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- PDB-6kxi: Crystal Structure Of NDM-1 Metallo-beta-lactamase In Complex With... -

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Basic information

Entry
Database: PDB / ID: 6kxi
TitleCrystal Structure Of NDM-1 Metallo-beta-lactamase In Complex With Inhibitor NO9
ComponentsBeta-lactamase
KeywordsHYDROLASE
Function / homology
Function and homology information


: / 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
2,5-dimethyl-4-sulfamoyl-furan-3-carboxylic acid / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsWachino, J.
CitationJournal: Mbio / Year: 2020
Title: Sulfamoyl Heteroarylcarboxylic Acids as Promising Metallo-beta-Lactamase Inhibitors for Controlling Bacterial Carbapenem Resistance.
Authors: Wachino, J.I. / Jin, W. / Kimura, K. / Kurosaki, H. / Sato, A. / Arakawa, Y.
History
DepositionSep 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Nov 22, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,30614
Polymers52,0912
Non-polymers1,21512
Water11,313628
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-134 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.550, 73.660, 77.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase / Beta-lactamase NDM-1 / BlaNDM-1 / BlaNDM-1 metallo beta lactamase / Metallo-beta-lactamase / NDM-1 ...Beta-lactamase NDM-1 / BlaNDM-1 / BlaNDM-1 metallo beta lactamase / Metallo-beta-lactamase / NDM-1 / NDM-1 metallo-beta-lactamase / New Delhi metallo-beta-lactamase NDM-1 / Subclass B1 metallo-beta-lactamase / Subclass B1 metallo-beta-lactamase NDM-1


Mass: 26045.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaNDM-1, bla NDM-1, APU18_05360, AZ95_0035, BANRA_05542, BET08_16280, BVL39_26630, C6985_28190, D3O91_26550, DWB25_28700, ECS01_0033, EJC75_01690, MS6198_A142, NDM1Dok01_N0175, pNDM102337_147, pNDM10505_149
Production host: Escherichia coli (E. coli) / References: UniProt: E5KIY2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NO9 / 2,5-dimethyl-4-sulfamoyl-furan-3-carboxylic acid


Mass: 219.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9NO5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium Sulfate, 0.1M Bis-Tris [pH 6.1], 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→42.624 Å / Num. obs: 83907 / % possible obs: 100 % / Redundancy: 12 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 16.9
Reflection shellResolution: 1.38→1.45 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.205 / Num. unique obs: 12092 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4eyb

4eyb


Resolution: 1.38→42.624 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.671 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.051
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1573 4159 4.961 %
Rwork0.1362 --
all0.137 --
obs-83827 99.993 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.041 Å2
Baniso -1Baniso -2Baniso -3
1-0.093 Å20 Å20 Å2
2---0.105 Å20 Å2
3---0.012 Å2
Refinement stepCycle: LAST / Resolution: 1.38→42.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 54 628 4148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0133726
X-RAY DIFFRACTIONr_bond_other_d00.0173344
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.6455082
X-RAY DIFFRACTIONr_angle_other_deg1.4891.5797764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.175.246508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.25123.176170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00215557
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg10.542152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8651516
X-RAY DIFFRACTIONr_chiral_restr0.0770.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024606
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02748
X-RAY DIFFRACTIONr_nbd_refined0.2140.2771
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.23187
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21781
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21545
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2423
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0760.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.218
X-RAY DIFFRACTIONr_nbd_other0.2180.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.245
X-RAY DIFFRACTIONr_mcbond_it1.4330.9421901
X-RAY DIFFRACTIONr_mcbond_other1.4270.941900
X-RAY DIFFRACTIONr_mcangle_it2.3471.4062380
X-RAY DIFFRACTIONr_mcangle_other2.3471.4072381
X-RAY DIFFRACTIONr_scbond_it2.1131.1661825
X-RAY DIFFRACTIONr_scbond_other2.1141.1671822
X-RAY DIFFRACTIONr_scangle_it3.2121.6542684
X-RAY DIFFRACTIONr_scangle_other3.2141.6552679
X-RAY DIFFRACTIONr_lrange_it5.17913.1134346
X-RAY DIFFRACTIONr_lrange_other5.06212.5424239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.38-1.4160.1883010.15258180.15461190.9540.9641000.139
1.416-1.4550.1763170.14256340.14359510.9620.9681000.131
1.455-1.4970.1422600.13555610.13558230.9710.97399.96570.128
1.497-1.5430.1572610.13453810.13556430.9670.97199.98230.129
1.543-1.5930.1652520.13752290.13854810.9660.9721000.133
1.593-1.6490.1772610.13750360.13952970.9610.9711000.135
1.649-1.7110.1562360.1348900.13251260.9710.9741000.13
1.711-1.7810.1392230.12947070.1349300.9750.9761000.133
1.781-1.860.1752180.13345470.13547650.9630.9731000.139
1.86-1.9510.1781890.1343440.13145330.9630.9751000.141
1.951-2.0560.1452020.13141250.13243270.9730.9761000.144
2.056-2.180.1392180.13138860.13141040.9760.9771000.146
2.18-2.330.1572110.1336440.13138550.9710.9751000.148
2.33-2.5160.1562460.13333650.13536110.9710.9771000.155
2.516-2.7560.1511700.13131530.13233230.9760.9771000.155
2.756-3.0790.1541640.13928800.1430440.9690.9731000.164
3.079-3.5530.1441460.13825490.13826950.9750.9771000.167
3.553-4.3440.1551080.13421840.13522920.9730.9791000.165
4.344-6.1110.144850.14917410.14918260.9750.9771000.191
6.111-42.6240.194910.1819950.18210860.9630.9671000.224

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