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- PDB-3ww0: Crystal structure of F97A mutant, a new nuclear transport recepto... -

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Basic information

Entry
Database: PDB / ID: 3ww0
TitleCrystal structure of F97A mutant, a new nuclear transport receptor of Hsp70
Components(Protein Hikeshi) x 2
KeywordsTRANSPORT PROTEIN / Nuclear transport receptor
Function / homology
Function and homology information


nuclear import signal receptor activity / Golgi organization / Regulation of HSF1-mediated heat shock response / Hsp70 protein binding / lung development / protein import into nucleus / protein transport / cellular response to heat / nuclear body / nuclear speck ...nuclear import signal receptor activity / Golgi organization / Regulation of HSF1-mediated heat shock response / Hsp70 protein binding / lung development / protein import into nucleus / protein transport / cellular response to heat / nuclear body / nuclear speck / nucleoplasm / nucleus / cytosol
Similarity search - Function
Hikeshi-like domain / OPI10 family / : / Hikeshi-like, N-terminal domain / Hikeshi-like, C-terminal domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSong, J. / Kose, S. / Watanabe, A. / Son, S.Y. / Choi, S. / Hong, R.H. / Yamashita, E. / Park, I.Y. / Imamoto, N. / Lee, S.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural and functional analysis of Hikeshi, a new nuclear transport receptor of Hsp70s
Authors: Song, J. / Kose, S. / Watanabe, A. / Son, S.Y. / Choi, S. / Hong, H. / Yamashita, E. / Park, I.Y. / Imamoto, N. / Lee, S.J.
History
DepositionJun 12, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Hikeshi
B: Protein Hikeshi


Theoretical massNumber of molelcules
Total (without water)43,3602
Polymers43,3602
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-51 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.483, 85.483, 68.943
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Protein Hikeshi


Mass: 21708.646 Da / Num. of mol.: 1 / Mutation: F97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C11orf73, HSPC138, HSPC179, HSPC248 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53FT3
#2: Protein Protein Hikeshi


Mass: 21651.596 Da / Num. of mol.: 1 / Mutation: F97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C11orf73, HSPC138, HSPC179, HSPC248 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53FT3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.35 Å3/Da / Density % sol: 63.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M Tris-HCl (pH 7.4), 1M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9192 Å
DetectorDetector: AREA DETECTOR / Date: Nov 8, 2013 / Details: 0.9192
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9192 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 19951 / Num. obs: 12674

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXAutoSolmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→42.741 Å / SU ML: 0.29 / σ(F): 1.98 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2241 994 5.11 %
Rwork0.1955 --
obs0.1969 12673 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→42.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2731 0 0 69 2800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032791
X-RAY DIFFRACTIONf_angle_d0.7353792
X-RAY DIFFRACTIONf_dihedral_angle_d13.827974
X-RAY DIFFRACTIONf_chiral_restr0.03417
X-RAY DIFFRACTIONf_plane_restr0.003490
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.63210.29441430.24772642100
2.6321-2.7970.28791540.23332613100
2.797-3.01290.30111660.24342628100
3.0129-3.3160.24871480.21282633100
3.316-3.79560.20221390.18792653100
3.7956-4.78110.19431270.16522644100
4.7811-42.74770.18711170.1857263899
Refinement TLS params.Method: refined / Origin x: -42.431 Å / Origin y: 0.9612 Å / Origin z: -0.5795 Å
111213212223313233
T0.2634 Å2-0.0075 Å20.042 Å2-0.3637 Å20.0089 Å2--0.2768 Å2
L0.3217 °2-0.1815 °20.4112 °2-2.2984 °2-0.0132 °2--0.7083 °2
S-0.0814 Å °-0.0248 Å °0.0332 Å °-0.0137 Å °0.0792 Å °0.0384 Å °-0.0142 Å °0.0636 Å °-0.0005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID -1:197 OR RESID 201:233 ) ) OR ( CHAIN B AND ( RESID 201:236 OR RESID 0:196 ) )A-1 - 197
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID -1:197 OR RESID 201:233 ) ) OR ( CHAIN B AND ( RESID 201:236 OR RESID 0:196 ) )A201 - 233
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID -1:197 OR RESID 201:233 ) ) OR ( CHAIN B AND ( RESID 201:236 OR RESID 0:196 ) )B201 - 236
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID -1:197 OR RESID 201:233 ) ) OR ( CHAIN B AND ( RESID 201:236 OR RESID 0:196 ) )B0 - 196

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