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- PDB-2fl5: Cofactor-containing antibodies: Crystal structure of the original... -

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Basic information

Entry
Database: PDB / ID: 2fl5
TitleCofactor-containing antibodies: Crystal structure of the original yellow antibody
Components
  • Immunoglobulin Igg1 Heavy chain
  • Immunoglobulin Igg1 Lambda Light Chain
KeywordsIMMUNE SYSTEM / human antibody / riboflavin-binding / cofactor / multiple myeloma / IGGGAR
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
RIBOFLAVIN / IGL@ protein / :
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Cofactor-containing antibodies: Crystal structure of the original yellow antibody.
Authors: Zhu, X. / Wentworth, P. / Kyle, R.A. / Lerner, R.A. / Wilson, I.A.
History
DepositionJan 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Currently there is no aminoacid sequence database reference available for the entities 1 and 2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Immunoglobulin Igg1 Lambda Light Chain
H: Immunoglobulin Igg1 Heavy chain
A: Immunoglobulin Igg1 Lambda Light Chain
B: Immunoglobulin Igg1 Heavy chain
C: Immunoglobulin Igg1 Lambda Light Chain
D: Immunoglobulin Igg1 Heavy chain
E: Immunoglobulin Igg1 Lambda Light Chain
F: Immunoglobulin Igg1 Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,96212
Polymers184,4568
Non-polymers1,5054
Water2,594144
1
L: Immunoglobulin Igg1 Lambda Light Chain
H: Immunoglobulin Igg1 Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4903
Polymers46,1142
Non-polymers3761
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-30 kcal/mol
Surface area19120 Å2
MethodPISA
2
A: Immunoglobulin Igg1 Lambda Light Chain
B: Immunoglobulin Igg1 Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4903
Polymers46,1142
Non-polymers3761
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-29 kcal/mol
Surface area19130 Å2
MethodPISA
3
C: Immunoglobulin Igg1 Lambda Light Chain
D: Immunoglobulin Igg1 Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4903
Polymers46,1142
Non-polymers3761
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-29 kcal/mol
Surface area19230 Å2
MethodPISA
4
E: Immunoglobulin Igg1 Lambda Light Chain
F: Immunoglobulin Igg1 Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4903
Polymers46,1142
Non-polymers3761
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-29 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.592, 111.105, 188.454
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
Immunoglobulin Igg1 Lambda Light Chain


Mass: 22418.754 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5FWF9
#2: Antibody
Immunoglobulin Igg1 Heavy chain


Mass: 23695.348 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6PJA4
#3: Chemical
ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 / Riboflavin


Mass: 376.364 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H20N4O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 298 K / pH: 7.5
Details: PEG 4000, di-ammonium hydrogen citrate, tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979751
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 7, 2004 / Details: FLAT MIRROR (VERTICAL FOCUSING)
RadiationMonochromator: SINGLE CRYSTAL SI(111) BENT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979751 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 42610 / % possible obs: 98.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 15.5
Reflection shellResolution: 3→3.07 Å / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8FAB

8fab


Resolution: 3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.29 2016 RANDOM
Rwork0.24 --
obs0.24 40272 -
all-43001 -
Displacement parametersBiso mean: 61.21 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12980 0 108 144 13232
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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