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- PDB-2xtp: Crystal structure of nucleotide-free human GIMAP2, amino acid res... -

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Basic information

Entry
Database: PDB / ID: 2xtp
TitleCrystal structure of nucleotide-free human GIMAP2, amino acid residues 1-260
ComponentsGTPASE IMAP FAMILY MEMBER 2
KeywordsIMMUNE SYSTEM / G PROTEIN
Function / homology
Function and homology information


lipid droplet / GTP binding / endoplasmic reticulum / nucleoplasm / identical protein binding
Similarity search - Function
AIG1-type guanine nucleotide-binding (G) domain / GTPase GIMA/IAN/Toc / AIG1 family / AIG1-type G domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GTPase IMAP family member 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsSchwefel, D. / Froehlich, C. / Daumke, O.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural Basis of Oligomerization in Septin-Like Gtpase of Immunity-Associated Protein 2 (Gimap2)
Authors: Schwefel, D. / Froehlich, C. / Eichhorst, J. / Wiesner, B. / Behlke, J. / Aravind, L. / Daumke, O.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Purification, Crystallization and Preliminary X- Ray Analysis of Human Gimap2.
Authors: Schwefel, D. / Frohlich, C. / Daumke, O.
History
DepositionOct 11, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPASE IMAP FAMILY MEMBER 2


Theoretical massNumber of molelcules
Total (without water)29,3551
Polymers29,3551
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.380, 60.910, 72.020
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 GTPASE IMAP FAMILY MEMBER 2 / IMMUNITY-ASSOCIATED PROTEIN 2 / HIMAP2 / GIMAP2


Mass: 29354.859 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q9UG22
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.15 Å3/Da / Density % sol: 42.62 % / Description: NONE
Crystal growpH: 7.5 / Details: 11-12% 2-PROPANOL, 15% GLYCEROL, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9797, 0.9849
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 23, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.98491
ReflectionResolution: 1.75→50 Å / Num. obs: 183804 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.6
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.2 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
XDSdata reduction
XDSdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.5→19.14 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.353 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20382 2085 5.1 %RANDOM
Rwork0.18009 ---
obs0.18128 38936 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.251 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2---0.83 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1712 0 0 179 1891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221797
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.9612431
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9045241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40624.68479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65115344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1541510
X-RAY DIFFRACTIONr_chiral_restr0.080.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021332
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6711.51121
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28721804
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2383676
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4814.5616
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→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 151 -
Rwork0.247 2817 -
obs--99.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.79520.24230.19470.3599-0.17660.64080.02720.0097-0.0452-0.00360.021-0.0311-0.0446-0.0164-0.04830.02670.0048-0.00390.0147-0.00620.019723.092349.56288.4488
20.88550.21950.01080.85680.70481.50970.01750.02930.0835-0.01840.01570.0887-0.07670.0274-0.03320.02790.00760.00410.00460.00090.023519.051554.804110.1244
30.4786-0.14460.01860.55490.02540.39270.0127-0.0298-0.03620.0084-0.0194-0.00770.0150.01380.00670.0145-0.0053-0.00070.00660.00640.012327.377642.810213.9628
49.7067-2.31061.36953.612-0.12294.20.1602-0.40490.34940.5161-0.17930.25670.0256-0.29590.01910.1592-0.0240.12040.1103-0.00320.10329.024848.687827.002
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 43
2X-RAY DIFFRACTION2A44 - 96
3X-RAY DIFFRACTION3A97 - 219
4X-RAY DIFFRACTION4A220 - 254

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