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- PDB-7w5q: The Kruppel-associated box (KRAB) domain of human zinc finger pro... -

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Basic information

Entry
Database: PDB / ID: 7w5q
TitleThe Kruppel-associated box (KRAB) domain of human zinc finger protein 568
ComponentsZinc finger protein 568
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


embryonic placenta morphogenesis / Generic Transcription Pathway / in utero embryonic development / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / metal ion binding / nucleus
Similarity search - Function
Krueppel-associated box (KRAB) profile. / KRAB box / krueppel associated box / Krueppel-associated box / KRAB domain superfamily / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Zinc finger protein 568
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsHan, C.W. / Jang, S.B.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1C1C2004755 Korea, Republic Of
CitationJournal: To Be Published
Title: Structure of the kruppel-associated box (KRAB) domain
Authors: Han, C.W. / Jang, S.B.
History
DepositionNov 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger protein 568
B: Zinc finger protein 568


Theoretical massNumber of molelcules
Total (without water)27,8812
Polymers27,8812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-8 kcal/mol
Surface area22490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.736, 147.094, 41.891
Angle α, β, γ (deg.)90.000, 90.006, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Zinc finger protein 568


Mass: 13940.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNF568 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3ZCX4

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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: 4.8 Å3/Da / Density % sol: 74.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Magnesium formate dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. obs: 13618 / % possible obs: 98.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 60.85 Å2 / CC1/2: 0.895 / Net I/σ(I): 31
Reflection shellResolution: 2.61→2.66 Å / Num. unique obs: 576 / CC1/2: 0.094

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX1.14_3260refinement
Cootmodel building
HKL-2000data reduction
PHASERphasing
CCP4idata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V65

1v65


Resolution: 2.73→41.89 Å / SU ML: 0.5015 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 37.4407 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3124 517 4.42 %
Rwork0.2436 11193 -
obs0.2468 11710 85.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.58 Å2
Refinement stepCycle: LAST / Resolution: 2.73→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1877 0 0 0 1877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121906
X-RAY DIFFRACTIONf_angle_d1.73652570
X-RAY DIFFRACTIONf_chiral_restr0.067285
X-RAY DIFFRACTIONf_plane_restr0.01334
X-RAY DIFFRACTIONf_dihedral_angle_d6.21991182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-30.3549810.25511452X-RAY DIFFRACTION44.97
3-3.440.34291400.25743205X-RAY DIFFRACTION99.49
3.44-4.330.28481560.23113264X-RAY DIFFRACTION99.74
4.33-41.890.31671400.24663272X-RAY DIFFRACTION98.78
Refinement TLS params.Method: refined / Origin x: 23.0292704609 Å / Origin y: -6.67902510344 Å / Origin z: 30.2667531724 Å
111213212223313233
T0.280211748068 Å20.0117909267211 Å2-0.0153096957224 Å2-0.286878455082 Å2-0.0128895066796 Å2--0.297639644848 Å2
L0.0439042936759 °20.0254707083203 °20.0228156974049 °2-0.0497267392566 °20.0909589919113 °2---0.0222782969382 °2
S0.00614223224423 Å °0.0306535566003 Å °0.000674323476293 Å °0.0813224247484 Å °-0.0378034606865 Å °0.0199463920552 Å °0.00224732456427 Å °0.0536983105727 Å °0.0208868516694 Å °
Refinement TLS groupSelection details: all

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