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- PDB-5zr8: Crystal Structure Of NDM-1 Metallo-beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 5zr8
TitleCrystal Structure Of NDM-1 Metallo-beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / metal 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWachino, J.
CitationJournal: To Be Published
Title: Crystal Structure Of NDM-1 Metallo-beta-lactamase
Authors: Wachino, J.
History
DepositionApr 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,77111
Polymers52,0912
Non-polymers6819
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-271 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.080, 73.900, 77.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / NDM-1 metallo-beta-lactamase / New Delhi metallo-beta-lactamase NDM-1 / New Delhi metallo-beta-lactamase-1 / 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, AM434_27040, APU18_05360, AZ95_0035, BET08_16280, BVL39_26630, CA268_28970, ECS01_0033, 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.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 1.96 Å3/Da / Density % sol: 37.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium Sulfate, 0.1 M Bis-Tris [pH 6.1], 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / 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: 1.5→53.56 Å / Num. obs: 66267 / % possible obs: 100 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 18.6
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.439 / Num. unique obs: 9562 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4eyb

4eyb


Resolution: 1.5→53.56 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.015 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16784 3365 5.1 %RANDOM
Rwork0.14632 ---
obs0.1474 62831 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.5→53.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 21 515 3954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193592
X-RAY DIFFRACTIONr_bond_other_d0.0010.023239
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9384886
X-RAY DIFFRACTIONr_angle_other_deg0.7733.0017498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8365476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.57324.51153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55315537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3981516
X-RAY DIFFRACTIONr_chiral_restr0.1060.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214089
X-RAY DIFFRACTIONr_gen_planes_other00.02716
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.821.1671856
X-RAY DIFFRACTIONr_mcbond_other1.7921.1651855
X-RAY DIFFRACTIONr_mcangle_it2.6531.7452321
X-RAY DIFFRACTIONr_mcangle_other2.6521.7472322
X-RAY DIFFRACTIONr_scbond_it2.9911.4561736
X-RAY DIFFRACTIONr_scbond_other2.991.4551737
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3052.0442557
X-RAY DIFFRACTIONr_long_range_B_refined5.52115.2984036
X-RAY DIFFRACTIONr_long_range_B_other5.48414.9813985
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 242 -
Rwork0.184 4593 -
obs--100 %

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