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- PDB-5b15: Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrol... -

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Basic information

Entry
Database: PDB / ID: 5b15
TitleCrystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Doripenem
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
Chem-DQM / Metallo-beta-lactamase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsWachino, J. / Arakawa, Y.
CitationJournal: To Be Published
Title: Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Doripenem
Authors: Wachino, J. / Arakawa, Y.
History
DepositionNov 23, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Data collection
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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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 / _pdbx_struct_oper_list.symmetry_operation / _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
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)28,77314
Polymers27,7541
Non-polymers1,01813
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-13 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.010, 40.920, 45.320
Angle α, β, γ (deg.)107.57, 102.56, 107.01
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, 353 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.: 7 / 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-DQM / (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-3-methyl-4-[(3~{S},5~{S})-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl]sulfanyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid / Hydrolyzed Doripenem


Mass: 438.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26N4O7S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.32 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG4000, Ammonium sulfate, Tris-Hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.39→40.7 Å / Num. obs: 39572 / % possible obs: 86.6 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.8
Reflection shellResolution: 1.39→1.47 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.072 / Mean I/σ(I) obs: 1.9 / % possible all: 84.7

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Processing

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

3vpe


Resolution: 1.39→40.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.721 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15829 1986 5 %RANDOM
Rwork0.13646 ---
obs0.13761 37585 86.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.434 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20.39 Å2-0.28 Å2
2--0.92 Å2-0.39 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.39→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 52 340 2313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192036
X-RAY DIFFRACTIONr_bond_other_d0.0010.021893
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.962777
X-RAY DIFFRACTIONr_angle_other_deg0.75234369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1375269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.12924.09683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87515318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2581512
X-RAY DIFFRACTIONr_chiral_restr0.10.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212337
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02453
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_it1.0880.791050
X-RAY DIFFRACTIONr_mcbond_other1.0870.7881049
X-RAY DIFFRACTIONr_mcangle_it1.5061.1881314
X-RAY DIFFRACTIONr_mcangle_other1.5071.1891315
X-RAY DIFFRACTIONr_scbond_it2.2391.048986
X-RAY DIFFRACTIONr_scbond_other2.2381.05987
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2781.4781459
X-RAY DIFFRACTIONr_long_range_B_refined5.0248.5622656
X-RAY DIFFRACTIONr_long_range_B_other5.0238.572657
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.393→1.429 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 129 -
Rwork0.16 2641 -
obs--81.83 %

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