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- PDB-2iwr: Gtpase Like Domain Of Centaurin Gamma 1 (Human) -

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Basic information

Entry
Database: PDB / ID: 2iwr
TitleGtpase Like Domain Of Centaurin Gamma 1 (Human)
ComponentsCENTAURIN GAMMA 1
KeywordsHYDROLASE / ANK REPEAT / ZINC-FINGER / GTP-BINDING / POLYMORPHISM / NUCLEOTIDE-BINDING / ALTERNATIVE SPLICING / PROTEIN TRANSPORT / GTPASE ACTIVATION / METAL-BINDING / NUCLEAR PROTEIN / PHOSPHORYLATION / SGC / ZINC / CENTG1 / GTPASE / ONCOGENE / TRANSPORT / STRUCTUAL GENOMICS CONSORTIUM / STRUCTURAL GENOMICS CONSORTIUM / STRUCTURAL GENOMICS
Function / homology
Function and homology information


Netrin-1 signaling / phosphatidylinositol 3-kinase regulator activity / phosphatidylinositol 3-kinase activator activity / Flemming body / endosomal transport / protein kinase activator activity / positive regulation of protein kinase activity / GTPase activator activity / negative regulation of protein catabolic process / protein transport ...Netrin-1 signaling / phosphatidylinositol 3-kinase regulator activity / phosphatidylinositol 3-kinase activator activity / Flemming body / endosomal transport / protein kinase activator activity / positive regulation of protein kinase activity / GTPase activator activity / negative regulation of protein catabolic process / protein transport / actin cytoskeleton organization / negative regulation of neuron apoptotic process / endosome / GTPase activity / protein kinase binding / GTP binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / 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 / small GTPase Rab1 family profile. / PH domain profile. / Pleckstrin homology domain. ...: / 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 / small GTPase Rab1 family profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Rab subfamily of small GTPases / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsElkins, J.M. / Soundararajan, M. / Yang, X. / Papagrigoriou, E. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Doyle, D.A. / Structural Genomics Consortium (SGC)
CitationJournal: Biochem.J. / Year: 2007
Title: The Centaurin Gamma-1 Gtpase-Like Domain Functions as an Ntpase.
Authors: Soundararajan, M. / Yang, X. / Elkins, J.M. / Sobott, F. / Doyle, D.A.
History
DepositionJul 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CENTAURIN GAMMA 1


Theoretical massNumber of molelcules
Total (without water)19,8471
Polymers19,8471
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.256, 62.146, 67.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CENTAURIN GAMMA 1 / ARF-GAP WITH GTP-BINDING PROTEIN-LIKE / ANKYRIN REPEAT AND PLECKSTRIN HOMOLOGY DOMAINS 2 / AGAP-2 / ...ARF-GAP WITH GTP-BINDING PROTEIN-LIKE / ANKYRIN REPEAT AND PLECKSTRIN HOMOLOGY DOMAINS 2 / AGAP-2 / PHOSPHATIDYLINOSITOL-3-KINASE ENHANCER / PIKE / GTP-BINDING AND GTPASE ACTIVATING PROTEIN 2 / GGAP2


Mass: 19847.256 Da / Num. of mol.: 1 / Fragment: GTPASE LIKE DOMAIN, RESIDUES 402-577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: IMAGE CONSORTIUM CLONE ID 5218187 / Plasmid: PLIC-SGC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99490
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.94 Å3/Da / Density % sol: 36.7 %
Crystal growpH: 6 / Details: 0.1M PCB PH6.0, 30% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: May 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→20.72 Å / Num. obs: 24972 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.7 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BMJ

2bmj


Resolution: 1.5→45.74 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.052 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1019 4.1 %RANDOM
Rwork0.15 ---
obs0.152 23903 99.3 %-
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: 21.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2---0.22 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1334 0 0 221 1555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211356
X-RAY DIFFRACTIONr_bond_other_d0.0020.02915
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9731826
X-RAY DIFFRACTIONr_angle_other_deg1.44132217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6455171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.57623.16760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2915230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0091513
X-RAY DIFFRACTIONr_chiral_restr0.110.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021509
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02283
X-RAY DIFFRACTIONr_nbd_refined0.3330.2297
X-RAY DIFFRACTIONr_nbd_other0.2210.2973
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2649
X-RAY DIFFRACTIONr_nbtor_other0.0870.2751
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2127
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3160.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8023923
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.62851367
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.8847522
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.45811459
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.242 48
Rwork0.174 1589

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