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- PDB-3ihw: Crystal structure of the Ras-like domain of CENTG3 -

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Basic information

Entry
Database: PDB / ID: 3ihw
TitleCrystal structure of the Ras-like domain of CENTG3
ComponentsCENTG3
KeywordsSIGNALING PROTEIN / ras / centaurin / gtpase / Structural Genomics / Structural Genomics Consortium / sgc / Alternative splicing / ANK repeat / Cytoplasm / GTP-binding / GTPase activation / Metal-binding / Nucleotide-binding / Phosphoprotein / Zinc / Zinc-finger
Function / homology
Function and homology information


polyubiquitin modification-dependent protein binding / GTPase activator activity / cell periphery / cellular response to reactive oxygen species / proteasome-mediated ubiquitin-dependent protein catabolic process / GTPase activity / GTP binding / signal transduction / membrane / metal ion binding ...polyubiquitin modification-dependent protein binding / GTPase activator activity / cell periphery / cellular response to reactive oxygen species / proteasome-mediated ubiquitin-dependent protein catabolic process / GTPase activity / GTP binding / signal transduction / membrane / metal ion binding / nucleus / 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 / Domain of unknown function DUF3447 / Small GTPase, Ras-type / small GTPase Ras family profile. / PH domain profile. ...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 / Domain of unknown function DUF3447 / Small GTPase, Ras-type / small GTPase Ras family profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Small GTPase / Ras family / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsNedyalkova, L. / Tempel, W. / Tong, Y. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the Ras-like domain of CENTG3
Authors: Nedyalkova, L. / Tempel, W. / Tong, Y. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionJul 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 21, 2020Group: Data collection / Database references / Category: diffrn_source / phasing / struct_ref_seq_dif / Item: _diffrn_source.type / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CENTG3


Theoretical massNumber of molelcules
Total (without water)20,8004
Polymers20,8001
Non-polymers03
Water90150
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.345, 54.176, 73.545
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CENTG3 / AGAP-3 / Centaurin-gamma-3 / MR1-interacting protein / MRIP-1 / CRAM-associated GTPase / CRAG


Mass: 20799.543 Da / Num. of mol.: 1 / Fragment: residues 90-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGAP3, CENTG3 / Plasmid: pET28-mhl (GI:134105571) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q96P47
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


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


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 16% PEG3350, 0.2M potassium fluoride, 0.1M Bis-Tris, pH 6.0, 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: Jun 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→20 Å / Num. obs: 13556 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.138 / Χ2: 1.967 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.92-1.996.70.9913242.328100
1.99-2.076.80.82513252.033100
2.07-2.166.80.60413282.09899.9
2.16-2.286.50.48413222.952100
2.28-2.426.90.33513361.616100
2.42-2.670.25513521.575100
2.6-2.8770.213571.819100
2.87-3.2870.11113661.593100
3.28-4.136.80.07413702.335100
4.13-206.60.04314761.465100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2BMJ

2bmj


Resolution: 1.92→19.72 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.2 / SU B: 4.496 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY. ARP/WARP, COOT and MOLPROBITY were also used during refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.278 682 5.077 %RANDOM
Rwork0.23 ---
obs0.233 13432 99.918 %-
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: 18.599 Å2
Baniso -1Baniso -2Baniso -3
1--1.489 Å20 Å20 Å2
2--0.299 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 1.92→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 3 50 1350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221326
X-RAY DIFFRACTIONr_bond_other_d0.0050.02874
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9631810
X-RAY DIFFRACTIONr_angle_other_deg1.00732139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4775176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.68624.13858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40215214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.293158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021507
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02276
X-RAY DIFFRACTIONr_mcbond_it0.8971.5843
X-RAY DIFFRACTIONr_mcbond_other0.2491.5344
X-RAY DIFFRACTIONr_mcangle_it1.5721362
X-RAY DIFFRACTIONr_scbond_it2.3093483
X-RAY DIFFRACTIONr_scangle_it3.6484.5443
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-1.9690.474480.3591496399.896
1.969-2.0230.415460.312907953100
2.023-2.0810.311450.28287592199.891
2.081-2.1440.329450.26383488299.66
2.144-2.2140.299420.238813855100
2.214-2.290.463310.34782085799.3
2.29-2.3750.258480.222763811100
2.375-2.4710.32370.226749786100
2.471-2.5790.316430.225707750100
2.579-2.7030.26400.231689729100
2.703-2.8460.275380.237652690100
2.846-3.0140.323380.231617655100
3.014-3.2170.212330.216579612100
3.217-3.4670.262290.218560589100
3.467-3.7870.238290.21507536100
3.787-4.2140.254300.189468498100
4.214-4.8290.135180.157424442100
4.829-5.8280.184180.212362380100
5.828-7.9040.297170.248302319100
7.904-19.720.44970.226208215100

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