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- PDB-5wcm: Crystal structure of the complex between class B3 beta-lactamase ... -

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Basic information

Entry
Database: PDB / ID: 5wcm
TitleCrystal structure of the complex between class B3 beta-lactamase BJP-1 and 4-nitrobenzene-sulfonamide - new refinement
ComponentsBlr6230 protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Hydrolase / ZINC ENZYME / SULFONAMIDE COMPLEX / HYDROLASE-INHIBITOR COMPLEX / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / metal ion binding
Similarity search - Function
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
4-nitrobenzenesulfonamide / Blr6230 protein
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsDocquier, J.D. / Benvenuti, M. / Calderone, V. / Menciassi, N. / Shabalin, I.G. / Raczynska, J.E. / Wlodawer, A. / Jaskolski, M. / Minor, W. / Mangani, S.
Citation
Journal: Antimicrob. Agents Chemother. / Year: 2010
Title: High-resolution crystal structure of the subclass B3 metallo-beta-lactamase BJP-1: rational basis for substrate specificity and interaction with sulfonamides.
Authors: Docquier, J.D. / Benvenuti, M. / Calderone, V. / Stoczko, M. / Menciassi, N. / Rossolini, G.M. / Mangani, S.
#1: Journal: Drug Resist. Updat. / Year: 2018
Title: A close look onto structural models and primary ligands of metallo-beta-lactamases.
Authors: Raczynska, J.E. / Shabalin, I.G. / Minor, W. / Wlodawer, A. / Jaskolski, M.
History
DepositionJun 30, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionJul 19, 2017ID: 3M8T
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Revision 1.3Oct 4, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr2_label_alt_id / _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_label_seq_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: Blr6230 protein
B: Blr6230 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,56015
Polymers57,4362
Non-polymers1,12413
Water14,718817
1
A: Blr6230 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3128
Polymers28,7181
Non-polymers5957
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Blr6230 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2477
Polymers28,7181
Non-polymers5296
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.352, 44.908, 76.635
Angle α, β, γ (deg.)79.340, 90.590, 61.680
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Blr6230 protein


Mass: 28717.814 Da / Num. of mol.: 2 / Fragment: residues 32-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110) (bacteria)
Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110 / Gene: blr6230 / Plasmid: PET-9A / 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.: 11 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-4NZ / 4-nitrobenzenesulfonamide


Mass: 202.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30-35% PEG 4000, 5MM ZNCL2, 0.5M SODIUM ACETATE, TRIS-HCL 0.1M, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 19, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 124424 / % possible obs: 82.1 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.022 / Rrim(I) all: 0.049 / Rsym value: 0.044 / Χ2: 0.818 / Net I/av σ(I): 28.6 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
1.2-1.223.60.2924.424290.9340.1750.3410.2920.92932
1.22-1.243.60.260.9540.1550.3030.93138.8
1.24-1.273.60.2320.9560.1380.2710.92346.6
1.27-1.293.60.2040.9570.1220.2380.90856.5
1.29-1.323.60.1780.9670.1070.2080.91970.5
1.32-1.353.70.1560.9720.0930.1820.88188.3
1.35-1.393.60.1350.9790.0810.1570.86789.2
1.39-1.423.70.1110.9840.0670.130.85789.3
1.42-1.463.70.10.9850.0590.1160.85190.1
1.46-1.513.80.0890.9870.0520.1030.83490.5
1.51-1.5740.0750.9910.0420.0860.80491.5
1.57-1.634.10.0660.9920.0360.0750.77592.5
1.63-1.74.40.0590.9930.0310.0670.78393.5
1.7-1.794.70.0540.9940.0270.0610.79294.3
1.79-1.95.30.050.9950.0240.0560.83596.3
1.9-2.055.70.0450.9960.0210.0490.81196.6
2.05-2.265.80.0410.9970.0190.0450.78497.1
2.26-2.595.80.0390.9970.0180.0430.7797.9
2.59-3.265.70.0370.9960.0170.0410.75798
3.26-504.90.0350.9920.0190.040.77992.4

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LVZ

3lvz


Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.182 / SU ML: 0.024 / SU R Cruickshank DPI: 0.0446 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.043
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1598 6083 4.9 %RANDOM
Rwork0.132 ---
obs0.1334 117432 81.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 248.99 Å2 / Biso mean: 18.358 Å2 / Biso min: 9.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20.04 Å2-0.03 Å2
2--0.06 Å2-0.03 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 37 829 4840
Biso mean--15.56 31.77 -
Num. residues----526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024191
X-RAY DIFFRACTIONr_bond_other_d0.0020.023830
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9695679
X-RAY DIFFRACTIONr_angle_other_deg1.06438909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7985540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84125.148169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31415692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6371514
X-RAY DIFFRACTIONr_chiral_restr0.0760.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214741
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02789
X-RAY DIFFRACTIONr_rigid_bond_restr5.02734191
X-RAY DIFFRACTIONr_sphericity_free18.7320.005516
X-RAY DIFFRACTIONr_sphericity_bonded11.3720.0054381
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 154 -
Rwork0.201 2859 -
all-3013 -
obs--26.78 %

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