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- PDB-6iip: Apo-form structure of the HRP3 PWWP domain -

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Basic information

Entry
Database: PDB / ID: 6iip
TitleApo-form structure of the HRP3 PWWP domain
ComponentsHepatoma-derived growth factor-related protein 3
KeywordsDNA BINDING PROTEIN / growth factor / PWWP domain / Hepatoma-derived growth factor-related protein 3
Function / homology
Function and homology information


negative regulation of microtubule depolymerization / microtubule polymerization / tubulin binding / growth factor activity / neuron projection development / microtubule binding / chromatin remodeling / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain
Similarity search - Domain/homology
Hepatoma-derived growth factor-related protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.951 Å
AuthorsWang, Z. / Tian, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570729 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Apo-form structure of the HRP3 PWWP domain
Authors: Wang, Z. / Tian, W.
History
DepositionOct 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Hepatoma-derived growth factor-related protein 3
B: Hepatoma-derived growth factor-related protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0969
Polymers20,2252
Non-polymers8717
Water5,296294
1
A: Hepatoma-derived growth factor-related protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5965
Polymers10,1121
Non-polymers4834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area5810 Å2
MethodPISA
2
B: Hepatoma-derived growth factor-related protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5004
Polymers10,1121
Non-polymers3873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.478, 39.931, 97.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hepatoma-derived growth factor-related protein 3 / HRP-3 / Hepatoma-derived growth factor 2 / HDGF-2


Mass: 10112.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDGFL3, HDGF2, HDGFRP3, CGI-142 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y3E1
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 1.85 Å3/Da / Density % sol: 33.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium sulphate, 0.1 M MES monohydrate, pH 6.5, and 30% w/v polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.91531 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91531 Å / Relative weight: 1
ReflectionResolution: 0.95→50 Å / Num. obs: 93005 / % possible obs: 97.4 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 52.6
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 4036 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EAE

3eae


Resolution: 0.951→30.876 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.93
RfactorNum. reflection% reflection
Rfree0.205 4627 4.98 %
Rwork0.1965 --
obs0.1969 92913 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.951→30.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1432 0 49 294 1775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061530
X-RAY DIFFRACTIONf_angle_d1.1622068
X-RAY DIFFRACTIONf_dihedral_angle_d15.408576
X-RAY DIFFRACTIONf_chiral_restr0.048183
X-RAY DIFFRACTIONf_plane_restr0.005265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9507-0.96150.37531360.37362723X-RAY DIFFRACTION91
0.9615-0.97280.34181810.34432778X-RAY DIFFRACTION94
0.9728-0.98470.30721320.30212857X-RAY DIFFRACTION96
0.9847-0.99720.31081240.28472824X-RAY DIFFRACTION94
0.9972-1.01030.25261560.2582846X-RAY DIFFRACTION96
1.0103-1.02410.22551230.22282868X-RAY DIFFRACTION95
1.0241-1.03870.22081620.20312856X-RAY DIFFRACTION97
1.0387-1.05430.1941350.20042874X-RAY DIFFRACTION96
1.0543-1.07070.21391370.1972914X-RAY DIFFRACTION97
1.0707-1.08830.2151410.20162904X-RAY DIFFRACTION97
1.0883-1.1070.21081650.19192879X-RAY DIFFRACTION97
1.107-1.12720.19951600.18842901X-RAY DIFFRACTION98
1.1272-1.14890.18921880.18162875X-RAY DIFFRACTION98
1.1489-1.17230.18361570.18512906X-RAY DIFFRACTION97
1.1723-1.19780.16241480.18532963X-RAY DIFFRACTION98
1.1978-1.22570.20051490.18442928X-RAY DIFFRACTION99
1.2257-1.25630.19051720.18632971X-RAY DIFFRACTION99
1.2563-1.29030.22471420.1893004X-RAY DIFFRACTION99
1.2903-1.32830.19191430.18183002X-RAY DIFFRACTION100
1.3283-1.37110.17081360.18542999X-RAY DIFFRACTION99
1.3711-1.42010.18131560.18142951X-RAY DIFFRACTION98
1.4201-1.4770.21091620.18613003X-RAY DIFFRACTION100
1.477-1.54420.19611740.18562991X-RAY DIFFRACTION100
1.5442-1.62560.20541670.19062992X-RAY DIFFRACTION100
1.6256-1.72750.18791550.19743033X-RAY DIFFRACTION100
1.7275-1.86080.2151590.19113013X-RAY DIFFRACTION99
1.8608-2.04810.18461660.19333027X-RAY DIFFRACTION99
2.0481-2.34430.20691620.19443079X-RAY DIFFRACTION100
2.3443-2.95320.23281630.213101X-RAY DIFFRACTION100
2.9532-30.89270.19421760.1863224X-RAY DIFFRACTION99

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