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- PDB-2jel: JEL42 FAB/HPR COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2jel
TitleJEL42 FAB/HPR COMPLEX
Components
  • (JEL42 FAB FRAGMENT) x 2
  • HISTIDINE-CONTAINING PROTEIN
KeywordsCOMPLEX (ANTIBODY/ANTIGEN) / ANTIBODY-PROTEIN COMPLEX / HISTIDINE-CONTAINING PROTEIN / MOLECULAR RECOGNITION / COMPLEX (ANTIBODY-ANTIGEN) / COMPLEX (ANTIBODY-ANTIGEN) complex
Function / homology
Function and homology information


phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / enzyme inhibitor activity / enzyme regulator activity / enzyme activator activity / cytosol
Similarity search - Function
Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. ...Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein HPr
Similarity search - Component
Biological speciesMus musculus (house mouse)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPrasad, L. / Waygood, E.B. / Lee, J.S. / Delbaere, L.T.J.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: The 2.5 A resolution structure of the jel42 Fab fragment/HPr complex
Authors: Prasad, L. / Waygood, E.B. / Lee, J.S. / Delbaere, L.T.J.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Evaluation of Mutagenesis for Epitope Mapping. Structure of an Antibody-Protein Antigen Complex
Authors: Prasad, L. / Sharma, S. / Vandonselaar, M. / Quail, J.W. / Lee, J.S. / Waygood, E.B. / Wilson, K.S. / Dauter, Z. / Delbaere, L.T.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Epitope Mapping by Mutagenesis Distinguishes between the Two Tertiary Structures of the Histidine-Containing Protein Hpr
Authors: Sharma, S. / Georges, F. / Delbaere, L.T. / Lee, J.S. / Klevit, R.E. / Waygood, E.B.
#3: Journal: J.Biol.Chem. / Year: 1989
Title: Crystallization of the Complex of a Monoclonal Fab Fragment with the Histidine-Containing Protein of the Phosphoenolpyruvate: Sugar Phosphotransferase System of Escherichia Coli
Authors: Delbaere, L.T. / Vandonselaar, M. / Quail, J.W. / Waygood, E.B. / Lee, J.S.
#4: Journal: J.Biol.Chem. / Year: 1988
Title: Structure Determination of a Monoclonal Fab Fragment Specific for Histidine-Containing Protein of the Phosphoenolpyruvate: Sugar Phosphotransferase System of Escherichia Coli
Authors: Prasad, L. / Vandonselaar, M. / Lee, J.S. / Delbaere, L.T.
History
DepositionFeb 24, 1998Processing site: BNL
SupersessionMay 27, 1998ID: 1JEL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Refinement description / Category: diffrn_detector / pdbx_database_status / software
Item: _diffrn_detector.detector / _pdbx_database_status.process_site / _software.name
Revision 1.4Apr 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
L: JEL42 FAB FRAGMENT
H: JEL42 FAB FRAGMENT
P: HISTIDINE-CONTAINING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2765
Polymers56,0843
Non-polymers1922
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-53 kcal/mol
Surface area22880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.850, 67.380, 77.090
Angle α, β, γ (deg.)90.00, 97.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody JEL42 FAB FRAGMENT


Mass: 23860.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#2: Antibody JEL42 FAB FRAGMENT


Mass: 23094.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#3: Protein HISTIDINE-CONTAINING PROTEIN / HPR


Mass: 9129.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AA04
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES OF THE FAB FRAGMENT ARE NUMBERED ACCORDING TO KABAT.

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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: 2.96 Å3/Da / Density % sol: 57 %
Crystal growpH: 5.8 / Details: pH 5.8
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Details: the molar ratio of Fab fragment to HPr was approximately 1:2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlFab fragment1drop
24 mg/mlHPr1drop
325 %satammonium sulfate1drop
425 mMphosphate1drop

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Apr 1, 1992 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→35 Å / Num. obs: 22067 / % possible obs: 96.6 % / Observed criterion σ(I): 5 / Redundancy: 2.7 % / Rsym value: 0.046 / Net I/σ(I): 11
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.19 / % possible all: 93
Reflection
*PLUS
Num. measured all: 47817 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 93 % / Num. unique obs: 1043 / Num. measured obs: 2784 / Rmerge(I) obs: 0.19

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Processing

Software
NameVersionClassification
MADNESdata collection
Agrovata(CCP4)data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
Agrovatadata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GLOOP2 FAB

Resolution: 2.5→6 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: INDIVIDUAL ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1014 5 %RANDOM
Rwork0.21 ---
obs0.21 20427 96 %-
Displacement parametersBiso mean: 36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.25 Å
Luzzati d res low-6 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 10 67 4014
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.322.85
X-RAY DIFFRACTIONx_mcangle_it4.644.5
X-RAY DIFFRACTIONx_scbond_it5.244.91
X-RAY DIFFRACTIONx_scangle_it6.847
LS refinement shellResolution: 2.5→2.56 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.39 114 4.9 %
Rwork0.34 1043 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2
LS refinement shell
*PLUS
Rfactor obs: 0.34

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