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- PDB-1jtd: Crystal structure of beta-lactamase inhibitor protein-II in compl... -

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Basic information

Entry
Database: PDB / ID: 1jtd
TitleCrystal structure of beta-lactamase inhibitor protein-II in complex with TEM-1 beta-lactamase
Components
  • TEM-1 beta-lactamase
  • beta-lactamase inhibitor protein II
KeywordsHYDROLASE/INHIBITOR / protein-protein complex / TEM-1 beta-lactamase / beta-lactamase inhibitor protein-II / BLIP-II / 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 TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Streptomyces exfoliatus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLim, D.C. / Park, H.U. / De Castro, L. / Kang, S.G. / Lee, H.S. / Jensen, S. / Lee, K.J. / Strynadka, N.C.J.
CitationJournal: 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.
History
DepositionAug 20, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_asym_id / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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: TEM-1 beta-lactamase
B: beta-lactamase inhibitor protein II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5277
Polymers56,3272
Non-polymers2005
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.525, 84.918, 147.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TEM-1 beta-lactamase


Mass: 28970.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 lamdaDE3 / References: UniProt: P62593, beta-lactamase
#2: Protein beta-lactamase inhibitor protein II


Mass: 27356.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces exfoliatus (bacteria) / Strain: SMF19 / References: UniProt: O87916
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG8000, calcium acetate, sodium cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris1drop
2150 mM1dropNaCl
310 mg/mlprotein1drop
424 %(w/v)PEG80001reservoir
520 mMcalcium acetate1reservoir
667 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 14, 1999 / Details: Osmic mirrors
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 27197 / Num. obs: 27197 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.39 % / Biso Wilson estimate: 18.8 Å2 / Rsym value: 0.053 / Net I/σ(I): 20
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 7.6 / Num. unique all: 2446 / Rsym value: 0.132 / % possible all: 89.5
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 92242 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 89.5 % / Rmerge(I) obs: 0.132

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Processing

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

Resolution: 2.3→24.54 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1832657.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1325 4.9 %RANDOM
Rwork0.178 ---
all0.1806 27197 --
obs-27127 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.8658 Å2 / ksol: 0.327549 e/Å3
Displacement parametersBiso mean: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20 Å2
2--3.85 Å20 Å2
3----5.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2.3→24.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 5 366 4323
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.931.5
X-RAY DIFFRACTIONc_mcangle_it2.572
X-RAY DIFFRACTIONc_scbond_it3.092
X-RAY DIFFRACTIONc_scangle_it3.942.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 217 4.9 %
Rwork0.18 4193 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.178 / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.931.5
X-RAY DIFFRACTIONc_scbond_it3.092
X-RAY DIFFRACTIONc_mcangle_it2.572
X-RAY DIFFRACTIONc_scangle_it3.942.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.248 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.18

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