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- PDB-3qhy: Structural, thermodynamic and kinetic analysis of the picomolar b... -

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Basic information

Entry
Database: PDB / ID: 3qhy
TitleStructural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases
Components
  • Beta-lactamase
  • Beta-lactamase inhibitory protein II
KeywordsHYDROLASE/HYDROLASE INHIBITOR / enyzme-inhibitor complex / beta-propeller / beta-lactamase / protein:protein interaction / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / ubiquitin protein ligase activity / response to antibiotic / metal ion binding
Similarity search - Function
: / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family ...: / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / 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 / 7 Propeller / Methylamine Dehydrogenase; Chain H / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-lactamase inhibitory protein II / Beta-lactamase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
Streptomyces exfoliatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsBrown, N.G. / Chow, D.C. / Sankaran, B. / Zwart, P. / Prasad, B.V.V. / Palzkill, T. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Analysis of the binding forces driving the tight interactions between beta-lactamase inhibitory protein-II (BLIP-II) and class A beta-lactamases.
Authors: Brown, N.G. / Chow, D.C. / Sankaran, B. / Zwart, P. / Prasad, B.V. / Palzkill, T.
History
DepositionJan 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase inhibitory protein II


Theoretical massNumber of molelcules
Total (without water)58,1212
Polymers58,1212
Non-polymers00
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-6 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.766, 87.177, 61.020
Angle α, β, γ (deg.)90.00, 114.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase / Beta-lactamase Bla1 / Beta-lactamase I


Mass: 29759.611 Da / Num. of mol.: 1 / Fragment: unp residues 39-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: bla1, BA_2507, GBAA2507, GBAA_2507 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93T42, beta-lactamase
#2: Protein Beta-lactamase inhibitory protein II


Mass: 28360.947 Da / Num. of mol.: 1 / Fragment: unp residues 41-311
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces exfoliatus (bacteria) / Gene: bliB / Production host: Escherichia coli (E. coli) / References: UniProt: O87916
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 0.1M Bicine, 13 % PEG 10,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2010
RadiationMonochromator: SINGLE CRYSTAL, CYLINDRICALLY BENT SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 37880 / % possible obs: 98.4 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.06→2.1 Å / % possible all: 91.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JTD

1jtd


Resolution: 2.06→49.95 Å / SU ML: 0.26 / σ(F): 1.93 / Phase error: 20.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 1884 4.97 %
Rwork0.169 --
obs0.172 37877 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.74 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7805 Å20 Å20.1636 Å2
2--3.7621 Å20 Å2
3----4.5426 Å2
Refinement stepCycle: LAST / Resolution: 2.06→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 0 508 4418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073987
X-RAY DIFFRACTIONf_angle_d1.0295422
X-RAY DIFFRACTIONf_dihedral_angle_d12.3031391
X-RAY DIFFRACTIONf_chiral_restr0.072608
X-RAY DIFFRACTIONf_plane_restr0.004708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0599-2.13350.3181740.2313478X-RAY DIFFRACTION95
2.1335-2.21890.21451780.18193543X-RAY DIFFRACTION98
2.2189-2.31990.26111810.17133585X-RAY DIFFRACTION98
2.3199-2.44220.2251780.17243598X-RAY DIFFRACTION98
2.4422-2.59520.20761920.16683588X-RAY DIFFRACTION99
2.5952-2.79560.22551730.16913629X-RAY DIFFRACTION99
2.7956-3.07690.23621880.16933601X-RAY DIFFRACTION99
3.0769-3.5220.22692200.16693613X-RAY DIFFRACTION99
3.522-4.43690.18631980.1493646X-RAY DIFFRACTION99
4.4369-49.96030.19062020.17183712X-RAY DIFFRACTION100

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