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- PDB-5zgx: Crystal structure of NDM-1 at pH7.5 (Succinate) with 1 molecule p... -

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Basic information

Entry
Database: PDB / ID: 5zgx
TitleCrystal structure of NDM-1 at pH7.5 (Succinate) with 1 molecule per asymmetric unit
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 / beta-lactamase activity / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 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: 0.95 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 10, 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)26,15210
Polymers25,6321
Non-polymers5209
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-54 kcal/mol
Surface area9700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.451, 59.885, 41.972
Angle α, β, γ (deg.)90.000, 97.940, 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: 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
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-OH / HYDROXIDE ION


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


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.01 Å3/Da / Density % sol: 38.89 % / Mosaicity: 0.171 ° / Mosaicity esd: 0.003 °
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: BL17U1 / Wavelength: 0.93924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 3, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93924 Å / Relative weight: 1
ReflectionResolution: 0.95→50 Å / Num. obs: 125535 / % possible obs: 98.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.076 / Χ2: 0.928 / Net I/σ(I): 13.6 / Num. measured all: 597678
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
0.95-0.983.70.485109780.769186.3
0.98-1.024.60.342126670.8381100
1.02-1.074.70.218126890.8561100
1.07-1.134.80.153126960.9481100
1.13-1.24.80.122127110.9771100
1.2-1.294.90.106126640.9581100
1.29-1.424.90.097127251.0131100
1.42-1.6250.094127411.2291100
1.62-2.0550.071127610.9571100
2.05-505.10.063129030.669199.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3q6x

3q6x
PDB Unreleased entry


Resolution: 0.95→33.88 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.378 / SU ML: 0.01 / SU R Cruickshank DPI: 0.0161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.016 / ESU R Free: 0.016
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1246 6297 5 %RANDOM
Rwork0.1126 ---
obs0.1132 119202 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.54 Å2 / Biso mean: 10.46 Å2 / Biso min: 3.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.01 Å2
2---0.23 Å20 Å2
3---0.26 Å2
Refinement stepCycle: final / Resolution: 0.95→33.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 27 301 2029
Biso mean--14.73 24.97 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191916
X-RAY DIFFRACTIONr_bond_other_d0.0010.021846
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9432612
X-RAY DIFFRACTIONr_angle_other_deg1.40434264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4755267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13424.52484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57715312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7871510
X-RAY DIFFRACTIONr_chiral_restr0.0810.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212246
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02446
X-RAY DIFFRACTIONr_rigid_bond_restr1.37533762
X-RAY DIFFRACTIONr_sphericity_free30.705552
X-RAY DIFFRACTIONr_sphericity_bonded7.34853949
LS refinement shellResolution: 0.95→0.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 369 -
Rwork0.294 7032 -
all-7401 -
obs--78.47 %

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