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- PDB-5zjc: Crystal structure of NDM-1 in complex with D-captopril derivative CY41 -

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Basic information

Entry
Database: PDB / ID: 5zjc
TitleCrystal structure of NDM-1 in complex with D-captopril derivative CY41
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / NDM-1 / metallo-beta-lactamase / antibiotic resistent / inhibitor / thio compounds / 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; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S)-2-methyl-3-sulfanyl-propan-1-ol / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsZhang, H. / Hao, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31670753 China
CitationJournal: to be published
Title: Crystal structure of NDM-1
Authors: Zhang, H. / Hao, Q.
History
DepositionMar 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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)25,9936
Polymers25,6321
Non-polymers3615
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-5 kcal/mol
Surface area9640 Å2
Unit cell
Length a, b, c (Å)41.610, 59.980, 42.067
Angle α, β, γ (deg.)90.000, 97.880, 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
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-9EX / (2S)-2-methyl-3-sulfanyl-propan-1-ol


Mass: 106.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.03 Å3/Da / Density % sol: 39.37 % / Mosaicity: 0.27 ° / Mosaicity esd: 0.004 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris pH5.5, 15% PEG 3350, 20mM L-proline

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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: Sep 22, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 0.96→50 Å / Num. obs: 119689 / % possible obs: 96.1 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.064 / Χ2: 0.947 / Net I/σ(I): 22.1 / Num. measured all: 747117
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
0.96-0.993.20.33483161.143166.9
0.99-1.034.20.206116751.026193.8
1.03-1.084.60.122123770.8461100
1.08-1.144.70.082124111.0071100
1.14-1.214.80.067124120.9191100
1.21-1.34.80.056124700.7771100
1.3-1.4360.064124540.6931100
1.43-1.649.90.084124381.0311100
1.64-2.079.80.059125010.9111100
2.07-509.30.062126351.091199.9

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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: 0.96→41.67 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.6 / SU ML: 0.014 / SU R Cruickshank DPI: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.022
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1455 5330 5 %RANDOM
Rwork0.1281 ---
obs0.1289 100828 86.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.09 Å2 / Biso mean: 22.936 Å2 / Biso min: 15.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.41 Å2
2---0.52 Å20 Å2
3---0.54 Å2
Refinement stepCycle: final / Resolution: 0.96→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 16 295 2008
Biso mean--26.65 35.2 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191837
X-RAY DIFFRACTIONr_bond_other_d0.0030.021685
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.9372509
X-RAY DIFFRACTIONr_angle_other_deg0.9843.0023918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5265250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21324.61578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0115288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.48158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212125
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02367
X-RAY DIFFRACTIONr_rigid_bond_restr1.06433522
X-RAY DIFFRACTIONr_sphericity_free17.1675195
X-RAY DIFFRACTIONr_sphericity_bonded4.90753575
LS refinement shellResolution: 0.964→0.989 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 44 -
Rwork0.22 941 -
all-985 -
obs--10.88 %
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)
11.16620.582-0.20143.68880.36110.68160.0134-0.09350.11030.0591-0.02440.1269-0.0469-0.00270.0110.0506-0.01160.02610.0884-0.01720.0271-2.5773-6.6739-1.7239
20.3040.0817-0.09141.12640.09460.67550.0053-0.035-0.0165-0.0483-0.0364-0.01650.00720.03410.0310.02580.00240.01870.05860.00050.01613.0007-14.3155-11.9292
31.0371-0.3526-0.17850.9478-0.02890.7091-0.02050.02360.0401-0.07530.00330.1635-0.0007-0.08570.01720.0231-0.0018-0.01220.0635-0.01030.0469-11.464-13.8394-16.9961
42.3510.02250.26180.9050.50811.5296-0.03540.14180.1088-0.06040.0650.1087-0.0791-0.1556-0.02950.0138-0.00010.01030.09780.00460.0701-18.5873-8.6176-13.0791
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 70
2X-RAY DIFFRACTION2A71 - 169
3X-RAY DIFFRACTION3A170 - 241
4X-RAY DIFFRACTION4A242 - 270

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