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- PDB-5gis: Crystal structure of a Fab fragment with its ligand peptide -

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Basic information

Entry
Database: PDB / ID: 5gis
TitleCrystal structure of a Fab fragment with its ligand peptide
Components
  • Heavy chain of Fab fragment
  • Light chain of Fab fragment
  • THR-LYS-PRO-ILE-THR-ILE-GLY-SER-HIS-ALA-HIS-GLY-ASP-GLN-TYR-LYS
KeywordsIMMUNE SYSTEM / Fab / peptide ligand / mutation
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / Maturation of TCA enzymes and regulation of TCA cycle / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADP+ metabolic process / 2-oxoglutarate metabolic process / glyoxylate cycle / tricarboxylic acid cycle / Mitochondrial protein degradation ...Citric acid cycle (TCA cycle) / Maturation of TCA enzymes and regulation of TCA cycle / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADP+ metabolic process / 2-oxoglutarate metabolic process / glyoxylate cycle / tricarboxylic acid cycle / Mitochondrial protein degradation / Transcriptional activation of mitochondrial biogenesis / NAD binding / peroxisome / carbohydrate metabolic process / mitochondrial matrix / magnesium ion binding / mitochondrion / extracellular exosome / cytosol
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Isocitrate dehydrogenase [NADP], mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsKitago, Y. / Kaneko, K.K. / Ogasawara, S. / Kato, Y. / Takagi, J.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2016
Title: Structural basis for multi-specific peptide recognition by the anti-IDH1/2 monoclonal antibody, MsMab-1.
Authors: Kitago, Y. / Kaneko, M.K. / Ogasawara, S. / Kato, Y. / Takagi, J.
History
DepositionJun 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Nov 13, 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
H: Heavy chain of Fab fragment
L: Light chain of Fab fragment
C: THR-LYS-PRO-ILE-THR-ILE-GLY-SER-HIS-ALA-HIS-GLY-ASP-GLN-TYR-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7656
Polymers53,4773
Non-polymers2883
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-63 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.050, 65.000, 67.130
Angle α, β, γ (deg.)90.00, 111.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Heavy chain of Fab fragment


Mass: 25712.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma / Production host: Mammalia (mammals)
#2: Antibody Light chain of Fab fragment


Mass: 26006.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma / Production host: Mammalia (mammals)
#3: Protein/peptide THR-LYS-PRO-ILE-THR-ILE-GLY-SER-HIS-ALA-HIS-GLY-ASP-GLN-TYR-LYS


Mass: 1756.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P48735*PLUS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Imidazole-HCl pH 6.5, 2.1 M Ammonium Sulfate, 0.2 M Potassium/Sodium Tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→45 Å / Num. obs: 34050 / % possible obs: 98.2 % / Redundancy: 5.8 % / Net I/σ(I): 12.3
Reflection shellResolution: 1.93→2.04 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata processing
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GIR

5gir


Resolution: 1.93→44.99 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.71 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21604 1700 5 %RANDOM
Rwork0.18614 ---
obs0.18766 32291 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.578 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20.27 Å2
2---0.49 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.93→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 15 260 3580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193416
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.9414649
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4125430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82124.211133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90115544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.371513
X-RAY DIFFRACTIONr_chiral_restr0.1010.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212526
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1581.9771726
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8752.9522151
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.992.2061690
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.71518.85814357
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 125 -
Rwork0.227 2364 -
obs--97.72 %

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