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- PDB-2g2w: Crystal Structure of the SHV D104K Beta-lactamase/Beta-lactamase ... -

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Basic information

Entry
Database: PDB / ID: 2g2w
TitleCrystal Structure of the SHV D104K Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) complex
Components
  • Beta-lactamase SHV-1
  • Beta-lactamase inhibitory protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / beta-lactamase / beta-lactamase inhibitor / protein-protein complex / BLIP / SHV / 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 SHV-1 / Beta-lactamase inhibitory protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
Streptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsReynolds, K.A. / Thomson, J.M. / Corbett, K.D. / Bethel, C.R. / Berger, J.M. / Kirsch, J.F. / Bonomo, R.A. / Handel, T.M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural and Computational Characterization of the SHV-1 beta-Lactamase-beta-Lactamase Inhibitor Protein Interface.
Authors: Reynolds, K.A. / Thomson, J.M. / Corbett, K.D. / Bethel, C.R. / Berger, J.M. / Kirsch, J.F. / Bonomo, R.A. / Handel, T.M.
History
DepositionFeb 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 20, 2024Group: Structure summary / Category: 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 SHV-1
B: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)46,4782
Polymers46,4782
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-9 kcal/mol
Surface area16890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.563, 44.825, 62.902
Angle α, β, γ (deg.)78.88, 88.94, 62.42
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is the complex between chain A (SHV D104K) and chain B (BLIP)

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Components

#1: Protein Beta-lactamase SHV-1 / PIT-2


Mass: 28921.111 Da / Num. of mol.: 1 / Mutation: D104K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: Bla, shv1 / Plasmid: pET24a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AD64, beta-lactamase
#2: Protein Beta-lactamase inhibitory protein / BLIP


Mass: 17556.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Plasmid: pET26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35804
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: 4% PEG 8000, 25mM cacodylate, 10 mM BisTris, 25mM NaCl, pH 6.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 19, 2005
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 35776 / Num. obs: 35776 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Rsym value: 0.03 / Net I/σ(I): 25.389
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 6.07 / Rsym value: 0.096 / % possible all: 89.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: polyalanine models of chain A from PDB 1SHV and chain B from PDB 1JTG

1shv

1jtg


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.158 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22183 1786 5 %RANDOM
Rwork0.17966 ---
obs0.18172 33986 95.82 %-
all-35772 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.821 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å2-2.1 Å21.24 Å2
2--1.43 Å2-2.06 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 0 193 3447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223315
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9534495
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.095426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7623.38142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17215544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2481528
X-RAY DIFFRACTIONr_chiral_restr0.0950.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022511
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21639
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22348
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7561.52173
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23823375
X-RAY DIFFRACTIONr_scbond_it2.02131302
X-RAY DIFFRACTIONr_scangle_it3.1814.51120
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 124 -
Rwork0.214 2285 -
obs--87.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5253-0.1241-0.35670.77060.39021.1739-0.00470.06750.0021-0.0531-0.00870.09560.0053-0.02380.0134-0.04670.0071-0.0223-0.02780.008-0.006216.510711.3804-11.5447
21.22370.62150.38170.6430.11510.1380.0802-0.0907-0.00340.066-0.08040.01290.0301-0.03740.0002-0.01980.01270.0183-0.04490.002-0.041917.9582-1.19813.3485
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA26 - 2921 - 265
2X-RAY DIFFRACTION2BB1 - 1651 - 165

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