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- PDB-6lip: Crystal structure of NDM-1 in complex with D-captopril derivative... -

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Basic information

Entry
Database: PDB / ID: 6lip
TitleCrystal structure of NDM-1 in complex with D-captopril derivative wss0218
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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-EEL / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.98 Å
AuthorsZhang, H. / Ma, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670753 China
CitationJournal: Bioorg.Med.Chem. / Year: 2020
Title: Structure-guided optimization of D-captopril for discovery of potent NDM-1 inhibitors.
Authors: Ma, G. / Wang, S. / Wu, K. / Zhang, W. / Ahmad, A. / Hao, Q. / Lei, X. / Zhang, H.
History
DepositionDec 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 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)26,0124
Polymers25,6321
Non-polymers3803
Water6,756375
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)41.732, 59.908, 42.295
Angle α, β, γ (deg.)90.000, 97.370, 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) / 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-EEL / (2R)-1-[3-sulfanyl-2-(sulfanylmethyl)propanoyl]pyrrolidine-2-carboxylic acid


Mass: 249.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 39.87 % / Mosaicity: 0.261 ° / Mosaicity esd: 0.003 °
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2017
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 0.98→50 Å / Num. obs: 113420 / % possible obs: 96 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.026 / Rrim(I) all: 0.071 / Χ2: 0.844 / Net I/σ(I): 14.1 / Num. measured all: 819276
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
0.98-1.025.60.60395440.7910.2750.6650.76481
1.02-1.067.20.383111940.9260.1530.4130.89295.1
1.06-1.17.30.224113060.9720.0890.2420.92995.8
1.1-1.167.30.146113580.9860.0580.1570.93396.4
1.16-1.237.40.109114510.9910.0430.1170.85797.2
1.23-1.337.40.081115280.9940.0320.0870.72797.8
1.33-1.467.40.068116460.9950.0270.0730.72998.6
1.46-1.687.50.069117220.9940.0270.0741.07199.3
1.68-2.117.40.044118430.9970.0170.0480.68799.8
2.11-507.50.062118280.990.0250.0670.83398.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XP6

5xp6


Resolution: 0.98→27.93 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.557 / SU ML: 0.013 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.021
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1443 5472 4.9 %RANDOM
Rwork0.1251 ---
obs0.1261 106562 94.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.09 Å2 / Biso mean: 20.823 Å2 / Biso min: 12.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å2-0.57 Å2
2---0.9 Å20 Å2
3---0.76 Å2
Refinement stepCycle: final / Resolution: 0.98→27.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 17 375 2093
Biso mean--19.8 34.49 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0151825
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171642
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.7662491
X-RAY DIFFRACTIONr_angle_other_deg1.4051.7623848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7975246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.88822.34681
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46415275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.415159
X-RAY DIFFRACTIONr_chiral_restr0.1710.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212107
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02340
X-RAY DIFFRACTIONr_rigid_bond_restr1.66633467
X-RAY DIFFRACTIONr_sphericity_free22.2425237
X-RAY DIFFRACTIONr_sphericity_bonded7.95253565
LS refinement shellResolution: 0.98→1.005 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 265 -
Rwork0.35 5230 -
all-5495 -
obs--62.78 %
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)
11.12990.2565-0.3343.22020.25541.04310.0208-0.09390.08960.1134-0.0190.1523-0.03040.0021-0.00180.0617-0.01310.02870.1169-0.01390.041614.96055.496720.2804
20.4186-0.0145-0.18690.92180.1030.74560.0025-0.0181-0.014-0.0238-0.04190.02840.0087-0.01240.03930.03260.00280.020.0805-0.00160.029416.928-1.95657.685
32.0108-0.4018-0.54580.67480.44210.74920.06760.28230.0441-0.0644-0.04680.1271-0.1181-0.1675-0.02080.0190.02210.00550.13280.00420.05750.59184.15354.3271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 70
2X-RAY DIFFRACTION2A71 - 216
3X-RAY DIFFRACTION3A217 - 270

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