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- PDB-1pzw: Crystal structure of the zinc finger associated domain of the Dro... -

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Basic information

Entry
Database: PDB / ID: 1pzw
TitleCrystal structure of the zinc finger associated domain of the Drosophila transcription factor Grauzone
ComponentsTranscription factor grauzone
KeywordsTRANSCRIPTION / dimerization / transcription regulation / treble-clef zinc finger / ZAD
Function / homology
Function and homology information


egg activation / cellularization / pole cell formation / homologous chromosome segregation / female meiotic nuclear division / cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
His-Me finger endonuclease fold - #20 / Transcription factor Grauzone / ZAD domain profile. / Zinc-finger associated domain (zf-AD) / Zinc finger, AD-type / Zinc-finger associated domain (zf-AD) / His-Me finger endonuclease fold / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. ...His-Me finger endonuclease fold - #20 / Transcription factor Grauzone / ZAD domain profile. / Zinc-finger associated domain (zf-AD) / Zinc finger, AD-type / Zinc-finger associated domain (zf-AD) / His-Me finger endonuclease fold / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcription factor grauzone
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJauch, R. / Bourenkov, G.P. / Chung, H.-R. / Urlaub, H. / Reidt, U. / Jaeckle, H. / Wahl, M.C.
CitationJournal: STRUCTURE / Year: 2003
Title: The zinc finger-associated domain of the Drosophila transcription factor grauzone is a novel zinc-coordinating protein-protein interaction module
Authors: Jauch, R. / Bourenkov, G.P. / Chung, H.-R. / Urlaub, H. / Reidt, U. / Wahl, M.C.
History
DepositionJul 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 14, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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: Transcription factor grauzone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2332
Polymers9,1671
Non-polymers651
Water1,00956
1
A: Transcription factor grauzone
hetero molecules

A: Transcription factor grauzone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4664
Polymers18,3352
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2060 Å2
ΔGint-23 kcal/mol
Surface area10200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)48.660, 48.660, 82.123
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212
DetailsThe biological unit is a dimer, the dimer is generated by the twofold axis: y, x, -z

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Components

#1: Protein Transcription factor grauzone / Zinc finger associated domain of Drosophila Grauzone / grauzone CG33133-PA


Mass: 9167.418 Da / Num. of mol.: 1 / Fragment: zinc finger associated domain (ZAD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: grauzone / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9U405
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.48 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 4000, ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
20.2 Mammonium acetate1reservoir
30.1 Msodium citrate1reservoirpH5.6
430 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.0500, 1.2828
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2003 / Details: mirrors
RadiationMonochromator: double Si(111) crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.051
21.28281
ReflectionResolution: 1.95→50 Å / Num. all: 7120 / Num. obs: 6907 / % possible obs: 97 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 52.6 Å2 / Rsym value: 0.042 / Net I/σ(I): 36.7
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 6.3 / Rsym value: 0.447 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.1refinement
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.404 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.213 / ESU R Free: 0.179
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. for refinement used also CNS 1.0
RfactorNum. reflection% reflectionSelection details
Rfree0.26691 322 4.7 %RANDOM
Rwork0.24083 ---
obs0.24204 6590 97.27 %-
all-6775 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.879 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms642 0 1 56 699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021657
X-RAY DIFFRACTIONr_bond_other_d0.0020.02575
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.913891
X-RAY DIFFRACTIONr_angle_other_deg0.83431336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175579
X-RAY DIFFRACTIONr_chiral_restr0.0660.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02736
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02137
X-RAY DIFFRACTIONr_nbd_refined0.2130.2183
X-RAY DIFFRACTIONr_nbd_other0.2340.2687
X-RAY DIFFRACTIONr_nbtor_other0.0850.2374
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.29
X-RAY DIFFRACTIONr_mcbond_it1.9793398
X-RAY DIFFRACTIONr_mcangle_it3.5564647
X-RAY DIFFRACTIONr_scbond_it3.2596259
X-RAY DIFFRACTIONr_scangle_it5.2119244
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.337 24
Rwork0.296 475
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)
112.3953-4.7373-1.17722.37740.15824.15390.66551.8736-0.2347-0.4912-0.58380.09810.1901-0.8568-0.08170.20130.021-0.09690.5604-0.02970.16353.24729.461823.9361
27.535-1.4051-2.0542.58692.42490.24710.33030.7420.9393-0.0521-0.0486-0.4699-0.7279-0.217-0.28170.3183-0.1259-0.06150.28220.27570.30757.48219.791628.8642
31.92470.23891.28872.87684.885911.8772-0.0731-0.08820.05150.24840.09040.39870.2513-0.524-0.01740.2352-0.0526-0.06040.17350.03240.27125.179713.850447.6017
40000000000000000.1853-0.0755-0.10390.2788-0.05680.2415.71316.848127.2863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 191 - 18
2X-RAY DIFFRACTION1AA51 - 5450 - 53
3X-RAY DIFFRACTION2AA20 - 5019 - 49
4X-RAY DIFFRACTION3AA55 - 8154 - 80
5X-RAY DIFFRACTION4AB1001
Software
*PLUS
Version: 5.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 15 Å / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.2

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