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- PDB-5axr: Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to 2-merc... -

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Basic information

Entry
Database: PDB / ID: 5axr
TitleCrystal Structure of Metallo-beta-Lactamase SMB-1 Bound to 2-mercaptoethanesulfonate
ComponentsMetallo-beta-lactamase
KeywordsHYDROLASE
Function / homology
Function and homology information


: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1-THIOETHANESULFONIC ACID / Metallo-beta-lactamase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWachino, J. / Arakawa, Y.
CitationJournal: To Be Published
Title: Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to 2-mercaptoethanesulfonate
Authors: Wachino, J. / Arakawa, Y.
History
DepositionJul 31, 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,16510
Polymers27,7541
Non-polymers4119
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-57 kcal/mol
Surface area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.112, 67.112, 46.717
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#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
#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.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O3S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, Lithium Chloride, MES

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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: Feb 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→58.13 Å / Num. obs: 13741 / % possible obs: 100 % / Redundancy: 11.6 % / Net I/σ(I): 42.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 10.7 / % possible all: 100

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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: 2.1→58.12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.455 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21437 763 5.6 %RANDOM
Rwork0.14967 ---
obs0.15318 12964 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0.34 Å20 Å2
2---0.67 Å20 Å2
3---2.19 Å2
Refinement stepCycle: LAST / Resolution: 2.1→58.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 15 183 2119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191967
X-RAY DIFFRACTIONr_bond_other_d0.0010.021851
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.942669
X-RAY DIFFRACTIONr_angle_other_deg0.68334260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0885258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67223.87580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73615311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7361512
X-RAY DIFFRACTIONr_chiral_restr0.0780.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212265
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02445
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_it2.4892.0871035
X-RAY DIFFRACTIONr_mcbond_other2.4652.0851034
X-RAY DIFFRACTIONr_mcangle_it3.4673.1141292
X-RAY DIFFRACTIONr_mcangle_other3.4663.1171293
X-RAY DIFFRACTIONr_scbond_it3.5432.398932
X-RAY DIFFRACTIONr_scbond_other3.5362.398932
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2913.4421378
X-RAY DIFFRACTIONr_long_range_B_refined6.71817.5682351
X-RAY DIFFRACTIONr_long_range_B_other6.62317.3742288
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 66 -
Rwork0.15 971 -
obs--100 %

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