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- PDB-1kr3: Crystal Structure of the Metallo beta-Lactamase from Bacteroides ... -

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Basic information

Entry
Database: PDB / ID: 1kr3
TitleCrystal Structure of the Metallo beta-Lactamase from Bacteroides fragilis (CfiA) in Complex with the Tricyclic Inhibitor SB-236050.
Componentsbeta-Lactamase, type II
KeywordsHYDROLASE / beta sandwich / protein-inhibitor complex / metallo / beta-lactamase
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / 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
Chem-113 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPayne, D.J. / Hueso-Rodrguez, J.A. / Boyd, H. / Concha, N.O. / Janson, C.A. / Gilpin, M. / Bateson, J.H. / Cheever, C. / Niconovich, N.L. / Pearson, S. ...Payne, D.J. / Hueso-Rodrguez, J.A. / Boyd, H. / Concha, N.O. / Janson, C.A. / Gilpin, M. / Bateson, J.H. / Cheever, C. / Niconovich, N.L. / Pearson, S. / Rittenhouse, S. / Tew, D. / Dez, E. / Prez, P. / de la Fuente, J. / Rees, M. / Rivera-Sagredo, A.
CitationJournal: ANTIMICROB.AGENTS CHEMOTHER. / Year: 2002
Title: Identification of a series of tricyclic natural products as potent broad-spectrum inhibitors of metallo-beta-lactamases
Authors: Payne, D.J. / Hueso-Rodrguez, J.A. / Boyd, H. / Concha, N.O. / Janson, C.A. / Gilpin, M. / Bateson, J.H. / Cheever, C. / Niconovich, N.L. / Pearson, S. / Rittenhouse, S. / Tew, D. / Dez, E. ...Authors: Payne, D.J. / Hueso-Rodrguez, J.A. / Boyd, H. / Concha, N.O. / Janson, C.A. / Gilpin, M. / Bateson, J.H. / Cheever, C. / Niconovich, N.L. / Pearson, S. / Rittenhouse, S. / Tew, D. / Dez, E. / Prez, P. / de la Fuente, J. / Rees, M. / Rivera-Sagredo, A.
History
DepositionJan 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-Lactamase, type II
B: beta-Lactamase, type II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,66910
Polymers50,7172
Non-polymers9528
Water72140
1
A: beta-Lactamase, type II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8355
Polymers25,3591
Non-polymers4764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-Lactamase, type II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8355
Polymers25,3591
Non-polymers4764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.800, 44.200, 58.500
Angle α, β, γ (deg.)92.80, 95.30, 98.00
Int Tables number1
Space group name H-MP1
Detailschain A and B do not form a functional dimer

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Components

#1: Protein beta-Lactamase, type II


Mass: 25358.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: CfiA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE) / References: UniProt: P25910, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-113 / 7,8-DIHYDROXY-1-METHOXY-3-METHYL-10-OXO-4,10-DIHYDRO-1H,3H-PYRANO[4,3-B]CHROMENE-9-CARBOXYLIC ACID


Mass: 322.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14O8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 32% PEG1000, 0.1M MES, 10microM ZnCl2, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
114 mg/mlprotein1drop
220 mMHEPES1droppH7.5
332 %PEG10001reservoir
40.1 MMES1reservoir
510000 mM1reservoirpH6.0ZnCl2

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.542 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 1, 1997 / Details: Ni-filtered
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.5→29 Å / Num. all: 15937 / Num. obs: 15937 / % possible obs: 75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 9.3
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1400 / Rsym value: 0.23 / % possible all: 56
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 10526 / % possible obs: 73.7 %
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.54 Å / % possible obs: 58 %

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
CNX2000.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native CfiA (1ZNB)

1znb


Resolution: 2.5→29.07 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 813475.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1082 10.3 %RANDOM
Rwork0.152 ---
all0.152 10526 --
obs0.152 10526 73.7 %-
Solvent computationSolvent model: MASK / Bsol: 60 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å2-0.67 Å20.66 Å2
2---2.77 Å21.89 Å2
3---2.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 52 40 3576
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_mcbond_it2.541.5
X-RAY DIFFRACTIONc_mcangle_it3.862
X-RAY DIFFRACTIONc_scbond_it4.112
X-RAY DIFFRACTIONc_scangle_it5.652.5
Refine LS restraints NCSNCS model details: CONSTRAINED MAIN CHAIN ATOMS
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 131 9.4 %
Rwork0.22 1262 -
obs--58.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2SB3.PARSB3.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.141
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17
LS refinement shell
*PLUS
Rfactor Rwork: 0.22

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