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- PDB-5eii: Structural determination of an protein complex of a Fab with incr... -

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Basic information

Entry
Database: PDB / ID: 5eii
TitleStructural determination of an protein complex of a Fab with increased solubility
Components
  • Fab Heavy Chain
  • Fab Light Chain
  • Histone chaperone ASF1
KeywordsIMMUNE SYSTEM / Antibody / Fab / Asf1 / 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 / DNA replication-dependent chromatin assembly / acetyltransferase activator activity / nucleosome disassembly / silent mating-type cassette heterochromatin formation / cellular response to stress / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair ...Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / DNA replication-dependent chromatin assembly / acetyltransferase activator activity / nucleosome disassembly / silent mating-type cassette heterochromatin formation / cellular response to stress / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair / positive regulation of transcription elongation by RNA polymerase II / protein modification process / nucleosome assembly / chromatin organization / regulation of gene expression / histone binding / chromosome, telomeric region / regulation of transcription by RNA polymerase II / chromatin / 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: 2.44 Å
AuthorsBailey, L.J. / Kossiakoff, A.A. / Chaperone-Enabled Studies of Epigenetic Regulation Enzymes (CEBS)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087519 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094588 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)HG006436 United States
Citation
Journal: To Be Published
Title: Structural determination of an protein complex of a Fab with increased solubility
Authors: Bailey, L.J. / Kossiakoff, A.A. / Schaefer, Z.P.
#1: Journal: To Be Published
Title: A polar ring endows improved specificity to an antibody fragment
Authors: Schaefer, Z.P. / Bailey, L.J. / Kossiakoff, A.A.
History
DepositionOct 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 13, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
A: Fab Heavy Chain
B: Fab Light Chain
G: Histone chaperone ASF1
H: Fab Heavy Chain
I: Histone chaperone ASF1
L: Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)132,2596
Polymers132,2596
Non-polymers00
Water7,728429
1
A: Fab Heavy Chain
B: Fab Light Chain
I: Histone chaperone ASF1


Theoretical massNumber of molelcules
Total (without water)66,1303
Polymers66,1303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-30 kcal/mol
Surface area25060 Å2
MethodPISA
2
G: Histone chaperone ASF1
H: Fab Heavy Chain
L: Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)66,1303
Polymers66,1303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-29 kcal/mol
Surface area26240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.486, 62.945, 161.828
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab Heavy Chain


Mass: 25084.887 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 Fab Light Chain


Mass: 23298.760 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)
#3: Protein Histone chaperone ASF1 / Anti-silencing function protein 1 / yASF1


Mass: 17746.012 Da / Num. of mol.: 2 / Fragment: UNP residues 1-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
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.: 429 / 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: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 293 K / Method: liquid diffusion
Details: Crystals were grown by hanging drop liquid diffusion by adding a solution containing 20% PEG 3350 and Sodium Acetate, pH 5.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.987 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.43723→46.3844 Å / Num. obs: 61283 / % possible obs: 99.4499 % / Redundancy: 3.6 % / Net I/σ(I): 12.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 2.44→46.384 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 3101 5.06 %
Rwork0.1851 --
obs0.1875 61283 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.44→46.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8627 0 0 429 9056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048838
X-RAY DIFFRACTIONf_angle_d0.71612043
X-RAY DIFFRACTIONf_dihedral_angle_d12.6865269
X-RAY DIFFRACTIONf_chiral_restr0.0461365
X-RAY DIFFRACTIONf_plane_restr0.0041530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4372-2.47530.34251460.27132363X-RAY DIFFRACTION90
2.4753-2.51590.31321530.2532636X-RAY DIFFRACTION100
2.5159-2.55930.32671510.23982611X-RAY DIFFRACTION100
2.5593-2.60580.29781330.24492636X-RAY DIFFRACTION100
2.6058-2.65590.28031470.24132624X-RAY DIFFRACTION100
2.6559-2.71010.31861560.23262669X-RAY DIFFRACTION100
2.7101-2.76910.35971530.24332629X-RAY DIFFRACTION100
2.7691-2.83350.33221420.24552615X-RAY DIFFRACTION100
2.8335-2.90430.30711370.23192641X-RAY DIFFRACTION100
2.9043-2.98280.28061140.22092660X-RAY DIFFRACTION100
2.9828-3.07060.27151410.2072654X-RAY DIFFRACTION100
3.0706-3.16970.27281310.21182664X-RAY DIFFRACTION100
3.1697-3.28290.24271450.20552645X-RAY DIFFRACTION100
3.2829-3.41430.23371500.19212638X-RAY DIFFRACTION100
3.4143-3.56970.23661440.17782657X-RAY DIFFRACTION100
3.5697-3.75780.21191330.17472654X-RAY DIFFRACTION100
3.7578-3.99310.22241400.16712657X-RAY DIFFRACTION100
3.9931-4.30120.19281180.1482707X-RAY DIFFRACTION100
4.3012-4.73370.14351450.12312654X-RAY DIFFRACTION100
4.7337-5.41770.17081320.1372718X-RAY DIFFRACTION100
5.4177-6.82230.21891410.1672696X-RAY DIFFRACTION100
6.8223-46.39270.18141490.18332754X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 6.3942 Å / Origin y: 5.5826 Å / Origin z: 34.589 Å
111213212223313233
T0.256 Å2-0.0078 Å2-0.0064 Å2-0.2785 Å2-0.0083 Å2--0.2536 Å2
L0.3422 °2-0.2033 °20.1035 °2-0.5867 °2-0.0969 °2--0.2027 °2
S-0.0343 Å °-0.1596 Å °-0.0083 Å °0.2232 Å °0.0578 Å °0.0093 Å °-0.0095 Å °0.0352 Å °-0.0208 Å °
Refinement TLS groupSelection details: all

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