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- PDB-1s6r: 908R class c beta-lactamase bound to iodo-acetamido-phenyl boroni... -

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Basic information

Entry
Database: PDB / ID: 1s6r
Title908R class c beta-lactamase bound to iodo-acetamido-phenyl boronic acid
Componentsbeta-lactamase
KeywordsHYDROLASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-IODO-ACETAMIDO PHENYLBORONIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 2.24 Å
AuthorsWouters, J.
CitationJournal: Cell.Mol.Life Sci. / Year: 2003
Title: Crystal structure of Enterobacter cloacae 908R class C beta-lactamase bound to iodo-acetamido-phenyl boronic acid, a transition-state analogue.
Authors: Wouters, J. / Fonze, E. / Vermeire, M. / Frere, J.M. / Charlier, P.
History
DepositionJan 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4022
Polymers39,0981
Non-polymers3051
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.381, 83.763, 95.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsasymetric unit corresponds to biological unit

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Components

#1: Protein beta-lactamase / Cephalosporinase


Mass: 39097.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: 908R / Production host: Escherichia coli (E. coli) / References: UniProt: Q93CA2, beta-lactamase
#2: Chemical ChemComp-IAP / 4-IODO-ACETAMIDO PHENYLBORONIC ACID


Mass: 304.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9BINO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M bicine buffer, 30% PEG (Mr 6000), pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, hanging drop / Details: Wouters, J., (2001) Acta Cryst., D57, 162.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mMHEPES1droppH8.2
35 mMEDTA1drop
42 mMdithiothreitol1drop
50.1 Mbicine1reservoirpH9.0
630 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.24→30 Å / Num. all: 13652 / Num. obs: 13652 / % possible obs: 83.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection
*PLUS
Num. obs: 11810 / % possible obs: 88.6 % / Num. measured all: 48365 / Rmerge(I) obs: 0.128

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 2.24→10 Å / Num. parameters: 11341 / Num. restraintsaints: 11667 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.293 659 5.6 %RANDOM
obs0.2257 9588 88.6 %-
all-11810 --
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2814
Refinement stepCycle: LAST / Resolution: 2.24→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 14 47 2817
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.016
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0201
X-RAY DIFFRACTIONs_zero_chiral_vol0.017
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.025
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.01
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor obs: 0.226 / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.02
X-RAY DIFFRACTIONs_chiral_restr0.017

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