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- PDB-1wej: IGG1 FAB FRAGMENT (OF E8 ANTIBODY) COMPLEXED WITH HORSE CYTOCHROM... -

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Basic information

Entry
Database: PDB / ID: 1wej
TitleIGG1 FAB FRAGMENT (OF E8 ANTIBODY) COMPLEXED WITH HORSE CYTOCHROME C AT 1.8 A RESOLUTION
Components
  • (E8 ANTIBODY) x 2
  • CYTOCHROME C
KeywordsCOMPLEX (ANTIBODY/ELECTRON TRANSPORT) / IMMUNOGLOBULIN / IGG1 KAPPA / FAB FRAGMENT / HORSE CYTOCHROME C / COMPLEX (ANTIBODY-ELECTRON TRANSPORT) / COMPLEX (ANTIBODY-ELECTRON TRANSPORT) complex
Function / homology
Function and homology information


cytochrome c-heme linkage / cytochrome complex / mitochondrial electron transport, cytochrome c to oxygen / immunoglobulin complex / mitochondrial electron transport, ubiquinol to cytochrome c / apoptotic signaling pathway / mitochondrial intermembrane space / adaptive immune response / electron transfer activity / lipid binding ...cytochrome c-heme linkage / cytochrome complex / mitochondrial electron transport, cytochrome c to oxygen / immunoglobulin complex / mitochondrial electron transport, ubiquinol to cytochrome c / apoptotic signaling pathway / mitochondrial intermembrane space / adaptive immune response / electron transfer activity / lipid binding / heme binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / : / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Immunoglobulin V-Type / Immunoglobulin V-set domain ...Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / : / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / : / : / Cytochrome c / Immunoglobulin kappa chain variable 12-41
Similarity search - Component
Biological speciesMus musculus (house mouse)
Equus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMylvaganam, S.E. / Paterson, Y. / Getzoff, E.D.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Structural basis for the binding of an anti-cytochrome c antibody to its antigen: crystal structures of FabE8-cytochrome c complex to 1.8 A resolution and FabE8 to 2.26 A resolution.
Authors: Mylvaganam, S.E. / Paterson, Y. / Getzoff, E.D.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Biochemical Implications from the Variable Gene Sequences of an Anti-Cytochrome C Antibody and Crystallographic Characterization of its Antigen-Binding Fragment in Free and Antigen-Complexed Forms
Authors: Mylvaganam, S.E. / Paterson, Y. / Kaiser, K. / Bowdish, K. / Getzoff, E.D.
#2: Journal: J.Immunol. / Year: 1985
Title: Monoclonal Antibodies to Horse Cytochrome C Expressing Four Distinct Idiotypes Distribute Among Two Sites on the Native Protein
Authors: Carbone, F.R. / Paterson, Y.
History
DepositionMar 26, 1998Processing site: BNL
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
L: E8 ANTIBODY
H: E8 ANTIBODY
F: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9405
Polymers59,2583
Non-polymers6822
Water11,476637
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-80 kcal/mol
Surface area24230 Å2
MethodPISA
2
F: CYTOCHROME C
hetero molecules

L: E8 ANTIBODY
H: E8 ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9405
Polymers59,2583
Non-polymers6822
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation1_554x,y,z-11
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-87 kcal/mol
Surface area24610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.580, 72.540, 94.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules F

#3: Protein CYTOCHROME C / CYT C / ANTIGEN


Mass: 11751.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: OBTAINED FROM SIGMA / Source: (natural) Equus caballus (horse) / Organ: HEART / References: UniProt: P00004

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Antibody , 2 types, 2 molecules LH

#1: Antibody E8 ANTIBODY / FAB E8


Mass: 23655.057 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Details: E8 ANTIBODY PURIFIED FROM ASCITES / Source: (natural) Mus musculus (house mouse) / Cell line: P3-X63-AG8.653 / Organ: SPLEEN / Strain: BALB/C / References: GenBank: 2072141, UniProt: P01635*PLUS
#2: Antibody E8 ANTIBODY / FAB E8


Mass: 23851.572 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Details: E8 ANTIBODY PURIFIED FROM ASCITES / Source: (natural) Mus musculus (house mouse) / Cell line: P3-X63-AG8.653 / Organ: SPLEEN / Strain: BALB-C / References: PIR: S49220

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Non-polymers , 3 types, 639 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 42 %
Crystal growpH: 6.4
Details: 50MM ZINC ACETATE BUFFER, PH 6.4, 25% (W/V) PEG 4000.
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 %(w/v)PEG40001reservoir
250 mMzinc acetate1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 48348 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 18.06 Å2 / Rsym value: 0.084 / Net I/σ(I): 36.6
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 12 / Rsym value: 0.282 / % possible all: 99.5
Reflection
*PLUS
Num. obs: 48334 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2.26 A RESOLUTION FABE8 X-RAY STRUCTURE (FREE FAB E8) (MYLVAGANAM ET AL., 1998, JMB, 281, 301-32; PDB ENTRY 1QBL) AND HORSE CYTOCHROME C 1.9 A X-RAY STRUCTURE (BUSHNELL ET. AL., 1990; ...Starting model: 2.26 A RESOLUTION FABE8 X-RAY STRUCTURE (FREE FAB E8) (MYLVAGANAM ET AL., 1998, JMB, 281, 301-32; PDB ENTRY 1QBL) AND HORSE CYTOCHROME C 1.9 A X-RAY STRUCTURE (BUSHNELL ET. AL., 1990; PDB ENTRY 1HRC).

1qbl

1hrc


Resolution: 1.8→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.256 -5 %
Rwork0.2 --
obs0.2 47993 94.1 %
Displacement parametersBiso mean: 21.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.942 Å2--
2---2.042 Å2-
3---2.07 Å2
Refine analyze
ObsFree
Luzzati d res low20 Å-
Luzzati sigma a0.33 Å0.299 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4166 0 43 637 4846
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.47
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.54
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
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree8 -5.1 %
Rwork0.316 5745 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.HEMETOPH19X.HEM
X-RAY DIFFRACTION2PARHCSDXB.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.199 / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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