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- PDB-5njw: Crystal Structure of BJP-1 metallo beta-lactamase in complex with... -

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Basic information

Entry
Database: PDB / ID: 5njw
TitleCrystal Structure of BJP-1 metallo beta-lactamase in complex with boric acid
ComponentsBlr6230 protein
KeywordsHYDROLASE / MBLs / 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
BORIC ACID / HYDROXIDE ION / DI(HYDROXYETHYL)ETHER / Blr6230 protein
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 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.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_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 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Blr6230 protein
B: Blr6230 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,80816
Polymers63,9652
Non-polymers84214
Water10,359575
1
A: Blr6230 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,55010
Polymers31,9831
Non-polymers5679
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Blr6230 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2586
Polymers31,9831
Non-polymers2755
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.370, 44.620, 76.120
Angle α, β, γ (deg.)78.80, 89.13, 61.79
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q89GW5

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Non-polymers , 6 types, 589 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BH3O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 2.07 Å3/Da / Density % sol: 40.57 % / Description: parallelepiped-shaped crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium Suplhate, 30-35 % PEG400, 0.5 M sodium acetate, pH 8.5

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.25→32.14 Å / Num. obs: 126849 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 5.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.5
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 120271 / CC1/2: 0.976 / % possible all: 95.48

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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: 1.25→32.14 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.276 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.042 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16209 6575 5.2 %RANDOM
Rwork0.1316 ---
obs0.13318 120271 95.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.645 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20.02 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.25→32.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4119 0 35 575 4729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194403
X-RAY DIFFRACTIONr_bond_other_d0.0030.024198
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9756007
X-RAY DIFFRACTIONr_angle_other_deg0.9339709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7225596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21225176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60815733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7441516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215047
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02925
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_it0.7980.9992261
X-RAY DIFFRACTIONr_mcbond_other0.7970.9992260
X-RAY DIFFRACTIONr_mcangle_it0.9531.5022844
X-RAY DIFFRACTIONr_mcangle_other0.9521.5032845
X-RAY DIFFRACTIONr_scbond_it0.9141.1432142
X-RAY DIFFRACTIONr_scbond_other0.9141.1432142
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.031.643146
X-RAY DIFFRACTIONr_long_range_B_refined1.67113.1474940
X-RAY DIFFRACTIONr_long_range_B_other1.67113.1574941
X-RAY DIFFRACTIONr_rigid_bond_restr1.40138601
X-RAY DIFFRACTIONr_sphericity_free14.2315368
X-RAY DIFFRACTIONr_sphericity_bonded3.16658708
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 465 -
Rwork0.171 8700 -
obs--93.25 %

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