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- PDB-2p57: GAP domain of ZNF289, an ID1-regulated zinc finger protein -

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Basic information

Entry
Database: PDB / ID: 2p57
TitleGAP domain of ZNF289, an ID1-regulated zinc finger protein
ComponentsGTPase-activating protein ZNF289
KeywordsMETAL BINDING PROTEIN / zinc finger / GAP / GTPASE activating protein / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


COPI coating of Golgi vesicle / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPI-dependent Golgi-to-ER retrograde traffic / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / GTPase activator activity / protein transport / Golgi membrane / Golgi apparatus / metal ion binding ...COPI coating of Golgi vesicle / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPI-dependent Golgi-to-ER retrograde traffic / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / GTPase activator activity / protein transport / Golgi membrane / Golgi apparatus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Arf GTPase activating protein / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADP-ribosylation factor GTPase-activating protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsTong, Y. / Dimov, S. / Shen, L. / Zhu, H. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. ...Tong, Y. / Dimov, S. / Shen, L. / Zhu, H. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: GAP domain of ZNF289, an ID1-regulated zinc finger protein
Authors: Tong, Y. / Dimov, S. / Shen, L. / Zhu, H. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionMar 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase-activating protein ZNF289
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1755
Polymers16,1091
Non-polymers654
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.027, 41.165, 72.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsnot known

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Components

#1: Protein GTPase-activating protein ZNF289


Mass: 16109.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNF289 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q8N6H7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 3.2M sodium formate, .09M sodium acetate, pH 4.6, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 11721 / % possible obs: 97.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.06 / Χ2: 1.737 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
1.8-1.8695.25.40.50411291.405
1.86-1.9496.55.40.34911111.774
1.94-2.0397.25.40.26811301.562
2.03-2.1397.25.40.19311521.741
2.13-2.2797.55.40.13811512.182
2.27-2.44985.40.09711711.709
2.44-2.6999.15.40.0811641.819
2.69-3.0898.85.40.05611971.718
3.08-3.8899.55.40.03812141.853
3.88-5098.95.10.02813021.603

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å22.71 Å
Translation2 Å22.71 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
ARP/wARPmodel building
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2CRW

2crw


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.185 / SU B: 2.524 / SU ML: 0.081 / ESU R: 0.138 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 559 4.782 %random
Rwork0.1955 ---
all0.198 ---
obs0.19773 11690 97.914 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.218 Å2
Baniso -1Baniso -2Baniso -3
1-0.699 Å20 Å20 Å2
2--0.036 Å20 Å2
3----0.735 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms981 0 4 41 1026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211008
X-RAY DIFFRACTIONr_bond_other_d0.0010.02678
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9011372
X-RAY DIFFRACTIONr_angle_other_deg0.99831634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5635133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.39122.70848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62715157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.185159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021173
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02233
X-RAY DIFFRACTIONr_nbd_refined0.2150.2215
X-RAY DIFFRACTIONr_nbd_other0.1920.2700
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2499
X-RAY DIFFRACTIONr_nbtor_other0.0850.2513
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.238
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3240.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.23
X-RAY DIFFRACTIONr_mcbond_it1.1211.5649
X-RAY DIFFRACTIONr_mcbond_other0.2721.5259
X-RAY DIFFRACTIONr_mcangle_it1.69421016
X-RAY DIFFRACTIONr_scbond_it2.3833410
X-RAY DIFFRACTIONr_scangle_it3.5594.5353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
1.8-1.8470.42370.2587630.26683995.352
1.847-1.8970.278450.2317840.23485696.846
1.897-1.9520.187390.2117450.2182794.8
1.952-2.0120.221340.1957320.19677798.584
2.012-2.0770.224320.1867310.18779196.46
2.077-2.150.26350.1866910.18974897.059
2.15-2.2310.28410.1796590.18570799.01
2.231-2.3210.239320.1836560.18671096.901
2.321-2.4240.191250.1776410.17768197.797
2.424-2.5410.185230.1996110.19963699.686
2.541-2.6780.284350.1885620.19460698.515
2.678-2.8390.311350.2165280.22157098.772
2.839-3.0330.218290.2225350.22157098.947
3.033-3.2730.283230.2074800.2150599.604
3.273-3.5810.153210.1934660.19148999.591
3.581-3.9960.174190.1854220.185441100
3.996-4.6010.226180.1513810.15440099.75
4.601-5.6020.26290.1853250.187334100
5.602-7.7880.319170.2472590.251276100
7.788-300.272100.2071600.21117696.591

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