAY DIFFRACTIONr_chiral_restr0.0740.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212213
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02384
X-RAY DIFFRACTIONr_rigid_bond_restr2.44533158
X-RAY DIFFRACTIONr_sphericity_free22.25548
X-RAY DIFFRACTIONr_sphericity_bonded7.46653398
LS refinement shellResolution: 0.98→1.005 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.133 287 -
Rwork0.114 5652 -
all-5939 -
obs--69.32 %

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