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- PDB-5aum: Crystal structure of a Fab fragment with the ligand peptide -

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Basic information

Entry
Database: PDB / ID: 5aum
TitleCrystal structure of a Fab fragment with the ligand peptide
Components
  • Heavy chain of Fab fragment
  • Light chain of Fab fragment
  • peptide RENLYFQGKDG
KeywordsIMMUNE SYSTEM/PEPTIDE / Antibody / peptide ligand / protease / ELISA / Western blotting / IMMUNE SYSTEM-PEPTIDE complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesRattus (rat)
Potyviridae (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKitago, Y. / Takagi, J.
CitationJournal: To Be Published
Title: Crystal structure of a Fab fragment with the ligand peptide
Authors: Kitago, Y. / Takagi, J.
History
DepositionApr 30, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: 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
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_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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Heavy chain of Fab fragment
A: Heavy chain of Fab fragment
B: Light chain of Fab fragment
L: Light chain of Fab fragment
C: peptide RENLYFQGKDG
D: peptide RENLYFQGKDG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6247
Polymers106,5596
Non-polymers651
Water10,647591
1
H: Heavy chain of Fab fragment
L: Light chain of Fab fragment
C: peptide RENLYFQGKDG


Theoretical massNumber of molelcules
Total (without water)53,2793
Polymers53,2793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-28 kcal/mol
Surface area19050 Å2
MethodPISA
2
A: Heavy chain of Fab fragment
B: Light chain of Fab fragment
D: peptide RENLYFQGKDG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3454
Polymers53,2793
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-28 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.768, 217.768, 52.236
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-301-

ZN

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Components

#1: Antibody Heavy chain of Fab fragment


Mass: 26009.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus (rat) / Cell: hybridoma / Cell (production host): hybridoma / Production host: Mammalia (mammals)
#2: Antibody Light chain of Fab fragment


Mass: 25941.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus (rat) / Cell: hybridoma / Cell (production host): hybridoma / Production host: Mammalia (mammals)
#3: Protein/peptide peptide RENLYFQGKDG


Mass: 1328.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The modified TEV protease recognition sequence / Source: (synth.) Potyviridae (virus)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / 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

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 % PEG 2000 MME, 0.5 M NaCl, 0.1 M Tris-HCl pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 88376 / % possible obs: 99.5 % / Redundancy: 5.3 % / Rsym value: 0.148 / Net I/σ(I): 26.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 5.1 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BFO

1bfo


Resolution: 2.05→45.69 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.529 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22055 4424 5 %RANDOM
Rwork0.18917 ---
obs0.19076 83738 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.895 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.12 Å20 Å2
2--0.23 Å2-0 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6609 0 1 591 7201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.026758
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9599210
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7255863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86924.016254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.828151086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2261532
X-RAY DIFFRACTIONr_chiral_restr0.0950.21071
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215028
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_it1.5962.5493476
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5143.8074331
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4182.7213280
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.39621.7610534
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: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 322 -
Rwork0.241 5914 -
obs--95.47 %

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