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- PDB-1jtg: CRYSTAL STRUCTURE OF TEM-1 BETA-LACTAMASE / BETA-LACTAMASE INHIBI... -

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Basic information

Entry
Database: PDB / ID: 1jtg
TitleCRYSTAL STRUCTURE OF TEM-1 BETA-LACTAMASE / BETA-LACTAMASE INHIBITOR PROTEIN COMPLEX
Components
  • BETA-LACTAMASE INHIBITORY PROTEINBeta-lactamase inhibitor protein
  • BETA-LACTAMASE TEM
KeywordsHYDROLASE / protein-protein complex / TEM-1 beta-lactamase / beta-lactamase inhibitor protein / BLIP
Function / homology
Function and homology information


regulation of beta-lactamase activity / beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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: 1.73 Å
AuthorsStrynadka, N.C.J. / Jensen, S.E. / Alzari, P.M. / James, M.N.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure and kinetic analysis of beta-lactamase inhibitor protein-II in complex with TEM-1 beta-lactamase.
Authors: Lim, D. / Park, H.U. / De Castro, L. / Kang, S.G. / Lee, H.S. / Jensen, S. / Lee, K.J. / Strynadka, N.C.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: A POTENT NEW MODE OF BETA-LACTAMASE INHIBITION REVEALED BY THE 1.7 A X-RAY CRYSTALLOGRAPHIC STRUCTURE OF THE TEM-1-BLIP COMPLEX.
Authors: C Strynadka, N. / Jensen, S.E. / Alzari, P.M. / James, M.N.
History
DepositionAug 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-LACTAMASE TEM
B: BETA-LACTAMASE INHIBITORY PROTEIN
C: BETA-LACTAMASE TEM
D: BETA-LACTAMASE INHIBITORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1616
Polymers93,0814
Non-polymers802
Water7,945441
1
A: BETA-LACTAMASE TEM
B: BETA-LACTAMASE INHIBITORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5813
Polymers46,5412
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-21 kcal/mol
Surface area16560 Å2
MethodPISA
2
C: BETA-LACTAMASE TEM
D: BETA-LACTAMASE INHIBITORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5813
Polymers46,5412
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-25 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.800, 126.300, 158.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains two biological units.

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Components

#1: Protein BETA-LACTAMASE TEM


Mass: 28984.076 Da / Num. of mol.: 2 / Mutation: I84V,V184A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Protein BETA-LACTAMASE INHIBITORY PROTEIN / Beta-lactamase inhibitor 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growpH: 8.8 / Details: pH 8.8

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.93
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 89586 / % possible obs: 88 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 17

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TEM-1 NATIVE

Resolution: 1.73→19.96 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2948138.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.205 4511 5 %RANDOM
Rwork0.173 ---
obs0.173 89586 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.4464 Å2 / ksol: 0.346053 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2--2.6 Å20 Å2
3----0.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.73→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6505 0 2 441 6948
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.591.5
X-RAY DIFFRACTIONc_mcangle_it3.352
X-RAY DIFFRACTIONc_scbond_it4.272
X-RAY DIFFRACTIONc_scangle_it6.022.5
LS refinement shellResolution: 1.73→1.84 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 678 5.2 %
Rwork0.265 12239 -
obs--81 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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