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- PDB-6j6w: Mutant K23N of heat shock factor 4-DBD -

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Basic information

Entry
Database: PDB / ID: 6j6w
TitleMutant K23N of heat shock factor 4-DBD
ComponentsHeat shock factor protein 4
KeywordsTRANSCRIPTION / transcriptional factor
Function / homology
Function and homology information


: / cell development / lens fiber cell differentiation / visual perception / epithelial cell proliferation / positive regulation of epithelial cell proliferation / positive regulation of cell differentiation / sequence-specific double-stranded DNA binding / protein phosphatase binding / transcription by RNA polymerase II ...: / cell development / lens fiber cell differentiation / visual perception / epithelial cell proliferation / positive regulation of epithelial cell proliferation / positive regulation of cell differentiation / sequence-specific double-stranded DNA binding / protein phosphatase binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
Heat shock factor (HSF)-type, DNA-binding / Heat shock transcription factor family / HSF-type DNA-binding / HSF-type DNA-binding domain signature. / heat shock factor / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Heat shock factor protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.693 Å
AuthorsXiao, Z.Y. / Cui, L.W. / Wang, S. / Liu, W.
CitationJournal: To Be Published
Title: Structure of the mutant K23N of heat shock factor 4-DBD at 1.69 Angstroms resolution.
Authors: Xiao, Z.Y. / Cui, L.W. / Wang, S. / Liu, W.
History
DepositionJan 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock factor protein 4
B: Heat shock factor protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6229
Polymers24,3442
Non-polymers2787
Water4,252236
1
A: Heat shock factor protein 4
B: Heat shock factor protein 4
hetero molecules

A: Heat shock factor protein 4
B: Heat shock factor protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,24418
Polymers48,6884
Non-polymers55614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area7900 Å2
ΔGint-38 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.632, 65.047, 80.556
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-381-

HOH

21B-383-

HOH

31B-390-

HOH

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Components

#1: Protein Heat shock factor protein 4 / / hHSF4 / Heat shock transcription factor 4 / HSTF 4


Mass: 12171.931 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSF4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9ULV5
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 295 K / Method: evaporation / Details: sodium nitrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.69→27.17 Å / Num. obs: 26197 / % possible obs: 99.4 % / Redundancy: 6.8 % / Net I/σ(I): 24.1
Reflection shellResolution: 1.69→1.73 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.693→27.169 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.15
RfactorNum. reflection% reflection
Rfree0.2052 1246 4.76 %
Rwork0.1711 --
obs0.1727 26196 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.693→27.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 16 236 1798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121629
X-RAY DIFFRACTIONf_angle_d1.2072201
X-RAY DIFFRACTIONf_dihedral_angle_d2.7541138
X-RAY DIFFRACTIONf_chiral_restr0.082227
X-RAY DIFFRACTIONf_plane_restr0.008290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6929-1.76070.24891120.20162453X-RAY DIFFRACTION87
1.7607-1.84080.23841440.19392673X-RAY DIFFRACTION96
1.8408-1.93780.22771410.18262745X-RAY DIFFRACTION98
1.9378-2.05920.19481330.16062771X-RAY DIFFRACTION99
2.0592-2.21810.16821450.1552790X-RAY DIFFRACTION99
2.2181-2.44120.20971220.16742811X-RAY DIFFRACTION99
2.4412-2.79420.22511370.18022863X-RAY DIFFRACTION100
2.7942-3.51920.18011590.1722840X-RAY DIFFRACTION100
3.5192-27.17230.21261530.1643004X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.37590.50690.52050.9590.03552.41080.0962-0.28090.19210.14610.0852-0.0012-0.0739-0.0341-0.05830.08530.00410.01030.1559-0.07790.0764-9.9073-24.461815.0408
21.4737-1.494-1.31656.06351.00513.71050.0482-0.31460.22620.49050.02310.2906-0.2994-0.2189-0.10730.14510.05430.03490.3295-0.17790.2119-11.4515-15.544824.784
32.72530.29920.06333.87470.28324.4686-0.0613-0.34190.05190.18240.0488-0.1865-0.21110.16280.06510.0883-0.0347-0.01560.1773-0.12180.2175-1.8119-17.500120.1285
43.7723-0.92441.66484.2592-0.28444.58190.0027-0.21780.62220.01770.0290.3246-0.6715-0.4371-0.01190.25080.03680.09830.0747-0.05460.2904-10.1244-12.89017.0442
52.9781-0.5455-0.05984.337-0.07412.45250.1071-0.02820.1938-0.1817-0.0113-0.0523-0.1485-0.0302-0.06820.0585-0.01360.01280.0582-0.02750.0619-6.9373-25.14716.5427
60.8128-0.66490.22672.8925-0.36344.59590.0031-0.05950.18310.20230.4088-1.0447-0.45131.057-0.4090.1999-0.0220.01480.2378-0.09720.25123.3382-26.41965.6679
71.14010.0821-0.40190.4009-0.22110.69840.13230.42420.4343-0.09540.13430.0856-0.1712-0.18050.14010.1142-0.00140.08080.16570.27550.1115-11.5652-17.5194-12.5661
82.4083-0.67811.57251.3605-0.92313.7868-0.00920.63120.6605-0.00770.07110.031-0.45360.08680.07270.22990.07720.0890.20560.19910.4315-16.2775-11.0385-8.0286
90.734-0.52940.15825.03920.16782.54920.030.14250.2804-0.03440.05560.3386-0.1673-0.2998-0.05130.0850.03320.02640.09520.05020.133-18.3258-23.8656-3.3545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 57 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 98 )
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 112 )
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 119 )
7X-RAY DIFFRACTION7chain 'B' and (resid 17 through 57 )
8X-RAY DIFFRACTION8chain 'B' and (resid 58 through 98 )
9X-RAY DIFFRACTION9chain 'B' and (resid 99 through 119 )

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