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- PDB-3d69: Crystal Structure of the Fab Fragment of an Anti-Factor IX Antibo... -

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Entry
Database: PDB / ID: 3d69
TitleCrystal Structure of the Fab Fragment of an Anti-Factor IX Antibody 10C12
Components(anti-factor IX antibody, 10C12) x 2
KeywordsIMMUNE SYSTEM / anticoagulant / 10C12 / Factor IX / Gla domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.77 Å
AuthorsShi, X.L. / Huang, M.D. / Zeng, T.
CitationJournal: CHIN.J.STRUCT.CHEM. / Year: 2008
Title: Crystal structure of Fab Fragment of an anti-Factor IX antibody 10C12
Authors: Shi, X.L. / Huang, M.D. / Zeng, T.
History
DepositionMay 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 2, 2013Group: Source and taxonomy
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: anti-factor IX antibody, 10C12
H: anti-factor IX antibody, 10C12
A: anti-factor IX antibody, 10C12
B: anti-factor IX antibody, 10C12


Theoretical massNumber of molelcules
Total (without water)93,5024
Polymers93,5024
Non-polymers00
Water00
1
A: anti-factor IX antibody, 10C12
B: anti-factor IX antibody, 10C12


Theoretical massNumber of molelcules
Total (without water)46,7512
Polymers46,7512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-22.4 kcal/mol
Surface area19490 Å2
MethodPISA
2
L: anti-factor IX antibody, 10C12
H: anti-factor IX antibody, 10C12


Theoretical massNumber of molelcules
Total (without water)46,7512
Polymers46,7512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-20.5 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.609, 159.609, 65.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Antibody anti-factor IX antibody, 10C12


Mass: 22950.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody anti-factor IX antibody, 10C12


Mass: 23800.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. IN CHAIN L AND A, RESIDUE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. IN CHAIN L AND A, RESIDUE NUMBER 10 IS SIMPLY SKIPPED. AUTHORS STATE THAT THE PROTEIN SEQUENCE IS IDENTICAL WITH 1NL0(PDB CODE). THE MISSING OF L10 IS DUE TO KABAT-WU NUMBERING.

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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: 4.45 Å3/Da / Density % sol: 72.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 3.0M ammonium sulfate, 0.1M HEPES, 2%MPD, pH7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C
DetectorDetector: CCD / Date: Sep 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.77→50 Å / Num. all: 17166 / Num. obs: 13950 / % possible obs: 82.2 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.217 / Rsym value: 0.009 / Net I/σ(I): 141.4

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NL0

1nl0


Resolution: 3.77→41.26 Å / Isotropic thermal model: isotropic / Cross valid method: thoughout
RfactorNum. reflection% reflectionSelection details
Rfree0.342 --random
Rwork0.249 ---
all-17166 --
obs-13950 82.2 %-
Displacement parametersBiso mean: 87.7 Å2
Refinement stepCycle: LAST / Resolution: 3.77→41.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6420 0 0 0 6420
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.6
LS refinement shellResolution: 3.77→3.94 Å / Rfactor Rfree error: 0.009
RfactorNum. reflection% reflection
Rfree0.342 13950 -
Rwork0.249 --
obs-17166 82.2 %

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