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- PDB-5b1u: Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrol... -

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Basic information

Entry
Database: PDB / ID: 5b1u
TitleCrystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Imipenem
ComponentsMetallo-beta-lactamase
KeywordsHYDROLASE/ANTIBIOTIC / HYDROLASE / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


: / 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
Chem-HIW / Metallo-beta-lactamase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsWachino, J. / Arakawa, Y.
CitationJournal: To be published
Title: Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Imipenem
Authors: Wachino, J. / Arakawa, Y.
History
DepositionDec 20, 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_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_symmetry

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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)28,83522
Polymers27,7541
Non-polymers1,08121
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-15 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.030, 41.460, 45.440
Angle α, β, γ (deg.)108.32, 102.78, 106.28
Int Tables number1
Space group name H-MP1

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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
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, 399 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.: 15 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-HIW / (2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-ca rboxylic acid / Hydrolyzed Imipenem


Mass: 317.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3O5S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG5000, Lithium sulfate, Tris-Hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→40.58 Å / Num. obs: 30412 / % possible obs: 93.6 % / Redundancy: 3.3 % / Net I/σ(I): 19
Reflection shellResolution: 1.57→1.65 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 11.9 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VPE

3vpe


Resolution: 1.57→40.58 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.967 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15472 1534 5 %RANDOM
Rwork0.12241 ---
obs0.12406 28877 93.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.866 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.29 Å2-0.23 Å2
2--0.49 Å2-0.28 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.57→40.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 53 378 2352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192050
X-RAY DIFFRACTIONr_bond_other_d0.0010.021912
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.9552798
X-RAY DIFFRACTIONr_angle_other_deg0.7434417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8695278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.5652485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19615326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6561513
X-RAY DIFFRACTIONr_chiral_restr0.0960.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212378
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02468
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_it0.8190.521055
X-RAY DIFFRACTIONr_mcbond_other0.8140.5191054
X-RAY DIFFRACTIONr_mcangle_it1.2670.7811322
X-RAY DIFFRACTIONr_mcangle_other1.2680.7821323
X-RAY DIFFRACTIONr_scbond_it2.0790.759995
X-RAY DIFFRACTIONr_scbond_other2.0780.76996
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0881.0451467
X-RAY DIFFRACTIONr_long_range_B_refined5.4596.512755
X-RAY DIFFRACTIONr_long_range_B_other5.1095.422516
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.568→1.609 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.153 118 -
Rwork0.113 2113 -
obs--92.5 %

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