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

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Basic information

Entry
Database: PDB / ID: 6kzl
TitleCrystal Structure Of NDM-1 Metallo-beta-lactamase In Complex With Inhibitor X2
ComponentsBeta-lactamase
KeywordsHYDROLASE
Function / homology
Function and homology information


antibiotic catabolic process / metal 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
Chem-E1C / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.763 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 24, 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)53,48415
Polymers52,0912
Non-polymers1,39313
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-85 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.720, 74.040, 77.430
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


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 / 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.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-E1C / 2,5-diethyl-1-methyl-4-sulfamoyl-pyrrole-3-carboxylic acid


Mass: 260.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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 Å3/Da / Density % sol: 38.6 %
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: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→77.43 Å / Num. obs: 40824 / % possible obs: 100 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.8
Reflection shellResolution: 1.76→1.86 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.474 / Num. unique obs: 5859 / % possible all: 99.9

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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: 1.763→53.513 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.181 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.112
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1916 2034 4.99 %
Rwork0.148 --
all0.15 --
obs-40758 99.971 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.359 Å2
Baniso -1Baniso -2Baniso -3
1-0.145 Å20 Å20 Å2
2---0.392 Å20 Å2
3---0.247 Å2
Refinement stepCycle: LAST / Resolution: 1.763→53.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3537 0 65 478 4080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133719
X-RAY DIFFRACTIONr_bond_other_d00.0173345
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.6435081
X-RAY DIFFRACTIONr_angle_other_deg1.3341.5867753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0885489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30423.125176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76215551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6881517
X-RAY DIFFRACTIONr_chiral_restr0.0630.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02752
X-RAY DIFFRACTIONr_nbd_refined0.2070.2785
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.23227
X-RAY DIFFRACTIONr_nbtor_refined0.1580.21792
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21483
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2349
X-RAY DIFFRACTIONr_metal_ion_refined0.0810.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2350.215
X-RAY DIFFRACTIONr_nbd_other0.2370.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.224
X-RAY DIFFRACTIONr_mcbond_it1.8961.971920
X-RAY DIFFRACTIONr_mcbond_other1.891.9671919
X-RAY DIFFRACTIONr_mcangle_it2.6922.9422400
X-RAY DIFFRACTIONr_mcangle_other2.6962.9442401
X-RAY DIFFRACTIONr_scbond_it2.7322.2411799
X-RAY DIFFRACTIONr_scbond_other2.7322.2411800
X-RAY DIFFRACTIONr_scangle_it3.9913.242674
X-RAY DIFFRACTIONr_scangle_other3.9913.242675
X-RAY DIFFRACTIONr_lrange_it5.69124.84284
X-RAY DIFFRACTIONr_lrange_other5.63824.5424230
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
1.763-1.8090.211480.17228200.17429690.9270.9499.96630.148
1.809-1.8580.2281390.15927360.16228800.9340.94799.82640.136
1.858-1.9120.2121440.15126760.15428200.9430.9561000.129
1.912-1.9710.21730.14325640.14727380.950.96299.96350.124
1.971-2.0350.1951310.15225170.15426480.9470.9591000.134
2.035-2.1070.1931320.15124510.15325830.9510.9611000.135
2.107-2.1860.2181250.14523760.14925010.9410.961000.131
2.186-2.2750.1771420.12722580.1324000.9620.9721000.114
2.275-2.3760.1811250.13821770.1423020.9610.9671000.127
2.376-2.4920.245980.14521010.14921990.9330.9611000.136
2.492-2.6260.1891000.13920070.14121070.9620.9651000.13
2.626-2.7850.176640.14419280.14519920.960.9651000.139
2.785-2.9770.17790.15118000.15218790.9620.9641000.145
2.977-3.2150.202610.14617130.14817740.9580.9691000.146
3.215-3.520.177670.15915460.1616130.9640.9671000.162
3.52-3.9340.168830.14813930.1514760.9680.9731000.154
3.934-4.5380.149740.13112390.13213130.9740.9771000.142
4.538-5.5480.186680.14310670.14511350.9680.9761000.154
5.548-7.8040.206490.1628480.1648970.9610.971000.173
7.804-53.5130.268320.1975070.2015440.9310.96599.08090.208

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