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

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Basic information

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


Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process ...Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / response to steroid hormone / female gonad development / peroxisomal matrix / tricarboxylic acid cycle / glutathione metabolic process / Peroxisomal protein import / peroxisome / NAD binding / tertiary granule lumen / NADP binding / secretory granule lumen / ficolin-1-rich granule lumen / response to oxidative stress / cadherin binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / mitochondrion / extracellular exosome / extracellular region / identical protein binding / cytoplasm / 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] cytoplasmic
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

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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
A: Heavy chain of Fab fragment
B: Light chain of Fab fragment
C: LYS-PRO-ILE-ILE-ILE-GLY-SER-HIS-ALA-TYR-GLY-ASP
D: LYS-PRO-ILE-ILE-ILE-GLY-SER-HIS-ALA-TYR-GLY-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,97317
Polymers105,9856
Non-polymers98911
Water8,917495
1
H: Heavy chain of Fab fragment
L: Light chain of Fab fragment
C: LYS-PRO-ILE-ILE-ILE-GLY-SER-HIS-ALA-TYR-GLY-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5699
Polymers52,9923
Non-polymers5766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-94 kcal/mol
Surface area19770 Å2
MethodPISA
2
A: Heavy chain of Fab fragment
B: Light chain of Fab fragment
D: LYS-PRO-ILE-ILE-ILE-GLY-SER-HIS-ALA-TYR-GLY-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4058
Polymers52,9923
Non-polymers4125
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-63 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.110, 93.650, 70.560
Angle α, β, γ (deg.)90.00, 107.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide LYS-PRO-ILE-ILE-ILE-GLY-SER-HIS-ALA-TYR-GLY-ASP


Mass: 1272.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75874*PLUS

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Antibody , 2 types, 4 molecules HALB

#1: Antibody Heavy chain of Fab fragment


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

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Non-polymers , 3 types, 506 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Imidazole-HCl pH 6.5, 2.0 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: May 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→48.3 Å / Num. obs: 64311 / % possible obs: 99.5 % / Redundancy: 5.1 % / Net I/σ(I): 13.3
Reflection shellResolution: 1.93→2.05 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2341)refinement
XDSdata processing
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EBQ

4ebq


Resolution: 1.93→38.435 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 3201 4.98 %
Rwork0.1815 --
obs0.184 64281 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→38.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6613 0 53 495 7161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136853
X-RAY DIFFRACTIONf_angle_d1.2589342
X-RAY DIFFRACTIONf_dihedral_angle_d11.6374102
X-RAY DIFFRACTIONf_chiral_restr0.0721052
X-RAY DIFFRACTIONf_plane_restr0.0081175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.95880.3581170.27072596X-RAY DIFFRACTION97
1.9588-1.98940.30231390.25192636X-RAY DIFFRACTION100
1.9894-2.0220.31291450.23542660X-RAY DIFFRACTION100
2.022-2.05690.25631350.23272636X-RAY DIFFRACTION100
2.0569-2.09430.28371450.22712639X-RAY DIFFRACTION100
2.0943-2.13460.28621410.2172659X-RAY DIFFRACTION100
2.1346-2.17810.27961340.20842650X-RAY DIFFRACTION100
2.1781-2.22550.25591440.19752651X-RAY DIFFRACTION100
2.2255-2.27730.25431390.19042650X-RAY DIFFRACTION100
2.2773-2.33420.27151370.18882622X-RAY DIFFRACTION100
2.3342-2.39730.2411400.1982670X-RAY DIFFRACTION100
2.3973-2.46780.28511390.1992640X-RAY DIFFRACTION100
2.4678-2.54750.28481410.19822678X-RAY DIFFRACTION100
2.5475-2.63850.26731370.19522641X-RAY DIFFRACTION100
2.6385-2.74410.25481410.19392657X-RAY DIFFRACTION100
2.7441-2.8690.2631440.19832661X-RAY DIFFRACTION100
2.869-3.02020.26141360.20462653X-RAY DIFFRACTION100
3.0202-3.20930.23311410.19232666X-RAY DIFFRACTION100
3.2093-3.4570.22421410.17962676X-RAY DIFFRACTION100
3.457-3.80460.21551410.16372650X-RAY DIFFRACTION100
3.8046-4.35440.18021410.1342683X-RAY DIFFRACTION100
4.3544-5.48360.14321400.12532681X-RAY DIFFRACTION100
5.4836-38.44270.18021430.16722725X-RAY DIFFRACTION100
Refinement TLS params.

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 °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.11110.69890.15871.69720.42970.9240.0134-0.10750.15480.1592-0.03650.2436-0.0442-0.077800.16920.01840.01230.17050.00520.247816.53315.746-14.547
21.0187-0.311-0.09661.22750.32010.69280.0159-0.0040.0278-0.136-0.0716-0.07410.00120.055300.226-0.00480.03950.16930.00850.16941.055333.347-25.1103
31.00330.0288-0.46850.39560.37481.5164-0.12280.0402-0.1279-0.05220.0119-0.02560.1120.0098-00.1755-0.01640.03280.16820.01360.22826.1924.453-27.952
41.06770.58350.62480.97720.99111.19850.0875-0.0427-0.11950.14060.0732-0.20030.10780.0094-00.19460.0107-0.04160.1462-0.00390.166250.306420.5876-20.9949
51.02090.0666-0.04762.2167-0.39080.47220.0534-0.0438-0.0336-0.1129-0.0413-0.29240.00890.0672-00.1566-0.02260.00050.1781-0.01410.18650.873-7.5-21.657
60.7850.4259-0.0161.2183-0.07451.0439-0.01340.06580.0648-0.06530.03670.0494-0.0578-0.143300.15860.01740.00350.16830.01070.1258-4.528-5.051-27.168
71.336-0.7975-0.15981.4380.00410.56430.0559-0.0517-0.01050.0891-0.01040.1158-0.0909-0.003-00.2119-0.02650.03990.1673-0.01970.15441.051-0.919-17.672
80.9880.2493-0.34760.7108-0.59081.17140.0772-0.06370.1440.2424-0.0380.0353-0.12280.01980.00010.2287-0.00470.07920.1492-0.00520.21846.4074.251-27.763
90.01710.01930.02740.00240.020.0394-0.0825-0.03270.032-0.0154-0.14310.0280.16410.149400.1832-0.0373-0.01230.26630.07110.3623-29.864-19.876-2.084
100.1007-0.05070.08240.0053-0.00710.0939-0.23320.04410.45-0.155-0.06720.0084-0.2775-0.1471-0.0020.2681-0.06230.07880.2433-0.01360.302938.96642.118-17.129
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 21:128 )A21 - 128
2X-RAY DIFFRACTION2( CHAIN A AND RESID 135:213 )A135 - 213
3X-RAY DIFFRACTION3( CHAIN B AND RESID 20:127 )B20 - 127
4X-RAY DIFFRACTION4( CHAIN B AND RESID 130:211 )B130 - 211
5X-RAY DIFFRACTION5( CHAIN C AND RESID 126:132 )C126 - 132
6X-RAY DIFFRACTION6( CHAIN C AND RESID 134:137 )C134 - 137
7X-RAY DIFFRACTION7( CHAIN D AND RESID 126:127 )D126 - 127
8X-RAY DIFFRACTION8( CHAIN D AND RESID 130:135 )D130 - 135
9X-RAY DIFFRACTION9( CHAIN A AND RESID 301:302 )A301 - 302
10X-RAY DIFFRACTION9( CHAIN H AND RESID 301:303 )H301 - 303
11X-RAY DIFFRACTION9( CHAIN B AND RESID 301:301 )B301
12X-RAY DIFFRACTION9( CHAIN L AND RESID 301:303 )L301 - 303
13X-RAY DIFFRACTION10( CHAIN A AND RESID 303:304 )A303 - 304

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