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- PDB-2olm: ArfGap domain of HIV-1 Rev binding protein -

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Basic information

Entry
Database: PDB / ID: 2olm
TitleArfGap domain of HIV-1 Rev binding protein
ComponentsNucleoporin-like protein RIP
KeywordsHYDROLASE REGULATOR / ARFGAP / gtpase-activating protein / rev-interacting protein / HIV / human immunodeficiency virus / AIDS / nucleoporin / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


spermatid nucleus differentiation / acrosome assembly / intermediate filament organization / mRNA export from nucleus / nuclear pore / GTPase activator activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / cytoplasmic vesicle / intracellular membrane-bounded organelle ...spermatid nucleus differentiation / acrosome assembly / intermediate filament organization / mRNA export from nucleus / nuclear pore / GTPase activator activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / cytoplasmic vesicle / intracellular membrane-bounded organelle / DNA binding / RNA binding / metal ion binding / cytosol / cytoplasm
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
Unknown ligand / Arf-GAP domain and FG repeat-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 Å
AuthorsTong, Y. / Tempel, W. / Shen, L. / Dimov, S. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. ...Tong, Y. / Tempel, W. / Shen, L. / Dimov, S. / 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: ArfGap domain of HIV-1 Rev binding protein
Authors: Tong, Y. / Tempel, W. / Shen, L. / Dimov, S. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
History
DepositionJan 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoporin-like protein RIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,50815
Polymers16,1591
Non-polymers35014
Water1,35175
1
A: Nucleoporin-like protein RIP
hetero molecules

A: Nucleoporin-like protein RIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,01630
Polymers32,3172
Non-polymers69928
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)57.883, 57.883, 83.696
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-202-

UNL

21A-202-

UNL

31A-202-

UNL

41A-1009-

UNX

51A-2070-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nucleoporin-like protein RIP / HIV-1 Rev-binding protein / Rev-interacting protein / Rev/Rex activation domain-binding protein


Mass: 16158.546 Da / Num. of mol.: 1 / Fragment: ArfGap domain: Residues 4-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRB, RAB, RIP / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P52594

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Non-polymers , 6 types, 89 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 9 / Source method: obtained synthetically
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.3 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.27M Ammonium phosphate, 0.09M BTP, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 45446 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.055 / Χ2: 1.437 / Net I/σ(I): 18.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.48-1.534.40.23744490.625197.3
1.53-1.596.60.19145520.641100
1.59-1.677.40.14845690.7081100
1.67-1.757.50.11545460.7931100
1.75-1.867.60.09345410.9971100
1.86-2.017.60.07445441.3371100
2.01-2.217.60.0645701.691100
2.21-2.537.70.05445662.0291100
2.53-3.197.70.04745392.2551100
3.19-507.50.04245702.75199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å29.26 Å
Translation2.5 Å29.26 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
ADSCQUANTUMdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IQJ

2iqj


Resolution: 1.48→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.193 / WRfactor Rwork: 0.18 / SU B: 0.992 / SU ML: 0.039 / Cross valid method: FREE-R / ESU R: 0.068 / ESU R Free: 0.066 / Stereochemistry target values: Engh & Huber
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. arp/warp, molprobity, coot programs were also used in the refinement. 3. Residue UNL is a molecule of unknown nature that has been ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. arp/warp, molprobity, coot programs were also used in the refinement. 3. Residue UNL is a molecule of unknown nature that has been modeled in density resembling an aromatic 6-membered ring.
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 1239 5.061 %random
Rwork0.1797 ---
all0.18 ---
obs-24481 99.825 %-
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: 12.863 Å2
Baniso -1Baniso -2Baniso -3
1-0.172 Å20 Å20 Å2
2--0.172 Å20 Å2
3----0.344 Å2
Refinement stepCycle: LAST / Resolution: 1.48→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 33 75 1164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221120
X-RAY DIFFRACTIONr_bond_other_d0.0020.02796
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9681512
X-RAY DIFFRACTIONr_angle_other_deg0.92231937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8425138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20123.72551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.65715200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.554158
X-RAY DIFFRACTIONr_chiral_restr0.0950.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021225
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02229
X-RAY DIFFRACTIONr_nbd_refined0.2120.2201
X-RAY DIFFRACTIONr_nbd_other0.2010.2821
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2557
X-RAY DIFFRACTIONr_nbtor_other0.0850.2548
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.249
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.26
X-RAY DIFFRACTIONr_mcbond_it2.2682727
X-RAY DIFFRACTIONr_mcbond_other0.4952267
X-RAY DIFFRACTIONr_mcangle_it2.68331094
X-RAY DIFFRACTIONr_scbond_it2.8352488
X-RAY DIFFRACTIONr_scangle_it4.1163415
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 (%)
1.48-1.5190.253910.216700.203179098.38
1.519-1.560.206850.17616310.1771716100
1.56-1.6050.221980.17115950.1731693100
1.605-1.6540.178710.1715530.171624100
1.654-1.7090.217840.16415120.1671596100
1.709-1.7680.173820.15714440.1581526100
1.768-1.8350.194760.16614160.1681492100
1.835-1.9090.205740.17413640.1751438100
1.909-1.9940.177720.16513180.1661390100
1.994-2.0910.203660.15912450.1611311100
2.091-2.2030.164830.16511860.1651269100
2.203-2.3360.151460.16811440.1671190100
2.336-2.4960.161540.17210820.1721136100
2.496-2.6950.168620.1759920.1751054100
2.695-2.950.232450.1849420.186987100
2.95-3.2940.173360.1918630.19899100
3.294-3.7960.214380.1777650.179803100
3.796-4.630.143310.1746640.17369799.713
4.63-6.4720.275290.2255300.227559100
6.472-300.336160.2873260.28935496.61

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