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- PDB-3ci9: Crystal Structure of the human HSBP1 -

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Basic information

Entry
Database: PDB / ID: 3ci9
TitleCrystal Structure of the human HSBP1
ComponentsHeat shock factor-binding protein 1
KeywordsTRANSCRIPTION / triple helix / Nucleus
Function / homology
Function and homology information


cellular heat acclimation / HSF1-dependent transactivation / HSF1 activation / Attenuation phase / regulation of cellular response to heat / transcription corepressor activity / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus ...cellular heat acclimation / HSF1-dependent transactivation / HSF1 activation / Attenuation phase / regulation of cellular response to heat / transcription corepressor activity / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Heat shock factor binding 1 / Heat shock factor binding protein 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #430 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Heat shock factor-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsLiu, X. / Xu, L. / Liu, Y. / Zhu, G. / Zhang, X.C. / Li, X. / Rao, Z.
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of the hexamer of human heat shock factor binding protein 1
Authors: Liu, X. / Xu, L. / Liu, Y. / Tong, X. / Zhu, G. / Zhang, X.C. / Li, X. / Rao, Z.
History
DepositionMar 11, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Category: 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

Downloads & links

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Assembly

Deposited unit
A: Heat shock factor-binding protein 1
B: Heat shock factor-binding protein 1


Theoretical massNumber of molelcules
Total (without water)10,9642
Polymers10,9642
Non-polymers00
Water39622
1
A: Heat shock factor-binding protein 1
B: Heat shock factor-binding protein 1

A: Heat shock factor-binding protein 1
B: Heat shock factor-binding protein 1

A: Heat shock factor-binding protein 1
B: Heat shock factor-binding protein 1


Theoretical massNumber of molelcules
Total (without water)32,8936
Polymers32,8936
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area11940 Å2
ΔGint-114 kcal/mol
Surface area14590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.226, 35.226, 233.266
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein/peptide Heat shock factor-binding protein 1 / Nasopharyngeal carcinoma- associated antigen 13 / NPC-A-13


Mass: 5482.181 Da / Num. of mol.: 2 / Fragment: UNP residues 6-53 / Mutation: M30I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSBP1 / Plasmid: pET-28a-c(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75506
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.7M Ammonium Sulfate,15%(v/v) Glycerol, 20mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONBSRF 3W1A20.9799, 0.9802, 0.9000
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDDec 8, 2006
MAR CCD 165 mm2CCDJan 1, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97991
30.98021
40.91
Reflection twinType: hemihedral / Operator: h,-h-k,-l / Fraction: 0.366
ReflectionResolution: 1.7→50 Å / Num. all: 11912 / Num. obs: 10975 / % possible obs: 92.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.036 / Χ2: 1.237 / Net I/σ(I): 19.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.762.40.197180.88858.9
1.76-1.832.60.1829270.82779.7
1.83-1.9130.17211030.90693.4
1.91-2.023.20.11911790.91499.7
2.02-2.143.40.0811900.97299.9
2.14-2.313.30.05811971.208100
2.31-2.543.40.05212071.351100
2.54-2.913.30.04111821.643100
2.91-3.663.30.0311781.49899.4
3.66-503.50.02910941.69890.9

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.6 Å / D res low: 50 Å / FOM : 0.37 / Reflection: 3201
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97996.74-8.36
13 wavelength20.98024.35-12.03
13 wavelength30.93.48-2.11
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.6060.3390.3331.089
2Se46.390.2320.6060.3130.644
3Se600.610.3220.2160.633
Phasing MAD shell
Resolution (Å)FOM Reflection
9.39-500.74148
5.92-9.390.64276
4.62-5.920.6344
3.92-4.620.56408
3.46-3.920.4458
3.13-3.460.27490
2.88-3.130.19550
2.68-2.880.11527
Phasing dmFOM : 0.64 / FOM acentric: 0.64 / FOM centric: 0 / Reflection: 3289 / Reflection acentric: 3289 / Reflection centric: 0
Phasing dm shell
Resolution (Å)FOM FOM acentricReflectionReflection acentric
7.4-30.1450.80.8142142
4.6-7.40.730.73444444
3.7-4.60.70.7559559
3.3-3.70.710.71545545
2.8-3.30.620.6210051005
2.6-2.80.450.45594594

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Processing

Software
NameVersionClassificationNB
SOLVE2.05phasing
RESOLVE2.05phasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→25.53 Å / σ(F): 163
Details: HEMIHEDRAL TWINNING OPERATOR (H,-H-K,-L). TWINNING FRACTION 0.366.
RfactorNum. reflection% reflection
Rfree0.234 910 9.1 %
Rwork0.195 --
all-10054 -
obs-9441 93.9 %
Solvent computationBsol: 75.437 Å2
Displacement parametersBiso mean: 41.147 Å2
Baniso -1Baniso -2Baniso -3
1--7.95 Å2-6.159 Å20 Å2
2---7.95 Å20 Å2
3---15.9 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms710 0 0 22 732
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0951.5
X-RAY DIFFRACTIONc_scbond_it1.9182
X-RAY DIFFRACTIONc_mcangle_it1.8312
X-RAY DIFFRACTIONc_scangle_it2.8922.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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