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- PDB-5aya: Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to L-captopril -

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Basic information

Entry
Database: PDB / ID: 5aya
TitleCrystal Structure of Metallo-beta-Lactamase SMB-1 Bound to L-captopril
ComponentsMetallo-beta-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
L-CAPTOPRIL / Metallo-beta-lactamase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsWachino, J. / Arakawa, Y.
CitationJournal: To Be Published
Title: Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to L-captopril
Authors: Wachino, J. / Arakawa, Y.
History
DepositionAug 12, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3408
Polymers27,7541
Non-polymers5867
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-14 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.097, 68.097, 49.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Metallo-beta-lactamase


Mass: 27754.043 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 19-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: SMB-1 / Production host: Escherichia coli (E. coli) / References: UniProt: G5ELM3, beta-lactamase

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Non-polymers , 5 types, 129 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-X8Z / L-CAPTOPRIL


Mass: 217.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO3S / Comment: medication*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG4000, Lithium Sulfate, Tris-Hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 16635 / % possible obs: 99.6 % / Redundancy: 11 % / Net I/σ(I): 64.2
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 17.1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VPE

3vpe


Resolution: 2.02→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.271 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28188 904 5.4 %RANDOM
Rwork0.2098 ---
obs0.21354 15711 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.209 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å2-0.52 Å20 Å2
2---1.04 Å20 Å2
3---3.37 Å2
Refinement stepCycle: LAST / Resolution: 2.02→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 28 122 2071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191983
X-RAY DIFFRACTIONr_bond_other_d0.0010.021860
X-RAY DIFFRACTIONr_angle_refined_deg1.121.9492692
X-RAY DIFFRACTIONr_angle_other_deg0.64834282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2045258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03123.87580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43615311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4971512
X-RAY DIFFRACTIONr_chiral_restr0.0680.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212277
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02445
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_it4.8333.8551035
X-RAY DIFFRACTIONr_mcbond_other4.8313.8511034
X-RAY DIFFRACTIONr_mcangle_it5.9885.7541292
X-RAY DIFFRACTIONr_mcangle_other5.9885.7581293
X-RAY DIFFRACTIONr_scbond_it4.6384.193948
X-RAY DIFFRACTIONr_scbond_other4.6424.189946
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2566.1411400
X-RAY DIFFRACTIONr_long_range_B_refined8.32431.7832326
X-RAY DIFFRACTIONr_long_range_B_other8.33531.7362284
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.022→2.074 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 69 -
Rwork0.245 1183 -
obs--100 %

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