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- PDB-1yuh: FAB FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1yuh
TitleFAB FRAGMENT
Components
  • 88C6/12 FAB (HEAVY CHAIN)
  • 88C6/12 FAB (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / ANTI-NITROPHENOL / LAMBDA LIGHT CHAIN / IMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-NP / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsYuhasz, S.C. / Amzel, L.M. / Parry, C. / Strand, M.
Citation
Journal: Mol.Immunol. / Year: 1995
Title: Structural analysis of affinity maturation: the three-dimensional structures of complexes of an anti-nitrophenol antibody.
Authors: Yuhasz, S.C. / Parry, C. / Strand, M. / Amzel, L.M.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallization and Preliminary X-Ray Diffraction Studies of an Anti-4-Hydroxy-3-Nitrophenylacetic Acid Monoclonal Antibody Fab Fragment Complexed with Immunizing and Heteroclitic Haptens
Authors: Yuhasz, S.C. / Ysern, X. / Strand, M. / Amzel, L.M.
History
DepositionJan 30, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2013Group: Source and taxonomy
Revision 1.4Mar 21, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.pdbx_collection_date / _pdbx_database_status.process_site
Revision 1.5Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _struct_ref_seq_dif.details / _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: 88C6/12 FAB (LIGHT CHAIN)
H: 88C6/12 FAB (HEAVY CHAIN)
A: 88C6/12 FAB (LIGHT CHAIN)
B: 88C6/12 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8346
Polymers92,2134
Non-polymers6212
Water724
1
L: 88C6/12 FAB (LIGHT CHAIN)
H: 88C6/12 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4173
Polymers46,1072
Non-polymers3101
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-20 kcal/mol
Surface area19250 Å2
MethodPISA
2
A: 88C6/12 FAB (LIGHT CHAIN)
B: 88C6/12 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4173
Polymers46,1072
Non-polymers3101
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-22 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.200, 86.900, 131.100
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: Antibody 88C6/12 FAB (LIGHT CHAIN)


Mass: 22672.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 387376
#2: Antibody 88C6/12 FAB (HEAVY CHAIN)


Mass: 23434.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 3399661
#3: Chemical ChemComp-NP / 4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC ACID


Mass: 310.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N2O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsIN THE NUMBERING SCHEME USED IN THIS ENTRY, THE LIGHT CHAIN RESIDUES FOR MOLECULE 1 ARE VL1 2 - ...IN THE NUMBERING SCHEME USED IN THIS ENTRY, THE LIGHT CHAIN RESIDUES FOR MOLECULE 1 ARE VL1 2 - 109, CL1 110 - 212 AND THE HEAVY CHAIN RESIDUES ARE VH1 1 - 117, CH1 118 - 218, RESPECTIVELY. MOLECULE 2 DEFINES THE LIGHT CHAIN RESIDUES AS VL2 2 - 109, CL2 110 - 212, AND HEAVY CHAIN RESIDUES AS VH2 1 - 117 AND CH2 118 - 218, RESPECTIVELY. THE WATERS ARE NUMBERED 990 - 994 AND THE 2 NITROPHENOL-EPSILON-AMINO CAPROIC MOLECULES LABELED AS NP ARE NUMBERED 995 AND 996.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal grow
*PLUS
pH: 6.52 / Method: vapor diffusion, hanging drop / Details: Yuhasz, S.C., (1989) J.Mol.Biol., 209, 319.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122 mg/mlFab1drop
220 mMsodium phosphate1reservoir
332 %(w/v)PEG34001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 16470 / % possible obs: 70.3 % / Rmerge(I) obs: 0.047
Reflection
*PLUS
Highest resolution: 3 Å

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Processing

Software
NameClassification
XENGENdata collection
X-PLORrefinement
XENGENdata reduction
RefinementResolution: 3→6 Å / σ(F): 2
Details: IN THE NUMBERING SCHEME USED IN THIS ENTRY, THE LIGHT CHAIN RESIDUES FOR MOLECULE 1 ARE VL1 2 - 109, CL1 110 - 212 AND THE HEAVY CHAIN RESIDUES ARE VH1 1 - 117, CH1 118 - 218, RESPECTIVELY. ...Details: IN THE NUMBERING SCHEME USED IN THIS ENTRY, THE LIGHT CHAIN RESIDUES FOR MOLECULE 1 ARE VL1 2 - 109, CL1 110 - 212 AND THE HEAVY CHAIN RESIDUES ARE VH1 1 - 117, CH1 118 - 218, RESPECTIVELY. MOLECULE 2 DEFINES THE LIGHT CHAIN RESIDUES AS VL2 2 - 109, CL2 110 - 212, AND HEAVY CHAIN RESIDUES AS VH2 1 - 117 AND CH2 118 - 218, RESPECTIVELY. THE WATERS ARE NUMBERED 990 - 994 AND THE 2 NITROPHENOL-EPSILON-AMINO CAPROIC MOLECULES LABELED AS NP ARE NUMBERED 995 AND 996. RESIDUES NUMBERED 132 - 140 OF H AND B CHAINS WERE NOT FOUND IN THE ELECTRON DENSITY AND ARE PROBABLY DISORDERED.
RfactorNum. reflection
Rwork0.19 -
obs0.19 10275
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6482 0 44 4 6530
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg4.08
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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