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- PDB-5k0w: Crystal structure of the metallo-beta-lactamase GOB-18 from Eliza... -

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Basic information

Entry
Database: PDB / ID: 5k0w
TitleCrystal structure of the metallo-beta-lactamase GOB-18 from Elizabethkingia meningoseptica
ComponentsClass B carbapenemase GOB-18
KeywordsHYDROLASE / metallo-beta-lactamase / B3 lactamase / zinc hydrolase / hydrolysis of beta-lactam antibiotics
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
Class B carbapenemase GOB-18
Similarity search - Component
Biological speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsBuschiazzo, A. / Larrieux, N. / Vila, A.J. / Lisa, M.N. / Moran-Barrio, J.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2016
Title: Crystal Structure of the Metallo-beta-Lactamase GOB in the Periplasmic Dizinc Form Reveals an Unusual Metal Site.
Authors: Moran-Barrio, J. / Lisa, M.N. / Larrieux, N. / Drusin, S.I. / Viale, A.M. / Moreno, D.M. / Buschiazzo, A. / Vila, A.J.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class B carbapenemase GOB-18
B: Class B carbapenemase GOB-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,37415
Polymers66,7362
Non-polymers63713
Water1,38777
1
A: Class B carbapenemase GOB-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,83911
Polymers33,3681
Non-polymers47110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Class B carbapenemase GOB-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5344
Polymers33,3681
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.000, 48.510, 88.940
Angle α, β, γ (deg.)90.00, 100.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Class B carbapenemase GOB-18


Mass: 33368.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q4JRB6
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2M NaCl, 2M (NH4)2SO4, 0.1M Tris.HCl

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.61→24.33 Å / Num. obs: 16108 / % possible obs: 96.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 37.56 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 9.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K07

1k07


Resolution: 2.61→24.33 Å / Cor.coef. Fo:Fc: 0.8956 / Cor.coef. Fo:Fc free: 0.8484 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.327
RfactorNum. reflection% reflectionSelection details
Rfree0.2422 955 5.93 %RANDOM
Rwork0.1919 ---
obs0.195 16107 96.74 %-
Displacement parametersBiso mean: 29.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.1099 Å20 Å211.5317 Å2
2--4.475 Å20 Å2
3----4.5849 Å2
Refine analyzeLuzzati coordinate error obs: 0.324 Å
Refinement stepCycle: 1 / Resolution: 2.61→24.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4381 0 18 77 4476
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094491HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.116064HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1579SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes119HARMONIC2
X-RAY DIFFRACTIONt_gen_planes631HARMONIC5
X-RAY DIFFRACTIONt_it4491HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion21.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion582SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance18HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5079SEMIHARMONIC4
LS refinement shellResolution: 2.61→2.79 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2892 151 5.43 %
Rwork0.2298 2628 -
all0.2331 2779 -
obs--96.74 %

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