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- PDB-5gvb: SepB domain of human AND-1 -

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Basic information

Entry
Database: PDB / ID: 5gvb
TitleSepB domain of human AND-1
ComponentsWD repeat and HMG-box DNA-binding protein 1
KeywordsREPLICATION / PEPTIDE BINDING PROTEIN / SepB / 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 / SAD / Resolution: 2.75 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 5, 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.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,5151
Polymers50,5151
Non-polymers00
Water1,62190
1
A: WD repeat and HMG-box DNA-binding protein 1

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

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


Theoretical massNumber of molelcules
Total (without water)151,5453
Polymers151,5453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10890 Å2
ΔGint-59 kcal/mol
Surface area50470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)249.646, 249.646, 249.646
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432

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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: 50514.883 Da / Num. of mol.: 1 / Fragment: UNP residues 416-850
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDHD1, AND1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75717
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 3.21 Å3/Da / Density % sol: 61.66 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 2.5M sodium formate pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 34000 / % possible obs: 99.9 % / Redundancy: 19.8 % / Biso Wilson estimate: 48.68 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 10.9
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 18.7 % / Rmerge(I) obs: 0.698 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data processing
SCALEPACKdata scaling
SHELXDEphasing
PHENIXmodel building
DENZOdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.75→41.61 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.78 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.254 3193 9.93 %
Rwork0.209 --
obs0.214 32164 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.5 Å2
Refinement stepCycle: LAST / Resolution: 2.75→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3172 0 0 90 3262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043336
X-RAY DIFFRACTIONf_angle_d0.7094521
X-RAY DIFFRACTIONf_dihedral_angle_d20.3781225
X-RAY DIFFRACTIONf_chiral_restr0.044497
X-RAY DIFFRACTIONf_plane_restr0.004579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7502-2.79120.42681360.32111283X-RAY DIFFRACTION99
2.7912-2.83480.41281380.30841257X-RAY DIFFRACTION100
2.8348-2.88130.4161430.32331284X-RAY DIFFRACTION99
2.8813-2.9310.38111400.29941261X-RAY DIFFRACTION99
2.931-2.98420.34841330.28431260X-RAY DIFFRACTION99
2.9842-3.04160.32291390.28881295X-RAY DIFFRACTION99
3.0416-3.10370.26611400.3021250X-RAY DIFFRACTION99
3.1037-3.17120.37511420.28241256X-RAY DIFFRACTION98
3.1712-3.24490.36751430.26421269X-RAY DIFFRACTION98
3.2449-3.3260.28181350.25011277X-RAY DIFFRACTION99
3.326-3.41590.29621330.24461215X-RAY DIFFRACTION97
3.4159-3.51640.2771430.22281268X-RAY DIFFRACTION97
3.5164-3.62980.27071310.19591242X-RAY DIFFRACTION97
3.6298-3.75940.22781430.19471246X-RAY DIFFRACTION98
3.7594-3.90990.22121340.18341230X-RAY DIFFRACTION97
3.9099-4.08770.21591320.17671247X-RAY DIFFRACTION96
4.0877-4.3030.20231510.15861230X-RAY DIFFRACTION97
4.303-4.57220.1721330.15891235X-RAY DIFFRACTION97
4.5722-4.92480.19121400.15261250X-RAY DIFFRACTION97
4.9248-5.41940.20991400.15491270X-RAY DIFFRACTION100
5.4194-6.20140.23711420.1951257X-RAY DIFFRACTION99
6.2014-7.80470.2041400.19791300X-RAY DIFFRACTION100
7.8047-41.61240.25061420.1991289X-RAY DIFFRACTION99

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