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- PDB-1hlk: METALLO-BETA-LACTAMASE FROM BACTEROIDES FRAGILIS IN COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 1hlk
TitleMETALLO-BETA-LACTAMASE FROM BACTEROIDES FRAGILIS IN COMPLEX WITH A TRICYCLIC INHIBITOR
ComponentsBETA-LACTAMASE, TYPE II
KeywordsHYDROLASE / alpha-beta structure / beta-sandwich
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 / 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
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-Rodriguez, J.A. / Boyd, H. / Concha, N.O. / Janson, C.A. / Gilpin, M. / Bateson, J.H. / Chever, C. / Niconovich, N.L. / Pearson, S. ...Payne, D.J. / Hueso-Rodriguez, J.A. / Boyd, H. / Concha, N.O. / Janson, C.A. / Gilpin, M. / Bateson, J.H. / Chever, C. / Niconovich, N.L. / Pearson, S. / Rittenhouse, S. / Tew, D. / Diez, E. / Perez, 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-Rodriguez, J.A. / Boyd, H. / Concha, N.O. / Janson, C.A. / Gilpin, M. / Bateson, J.H. / Chever, C. / Niconovich, N.L. / Pearson, S. / Rittenhouse, S. / Tew, D. / Diez, E. ...Authors: Payne, D.J. / Hueso-Rodriguez, J.A. / Boyd, H. / Concha, N.O. / Janson, C.A. / Gilpin, M. / Bateson, J.H. / Chever, C. / Niconovich, N.L. / Pearson, S. / Rittenhouse, S. / Tew, D. / Diez, E. / Perez, P. / de la Fuente, J. / Rees, M. / Rivera-Sagredo, A.
History
DepositionDec 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Aug 9, 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 / 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_asym_id / _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_asym_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_asym_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)50,56010
Polymers49,6082
Non-polymers9528
Water1,51384
1
A: BETA-LACTAMASE, TYPE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2805
Polymers24,8041
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)25,2805
Polymers24,8041
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
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Protein BETA-LACTAMASE, TYPE II / E.C.3.5.2.6 / METALLO-BETA-LACTAMASE / PENICILLINASE / CEPHALOSPORINASE / IMIPENEM-CEFOXITIN HYDROLYZING ENZYME


Mass: 24803.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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.: 84 / 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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20mM HEPES, pH 7.5, 32% PEG 1000, 01M MES, 10 uM ZnCl2, pH 6.0, VAPOR DIFFUSION, SITTING DROP at 294K
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
50.010 mM1reservoirpH6.0ZnCl2

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 10, 1990
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 10643 / Num. obs: 10643 / % possible obs: 73.8 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 9.2
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1400 / Rsym value: 0.23 / % possible all: 73.8
Reflection
*PLUS
Num. obs: 10526 / % possible obs: 73.7 %
Reflection shell
*PLUS
Lowest resolution: 2.54 Å / % possible obs: 58 %

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1znb

1znb


Resolution: 2.5→50 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1082 10 %random
Rwork0.165 ---
all0.159 10643 --
obs0.159 10526 73.8 %-
Solvent computationSolvent model: flat model
Displacement parametersBiso mean: 26.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 52 84 3622
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.87
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor all: 0.165 / Rfactor obs: 0.141 / Rfactor Rfree: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87

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