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- PDB-5ucb: Structure of antigen-Fab complex with engineered switch residue r... -

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Basic information

Entry
Database: PDB / ID: 5ucb
TitleStructure of antigen-Fab complex with engineered switch residue region.
Components
  • Fab Heavy Chain
  • Fab Light Chain
  • Histone chaperone ASF1
KeywordsIMMUNE SYSTEM / Antibody / Fab / Asf1 / histone chaperone / Structural Genomics / PSI-Biology / Chaperone-Enabled Studies of Epigenetic Regulation Enzymes / CEBS
Function / homology
Function and homology information


Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / silent mating-type cassette heterochromatin formation / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair / positive regulation of transcription elongation by RNA polymerase II ...Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / silent mating-type cassette heterochromatin formation / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair / positive regulation of transcription elongation by RNA polymerase II / regulation of protein phosphorylation / protein modification process / nucleosome assembly / chromatin organization / histone binding / regulation of gene expression / chromosome, telomeric region / chromatin / regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Histone chaperone ASF1-like / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Histone chaperone ASF1
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.521 Å
AuthorsBailey, L.J. / Kossiakoff, A.A. / Chaperone-Enabled Studies of Epigenetic Regulation Enzymes (CEBS)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 087519 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 117372 United States
CitationJournal: To Be Published
Title: Antibody Switch Residue Engineering for Improved Crystallization Chaperones
Authors: Bailey, L.J. / Kossiakoff, A.A.
History
DepositionDec 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab Heavy Chain
L: Fab Light Chain
B: Histone chaperone ASF1


Theoretical massNumber of molelcules
Total (without water)63,4213
Polymers63,4213
Non-polymers00
Water11,548641
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-33 kcal/mol
Surface area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.378, 49.180, 84.707
Angle α, β, γ (deg.)106.29, 95.71, 100.13
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Fab Heavy Chain


Mass: 23182.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab Light Chain


Mass: 22866.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein Histone chaperone ASF1 / Anti-silencing function protein 1 / yASF1


Mass: 17371.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ASF1, CIA1, YJL115W, J0755 / Production host: Escherichia coli (E. coli) / References: UniProt: P32447
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 18% PEG3350,

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.521→35.589 Å / Num. obs: 100518 / % possible obs: 95.81 % / Redundancy: 3.2 % / Biso Wilson estimate: 26.76 Å2 / Net I/σ(I): 32.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 1.521→35.589 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 15.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1688 5020 4.99 %
Rwork0.1381 --
obs0.1396 100518 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.521→35.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 0 641 5097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084568
X-RAY DIFFRACTIONf_angle_d0.956228
X-RAY DIFFRACTIONf_dihedral_angle_d10.1742724
X-RAY DIFFRACTIONf_chiral_restr0.064704
X-RAY DIFFRACTIONf_plane_restr0.006794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5215-1.53880.20781400.1472964X-RAY DIFFRACTION87
1.5388-1.55690.19041860.14123093X-RAY DIFFRACTION94
1.5569-1.57580.17841660.13173152X-RAY DIFFRACTION94
1.5758-1.59580.19111600.12523093X-RAY DIFFRACTION95
1.5958-1.61680.19591690.12913159X-RAY DIFFRACTION95
1.6168-1.63890.17231720.12423139X-RAY DIFFRACTION94
1.6389-1.66240.16321690.12073163X-RAY DIFFRACTION96
1.6624-1.68720.16021700.11523185X-RAY DIFFRACTION95
1.6872-1.71350.16521620.10913089X-RAY DIFFRACTION95
1.7135-1.74160.17871690.11623238X-RAY DIFFRACTION95
1.7416-1.77170.16341600.1223147X-RAY DIFFRACTION95
1.7717-1.80390.16231770.11943177X-RAY DIFFRACTION96
1.8039-1.83860.17141620.12613229X-RAY DIFFRACTION96
1.8386-1.87610.17711460.12443178X-RAY DIFFRACTION96
1.8761-1.91690.14651710.12673161X-RAY DIFFRACTION96
1.9169-1.96150.17261630.12743282X-RAY DIFFRACTION96
1.9615-2.01050.17431800.12853150X-RAY DIFFRACTION97
2.0105-2.06490.15181520.13023273X-RAY DIFFRACTION97
2.0649-2.12560.17961720.13123185X-RAY DIFFRACTION97
2.1256-2.19420.15861900.12983167X-RAY DIFFRACTION97
2.1942-2.27260.1451590.12643295X-RAY DIFFRACTION98
2.2726-2.36360.16761570.13943251X-RAY DIFFRACTION97
2.3636-2.47120.18651550.13843216X-RAY DIFFRACTION98
2.4712-2.60140.18261620.14713279X-RAY DIFFRACTION98
2.6014-2.76430.20271740.14853249X-RAY DIFFRACTION98
2.7643-2.97770.16731950.14673237X-RAY DIFFRACTION98
2.9777-3.27710.15061870.14253294X-RAY DIFFRACTION98
3.2771-3.75090.16581770.13643231X-RAY DIFFRACTION98
3.7509-4.7240.14911410.12533241X-RAY DIFFRACTION96
4.724-35.5990.18811770.16812981X-RAY DIFFRACTION90

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