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- PDB-3lhr: Crystal structure of the SCAN domain from Human ZNF24 -

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Basic information

Entry
Database: PDB / ID: 3lhr
TitleCrystal structure of the SCAN domain from Human ZNF24
ComponentsZinc finger protein 24
KeywordsTRANSCRIPTION REGULATOR / SCAN DOMAIN / protein structure initiative / center for eukaryotic structural genomics / PSI-2 / CESG / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation
Function / homology
Function and homology information


myelination / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding ...myelination / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding
Similarity search - Function
DNA breaking-rejoining enzymes fold / DNA breaking-rejoining enzymes / : / SCAN domain / SCAN domain superfamily / SCAN domain / SCAN box profile. / leucine rich region / Zinc finger, C2H2 type / zinc finger ...DNA breaking-rejoining enzymes fold / DNA breaking-rejoining enzymes / : / SCAN domain / SCAN domain superfamily / SCAN domain / SCAN box profile. / leucine rich region / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ETHYL MERCURY ION / DI(HYDROXYETHYL)ETHER / Zinc finger protein 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsVolkman, B.F. / Peterson, F.C. / Bingman, C.A. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be Published
Title: Crystal structure of the SCAN domain from Human ZNF24
Authors: Volkman, B.F. / Peterson, F.C. / Bingman, C.A. / Phillips Jr., G.N.
History
DepositionJan 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 30, 2013Group: Database references / Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger protein 24
B: Zinc finger protein 24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5267
Polymers21,9002
Non-polymers6255
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-27 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.055, 50.029, 91.301
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Zinc finger protein 24 / Zinc finger protein 191 / Zinc finger protein KOX17 / Retinoic acid suppression protein A / RSG-A / ...Zinc finger protein 191 / Zinc finger protein KOX17 / Retinoic acid suppression protein A / RSG-A / Zinc finger and SCAN domain-containing protein 3


Mass: 10950.171 Da / Num. of mol.: 2 / Fragment: SCAN BOX DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KOX17, ZNF191, ZNF24, ZSCAN3 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009[pREP4] / References: UniProt: P17028

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Non-polymers , 5 types, 117 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5Hg
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution at 1.5 mM concentration was mixed 1:1 with a reservoir solution composed of 100 mM HEPES buffer, pH 7.5, 40 mM MgCl2, 24% MEPEG 2000, 2 mM thimerosal. Crystals were ...Details: Protein solution at 1.5 mM concentration was mixed 1:1 with a reservoir solution composed of 100 mM HEPES buffer, pH 7.5, 40 mM MgCl2, 24% MEPEG 2000, 2 mM thimerosal. Crystals were cryoprotected with reservoir solution supplemented with 10% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 24, 2006 / Details: Silicon <111> monochromator, KB mirrors
RadiationMonochromator: SILICON <111> / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 15875 / % possible obs: 97.3 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.082 / Χ2: 1.075 / Net I/σ(I): 12.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.456 / Num. unique all: 1216 / Χ2: 0.965 / % possible all: 76.5

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.9 Å / D res low: 33.72 Å / FOM acentric: 0.282 / FOM centric: 0.083 / Reflection acentric: 13659 / Reflection centric: 2215
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_11.933.7200136592215
ANO_11.933.720.8480134930
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_18.26-33.7200126106
ISO_15.93-8.2600254113
ISO_14.87-5.9300348111
ISO_14.23-4.8700411110
ISO_13.79-4.2300482119
ISO_13.46-3.7900522111
ISO_13.21-3.4600591111
ISO_13-3.2100627114
ISO_12.83-300678112
ISO_12.69-2.8300712110
ISO_12.56-2.6900753113
ISO_12.45-2.5600793123
ISO_12.36-2.4500835111
ISO_12.27-2.3600853106
ISO_12.2-2.2700906116
ISO_12.13-2.200910116
ISO_12.06-2.1300970108
ISO_12-2.0600989110
ISO_11.95-200974108
ISO_11.9-1.950092587
ANO_18.26-33.721.58701260
ANO_15.93-8.262.33902540
ANO_14.87-5.932.14603480
ANO_14.23-4.871.82804110
ANO_13.79-4.231.68704820
ANO_13.46-3.791.68505220
ANO_13.21-3.461.63105910
ANO_13-3.211.5106270
ANO_12.83-31.34306780
ANO_12.69-2.831.15607120
ANO_12.56-2.691.00107530
ANO_12.45-2.560.8107930
ANO_12.36-2.450.69608350
ANO_12.27-2.360.58108530
ANO_12.2-2.270.47609060
ANO_12.13-2.20.40909100
ANO_12.06-2.130.34109690
ANO_12-2.060.27509820
ANO_11.95-20.24509400
ANO_11.9-1.950.21508010
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-5.483-6.146-35.941HG32.510.57
2-3.719-42.891-13.918HG32.330.48
3-2.878-41.39-12.07HG10.05
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
8.26-33.720.4970.084126106
5.93-8.260.5340.086254113
4.87-5.930.5010.116348111
4.23-4.870.4310.082411110
3.79-4.230.3890.072482119
3.46-3.790.3950.067522111
3.21-3.460.3870.068591111
3-3.210.4090.088627114
2.83-30.3960.084678112
2.69-2.830.3580.076712110
2.56-2.690.340.097753113
2.45-2.560.3210.08793123
2.36-2.450.290.07835111
2.27-2.360.2370.079853106
2.2-2.270.2270.071906116
2.13-2.20.1980.077910116
2.06-2.130.1790.08970108
2-2.060.1490.098989110
1.95-20.1320.086974108
1.9-1.950.120.10492587
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 15874
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.3-10061.10.763503
4.94-6.3600.85510
4.28-4.9459.90.902514
3.86-4.2861.90.895511
3.58-3.8659.10.895512
3.36-3.5867.80.87512
3.19-3.3668.40.862509
3.05-3.1962.60.864501
2.92-3.0562.70.835519
2.81-2.9263.70.846547
2.71-2.8165.80.83567
2.62-2.7166.30.814579
2.54-2.6269.20.851592
2.47-2.5465.30.848633
2.4-2.4768.60.84630
2.34-2.470.60.861658
2.28-2.3476.20.836650
2.23-2.2869.40.821706
2.18-2.2371.80.845686
2.13-2.18770.822716
2.09-2.1377.20.813719
2.04-2.09800.773752
2.01-2.0478.70.733750
1.97-2.0182.50.694752
1.9-1.9785.90.661346

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.9→33.73 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.854 / SU B: 3.299 / SU ML: 0.1 / SU R Cruickshank DPI: 0.158 / SU Rfree: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.243 793 5 %RANDOM
Rwork0.182 ---
obs0.184 15873 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.63 Å2 / Biso mean: 29.163 Å2 / Biso min: 13.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å20 Å2
2---0.16 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 0 15 112 1664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211600
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.9722172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1475189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41624.23992
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7215276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0521516
X-RAY DIFFRACTIONr_chiral_restr0.1330.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211258
X-RAY DIFFRACTIONr_mcbond_it1.4011.5939
X-RAY DIFFRACTIONr_mcangle_it2.46121534
X-RAY DIFFRACTIONr_scbond_it3.9023661
X-RAY DIFFRACTIONr_scangle_it6.3084.5635
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 52 -
Rwork0.25 959 -
all-1011 -
obs--86.56 %

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