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- PDB-3c7v: Structural Insight into the Kinetics and Delta-Cp of interactions... -

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Basic information

Entry
Database: PDB / ID: 3c7v
TitleStructural Insight into the Kinetics and Delta-Cp of interactions between TEM-1 Beta-Lactamase and BLIP
Components
  • Beta-lactamase
  • Beta-lactamase inhibitory protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / enzyme-inhibitor complex / Antibiotic resistance / Hydrolase / Plasmid / Secreted / 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 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Streptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsWang, J. / Chow, D.-C.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural insight into the kinetics and DeltaCp of interactions between TEM-1 beta-lactamase and beta-lactamase inhibitory protein (BLIP)
Authors: Wang, J. / Palzkill, T. / Chow, D.C.
History
DepositionFeb 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.4Oct 30, 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
B: Beta-lactamase inhibitory protein
C: Beta-lactamase
D: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)92,8974
Polymers92,8974
Non-polymers00
Water3,117173
1
A: Beta-lactamase
B: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)46,4482
Polymers46,4482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-11 kcal/mol
Surface area16350 Å2
MethodPISA
2
C: Beta-lactamase
D: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)46,4482
Polymers46,4482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-11 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.671, 129.044, 78.898
Angle α, β, γ (deg.)90.00, 91.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISTRPTRPAA26 - 2881 - 263
21HISHISTRPTRPCC26 - 2881 - 263
12ALAALAVALVALBB1 - 1651 - 165
22ALAALAVALVALDD1 - 1651 - 165

NCS ensembles :
ID
1
2

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Components

#1: Protein Beta-lactamase / Extended spectrum beta-lactamase / TEM extended spectrum beta-lactamase / Betalactamase TEM-116 / ...Extended spectrum beta-lactamase / TEM extended spectrum beta-lactamase / Betalactamase TEM-116 / Mutant extended- spectrum beta-lactamase / Beta lactamase


Mass: 28984.076 Da / Num. of mol.: 2 / Mutation: Y51A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaTEM-116 / Production host: Escherichia coli (E. coli)
References: UniProt: Q79DR3, UniProt: P62593*PLUS, beta-lactamase
#2: Protein Beta-lactamase inhibitory protein / BLIP


Mass: 17464.396 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.: 173 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 12% PEG 8000, 0.1M Phosphate-Citrate, 0.1M NaCl, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.3808 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3808 Å / Relative weight: 1
ReflectionResolution: 2.07→35.1 Å / Num. all: 43519 / Num. obs: 54728 / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 13.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JTG

1jtg


Resolution: 2.07→35.09 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.963 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23846 2789 5.1 %RANDOM
Rwork0.21441 ---
obs0.21563 51939 92.88 %-
all-43519 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.387 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.04 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.07→35.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6516 0 0 173 6689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226646
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9579016
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7965852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.63423.83282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.857151102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.111546
X-RAY DIFFRACTIONr_chiral_restr0.10.21020
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025018
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.23470
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.24734
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3790.2121
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2251.54232
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.85126770
X-RAY DIFFRACTIONr_scbond_it3.32932414
X-RAY DIFFRACTIONr_scangle_it4.9544.52246
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1052tight positional0.180.05
2B660tight positional0.20.05
1A978medium positional0.430.5
2B568medium positional0.410.5
1A1052tight thermal2.050.5
2B660tight thermal2.010.5
1A978medium thermal3.22
2B568medium thermal4.012
LS refinement shellResolution: 2.07→2.126 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 157 -
Rwork0.295 2880 -
obs--70.27 %
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)
10.0672-0.00680.02030.01640.05850.2398-0.00160.00160.00330.0172-0.0279-0.0267-0.0321-0.02430.02950.0165-0.01640.026-0.01270.02260.051315.708115.610865.7592
20.232-0.2939-0.2870.41870.2910.4684-0.046-0.00910.0270.050.0218-0.02130.01180.00660.0243-0.00650.00140.00930.0087-0.01180.04183.00816.732443.9235
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA26 - 2881 - 263
2X-RAY DIFFRACTION1CC26 - 2881 - 263
3X-RAY DIFFRACTION2BB1 - 1651 - 165
4X-RAY DIFFRACTION2DD1 - 1651 - 165

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