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- PDB-2b5r: 1B Lactamase / B Lactamase Inhibitor -

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Basic information

Entry
Database: PDB / ID: 2b5r
Title1B Lactamase / B Lactamase Inhibitor
Components
  • Beta-lactamase TEM
  • Beta-lactamase inhibitory protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protein-Protein complex / Structural Genomics / Israel Structural Proteomics Center / ISPC / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


regulation of beta-lactamase activity / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / extracellular region
Similarity search - Function
Beta-lactamase-inhibitor protein BLIP / Beta-lactamase-inhibitor protein BLIP domain superfamily / Beta-lactamase inhibitor (BLIP) / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / BamE-like / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family ...Beta-lactamase-inhibitor protein BLIP / Beta-lactamase-inhibitor protein BLIP domain superfamily / Beta-lactamase inhibitor (BLIP) / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / BamE-like / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-lactamase inhibitory protein / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Streptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRahat, O. / Albeck, S. / Meged, R. / Dym, O. / Screiber, G. / Israel Structural Proteomics Center (ISPC)
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Binding Hot Spots in the TEM1-BLIP Interface in Light of its Modular Architecture.
Authors: Reichmann, D. / Cohen, M. / Abramovich, R. / Dym, O. / Lim, D. / Strynadka, N.C. / Schreiber, G.
History
DepositionSep 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Dec 25, 2019Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Beta-lactamase TEM
C: Beta-lactamase inhibitory protein
B: Beta-lactamase TEM
D: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)92,9954
Polymers92,9954
Non-polymers00
Water9,458525
1
A: Beta-lactamase TEM
C: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)46,4982
Polymers46,4982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-10 kcal/mol
Surface area16680 Å2
MethodPISA
2
B: Beta-lactamase TEM
D: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)46,4982
Polymers46,4982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-9 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.799, 124.473, 157.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase TEM / TEM-1 / TEM-2 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2 / TEM-16/CAZ-7 / TEM-24/CAZ-6 / IRT-4 / ...TEM-1 / TEM-2 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2 / TEM-16/CAZ-7 / TEM-24/CAZ-6 / IRT-4 / Penicillinase


Mass: 28941.010 Da / Num. of mol.: 2 / Mutation: V84I, E104Y, Y105N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Protein Beta-lactamase inhibitory protein / BLIP


Mass: 17556.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P35804
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.27 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 298 K / pH: 8.5
Details: PEG 3350, NH4 Acetate, pH 8.5, Microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97565 Å
DetectorType: NONIUS CAD4 / Detector: CCD / Date: Jul 1, 2005
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97565 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 109217 / Num. obs: 109217 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.065 / Net I/σ(I): 18.5
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 7 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 4 / Num. unique all: 5385 / Rsym value: 0.329 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→48.3 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 10903 -Random
Rwork0.19 ---
all0.19 109041 --
obs0.19 109041 99.7 %-
Refinement stepCycle: LAST / Resolution: 1.65→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6522 0 0 525 7047
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_d1.9
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d1.76
LS refinement shellResolution: 1.65→1.75 Å
RfactorNum. reflection% reflection
Rfree0.264 1817 -
Rwork0.205 --
obs-16148 100 %

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