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- PDB-5gva: WD40 domain of human AND-1 -

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Basic information

Entry
Database: PDB / ID: 5gva
TitleWD40 domain of human AND-1
ComponentsWD repeat and HMG-box DNA-binding protein 1
KeywordsREPLICATION / WD40
Function / homology
Function and homology information


nuclear replication fork / DNA-templated DNA replication / mitotic cell cycle / DNA repair / chromatin binding / DNA binding / nucleoplasm / cytoplasm
Similarity search - Function
: / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily ...: / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
WD repeat and HMG-box DNA-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.851 Å
AuthorsGuan, C.C. / Li, J.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The structure and polymerase-recognition mechanism of the crucial adaptor protein AND-1 in the human replisome
Authors: Guan, C. / Li, J. / Sun, D. / Liu, Y. / Liang, H.
History
DepositionSep 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD repeat and HMG-box DNA-binding protein 1


Theoretical massNumber of molelcules
Total (without water)38,0231
Polymers38,0231
Non-polymers00
Water6,936385
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12410 Å2
Unit cell
Length a, b, c (Å)79.895, 79.895, 163.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-661-

HOH

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Components

#1: Protein WD repeat and HMG-box DNA-binding protein 1 / Acidic nucleoplasmic DNA-binding protein 1 / And-1


Mass: 38022.684 Da / Num. of mol.: 1 / Mutation: UNP residues 1-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDHD1, AND1 / Plasmid: pFastbac1 / Production host: Trichoplasta (insect) / References: UniProt: O75717
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 3.44 Å3/Da / Density % sol: 64.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 1.8M Ammonium citrate tribasic pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.91769 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91769 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 45822 / % possible obs: 99.5 % / Redundancy: 7.7 % / Net I/σ(I): 30.48
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5.9 % / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data processing
SCALEPACKdata scaling
SHELXDEphasing
PHENIXmodel building
DENZOdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 1.851→33.148 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7
RfactorNum. reflection% reflection
Rfree0.1884 2000 4.37 %
Rwork0.1701 --
obs0.1709 45816 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.851→33.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 0 385 2741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082587
X-RAY DIFFRACTIONf_angle_d1.0753539
X-RAY DIFFRACTIONf_dihedral_angle_d13.711971
X-RAY DIFFRACTIONf_chiral_restr0.069389
X-RAY DIFFRACTIONf_plane_restr0.006461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8507-1.8970.31171340.25092949X-RAY DIFFRACTION96
1.897-1.94830.23371420.22273087X-RAY DIFFRACTION100
1.9483-2.00560.19011400.20033076X-RAY DIFFRACTION100
2.0056-2.07030.25171400.1973079X-RAY DIFFRACTION100
2.0703-2.14430.24071410.18283086X-RAY DIFFRACTION100
2.1443-2.23010.20041420.18573105X-RAY DIFFRACTION100
2.2301-2.33160.20661410.18453093X-RAY DIFFRACTION100
2.3316-2.45450.22391440.19193139X-RAY DIFFRACTION100
2.4545-2.60820.22841410.19383113X-RAY DIFFRACTION100
2.6082-2.80950.22861450.18183150X-RAY DIFFRACTION100
2.8095-3.0920.20141440.16943170X-RAY DIFFRACTION100
3.092-3.5390.16231440.14933173X-RAY DIFFRACTION100
3.539-4.45710.13791480.13343213X-RAY DIFFRACTION100
4.4571-33.15380.17491540.17133383X-RAY DIFFRACTION99

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