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- PDB-2bmj: GTPase like domain of Centaurin Gamma 1 (Human) -

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Basic information

Entry
Database: PDB / ID: 2bmj
TitleGTPase like domain of Centaurin Gamma 1 (Human)
ComponentsCENTAURIN GAMMA 1
KeywordsHYDROLASE / GTPASE / STRUCTURAL GENOMICS CONSORTIUM / SGC / CENTAURIN ANK REPEAT / GTP-BINDING
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: 2.1 Å
AuthorsYang, X. / Elkins, J.M. / Soundararajan, M. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / 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
DepositionMar 14, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)19,6071
Polymers19,6071
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.151, 31.104, 81.928
Angle α, β, γ (deg.)90.00, 102.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CENTAURIN GAMMA 1


Mass: 19607.291 Da / Num. of mol.: 1 / Fragment: GTPASE LIKE DOMAIN, RESIDUES 66-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / 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.: 122 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES SER A64 AND MET A65 ARE CLONING ARTEFACTS

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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: 1.98 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M SPG PH 7.0; 30.0% PEG1000; 0.5% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU/MSC / Detector: IMAGE PLATE / Date: Feb 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30.6 Å / Num. obs: 43169 / % possible obs: 95.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.9 / % possible all: 89.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RAP

2rap


Resolution: 2.1→80.06 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.489 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 413 4.8 %RANDOM
Rwork0.163 ---
obs0.166 8240 94.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å2-0.28 Å2
2--1.4 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.1→80.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1329 0 0 122 1451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221346
X-RAY DIFFRACTIONr_bond_other_d0.0010.021261
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9661812
X-RAY DIFFRACTIONr_angle_other_deg0.85732914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6845172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.62123.3959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78415239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8891512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021505
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02278
X-RAY DIFFRACTIONr_nbd_refined0.1960.2232
X-RAY DIFFRACTIONr_nbd_other0.1930.21216
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2614
X-RAY DIFFRACTIONr_nbtor_other0.0840.2862
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1770.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2960.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0681.51107
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31421361
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1533560
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1724.5451
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 29
Rwork0.172 545
Refinement TLS params.Method: refined / Origin x: 8.087 Å / Origin y: 12.894 Å / Origin z: 21.505 Å
111213212223313233
T-0.1723 Å2-0.0208 Å20.0211 Å2--0.0874 Å20.0178 Å2---0.1773 Å2
L1.9714 °20.1452 °20.5561 °2-0.7468 °2-0.1431 °2--2.8437 °2
S0.0535 Å °-0.1015 Å °0.0643 Å °0.0565 Å °-0.0543 Å °0.0154 Å °0.0052 Å °0.1379 Å °0.0008 Å °

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