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- PDB-3c7u: Structural Insight into the Kinetics and Cp of interactions betwe... -

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Basic information

Entry
Database: PDB / ID: 3c7u
TitleStructural Insight into the Kinetics and Cp of interactions between TEM-1-Lactamase and BLIP
Components
  • Beta-lactamase inhibitory proteinBeta-lactamase inhibitor protein
  • Beta-lactamase
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: 2.2 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.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)92,8514
Polymers92,8514
Non-polymers00
Water4,161231
1
A: Beta-lactamase
B: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)46,4252
Polymers46,4252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-10 kcal/mol
Surface area16750 Å2
MethodPISA
2
C: Beta-lactamase
D: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)46,4252
Polymers46,4252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-9 kcal/mol
Surface area16800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.090, 129.476, 80.130
Angle α, β, γ (deg.)90.00, 91.86, 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: W150A
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 / Beta-lactamase inhibitor protein / BLIP


Mass: 17441.361 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 / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 15% PEG 8000, 0.1M Phosphate-Citrate, 0.1M NaCl, pH 4.5, 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: Aug 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3808 Å / Relative weight: 1
ReflectionResolution: 2→32.41 Å / Num. all: 54728 / Num. obs: 50562 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 12.5

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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: 2.2→32.41 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.914 / SU B: 10.593 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23202 2568 5.1 %RANDOM
Rwork0.20833 ---
obs0.20954 47994 99.74 %-
all-79830 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.484 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0.28 Å2
2--0.13 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6512 0 0 231 6743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0226640
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9599006
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5725852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1123.83282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.816151102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4861546
X-RAY DIFFRACTIONr_chiral_restr0.1370.21020
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025014
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.23066
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24591
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4670.2235
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3770.2149
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0991.54232
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.66726770
X-RAY DIFFRACTIONr_scbond_it3.66932408
X-RAY DIFFRACTIONr_scangle_it5.6144.52236
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 positional0.20.05
2B660tight positional0.170.05
1A978medium positional0.450.5
2B566medium positional0.380.5
1A1052tight thermal4.480.5
2B660tight thermal3.740.5
1A978medium thermal4.612
2B566medium thermal6.032
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 167 -
Rwork0.246 3446 -
obs--96.53 %
Refinement TLS params.

S32: 0.0008 Å ° / 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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00170.0014-0.00210.0012-0.00180.00260.0006-0.0003-0.0002-0.0004-0.0003-0.0002-0.0006-0.00030.018-0.00030.0167-0.00570.0002-0.00636.99715.59913.336
20.00560.0069-0.00680.0114-0.00630.0099-0.00070.0001-0.0010.0002-0.0004-0.001-0.00080.00110.0182-0.00020.0158-0.0056-0.0001-0.006419.63416.59935.336
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 288
2X-RAY DIFFRACTION1C26 - 288
3X-RAY DIFFRACTION2B1 - 165
4X-RAY DIFFRACTION2D1 - 165

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