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- PDB-4rrp: Crystal Structure of the Fab complexed with antigen Asf1p, Northe... -

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Basic information

Entry
Database: PDB / ID: 4rrp
TitleCrystal Structure of the Fab complexed with antigen Asf1p, Northeast Structural Genomics Consortium (NESG) Target PdR16
Components
  • Antigen Asf1p
  • Fab antibody, heavy chain
  • Fab antibody, light chain
KeywordsIMMUNE SYSTEM / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Chaperone-Enabled Studies of Epigenetic Regulation Enzymes / CEBS
Function / homologyHistone chaperone ASF1-like / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsKuzin, A. / Lew, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Oconnell, P.T. / Maglaqui, M. / Bailey, L. / Everett, J.K. / Acton, T.B. ...Kuzin, A. / Lew, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Oconnell, P.T. / Maglaqui, M. / Bailey, L. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Chaperone-Enabled Studies of Epigenetic Regulation Enzymes (CEBS) / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Fab complexed with antigen Asf1p, Northeast Structural Genomics Consortium (NESG) Target PdR16
Authors: Kuzin, A. / Lew, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Oconnell, P.T. / Maglaqui, M. / Bailey, L. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionNov 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Structure summary
Revision 1.2Jan 14, 2015Group: Derived calculations / Structure summary
Revision 1.3Feb 25, 2015Group: Structure summary
Revision 1.4Jul 22, 2015Group: Source and taxonomy
Revision 1.5Sep 20, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fab antibody, light chain
G: Fab antibody, heavy chain
B: Fab antibody, light chain
H: Fab antibody, heavy chain
C: Fab antibody, light chain
I: Fab antibody, heavy chain
D: Fab antibody, light chain
J: Fab antibody, heavy chain
E: Fab antibody, light chain
K: Fab antibody, heavy chain
F: Fab antibody, light chain
L: Fab antibody, heavy chain
M: Antigen Asf1p
N: Antigen Asf1p
O: Antigen Asf1p
P: Antigen Asf1p
Q: Antigen Asf1p
R: Antigen Asf1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)402,46519
Polymers402,35918
Non-polymers1061
Water4,017223
1
A: Fab antibody, light chain
G: Fab antibody, heavy chain
M: Antigen Asf1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1664
Polymers67,0603
Non-polymers1061
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Fab antibody, light chain
J: Fab antibody, heavy chain
P: Antigen Asf1p


Theoretical massNumber of molelcules
Total (without water)67,0603
Polymers67,0603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Fab antibody, light chain
H: Fab antibody, heavy chain
N: Antigen Asf1p


Theoretical massNumber of molelcules
Total (without water)67,0603
Polymers67,0603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Fab antibody, light chain
I: Fab antibody, heavy chain
O: Antigen Asf1p


Theoretical massNumber of molelcules
Total (without water)67,0603
Polymers67,0603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Fab antibody, light chain
K: Fab antibody, heavy chain
Q: Antigen Asf1p


Theoretical massNumber of molelcules
Total (without water)67,0603
Polymers67,0603
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Fab antibody, light chain
L: Fab antibody, heavy chain
R: Antigen Asf1p


Theoretical massNumber of molelcules
Total (without water)67,0603
Polymers67,0603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.725, 181.309, 259.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer,71.45 kD,90.4%

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Components

#1: Antibody
Fab antibody, light chain


Mass: 23590.217 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Protein selected by phage display / Production host: Escherichia coli (E. coli)
#2: Antibody
Fab antibody, heavy chain


Mass: 25410.324 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Protein selected by phage display / Production host: Escherichia coli (E. coli)
#3: Protein
Antigen Asf1p


Mass: 18059.211 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: AWRI796 / Gene: AWRI796_2536 / Production host: Escherichia coli (E. coli) / References: UniProt: E7KE71
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 291 K / pH: 5.5
Details: Protein solution 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution ammonium acetate 0.1M, BIS-TRIS 0.1M, PEG 10,000 17%(w/v), microbatch under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X3A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2013
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 6.8 % / Biso Wilson estimate: 38.72 Å2 / Rmerge(I) obs: 0.086

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Processing

Software
NameVersionClassificationNB
PHENIX1.9_1692refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGC

1qgc


Resolution: 2.79→49.69 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.35 / σ(F): 1.44 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 1999 1.84 %
Rwork0.183 --
obs0.185 108383 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.83 Å2
Refinement stepCycle: LAST / Resolution: 2.79→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26863 0 7 223 27093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00927588
X-RAY DIFFRACTIONf_angle_d1.21937531
X-RAY DIFFRACTIONf_dihedral_angle_d15.7319922
X-RAY DIFFRACTIONf_chiral_restr0.0444266
X-RAY DIFFRACTIONf_plane_restr0.0064793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.793-2.8630.34211340.23667109X-RAY DIFFRACTION94
2.863-2.94040.3771390.23217439X-RAY DIFFRACTION99
2.9404-3.02690.2781420.22057534X-RAY DIFFRACTION99
3.0269-3.12460.28521420.20787554X-RAY DIFFRACTION99
3.1246-3.23630.27951410.20127544X-RAY DIFFRACTION100
3.2363-3.36580.24651430.19297578X-RAY DIFFRACTION100
3.3658-3.5190.23031420.18757559X-RAY DIFFRACTION100
3.519-3.70440.24071440.18867666X-RAY DIFFRACTION100
3.7044-3.93640.32031420.19087577X-RAY DIFFRACTION100
3.9364-4.24020.25661440.1767654X-RAY DIFFRACTION100
4.2402-4.66660.21391440.1457662X-RAY DIFFRACTION100
4.6666-5.34120.19911450.14537690X-RAY DIFFRACTION100
5.3412-6.72670.21581460.17647788X-RAY DIFFRACTION100
6.7267-49.70050.23921510.18428030X-RAY DIFFRACTION100

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