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- PDB-5ngg: Crystal structure of the subclass B3 metallo-beta-lactamase BJP-1... -

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Basic information

Entry
Database: PDB / ID: 5ngg
TitleCrystal structure of the subclass B3 metallo-beta-lactamase BJP-1 in complex with acetate anion
ComponentsBlr6230 protein
KeywordsHYDROLASE / metallo-beta-lactamase / B3 acetate / BJP-1
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
ACETATE ION / Blr6230 protein
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsPozzi, C. / Di Pisa, F. / Benvenuti, M. / Mangani, S.
CitationJournal: Inorg.Chim.Acta. / Year: 2017
Title: Boric acid and acetate anion binding to subclass B3 metallo-Beta-lactamase BJP-1 provides clues for mechanism of action and inhibitor design
Authors: Di Pisa, F. / Pozzi, C. / Benvenuti, M. / Docquier, J.-D. / De Luca, F. / Mangani, S.
History
DepositionMar 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / pdbx_related_exp_data_set / Item: _audit_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: 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_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_label_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 / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 6, 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: Blr6230 protein
B: Blr6230 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,47610
Polymers63,9652
Non-polymers5118
Water11,295627
1
A: Blr6230 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2385
Polymers31,9831
Non-polymers2554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Blr6230 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2385
Polymers31,9831
Non-polymers2554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.310, 44.640, 75.910
Angle α, β, γ (deg.)78.88, 89.41, 61.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Blr6230 protein


Mass: 31982.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens USDA 110 (bacteria)
Gene: blr6230 / Plasmid: pET-BJP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q89GW5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 1.93 Å3/Da / Density % sol: 36.38 % / Description: Clusters of parallelepiped-shaped crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: BJP-1 (10 mg mL-1 in 0.1 M Tris-HCl pH 8.5 and 5 mM zinc(II) chloride) mixed with precipitant (0.2 M lithium sulfate, 30-35 % PEG4000, 0.5 M sodium acetate pH 8.5)
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 5, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.18→34.68 Å / Num. obs: 148959 / % possible obs: 94.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 6.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.8
Reflection shellResolution: 1.18→1.24 Å / Redundancy: 4 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3 / Num. unique obs: 21301 / CC1/2: 0.806 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LVZ

3lvz


Resolution: 1.18→34.68 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / Rfactor Rfree error: 0.03 / SU B: 0.888 / SU ML: 0.02 / SU R Cruickshank DPI: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.034 / SU Rfree Cruickshank DPI: 0.0336 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14601 7703 5.2 %RANDOM
Rwork0.12071 ---
obs0.122 141256 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.912 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2--0 Å2-0.01 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.18→34.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 14 627 4741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194458
X-RAY DIFFRACTIONr_bond_other_d0.0020.024221
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9716108
X-RAY DIFFRACTIONr_angle_other_deg2.06739760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7165612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.07324.944178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43715738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.021517
X-RAY DIFFRACTIONr_chiral_restr0.0840.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215190
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02947
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_it1.4872310
X-RAY DIFFRACTIONr_mcbond_other1.4842307
X-RAY DIFFRACTIONr_mcangle_it1.7182915
X-RAY DIFFRACTIONr_mcangle_other1.7192916
X-RAY DIFFRACTIONr_scbond_it1.622148
X-RAY DIFFRACTIONr_scbond_other1.622149
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1543174
X-RAY DIFFRACTIONr_long_range_B_refined3.065049
X-RAY DIFFRACTIONr_long_range_B_other2.7144948
X-RAY DIFFRACTIONr_rigid_bond_restr3.42833757
X-RAY DIFFRACTIONr_sphericity_free24.6535389
X-RAY DIFFRACTIONr_sphericity_bonded11.87653918
LS refinement shellResolution: 1.18→1.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 525 -
Rwork0.196 10234 -
obs--92.1 %

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