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- PDB-2xtm: Crystal structure of GDP-bound human GIMAP2, amino acid residues ... -

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Basic information

Entry
Database: PDB / ID: 2xtm
TitleCrystal structure of GDP-bound human GIMAP2, amino acid residues 1- 234
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
GTPase GIMA/IAN/Toc / AIG1-type guanine nucleotide-binding (G) domain / AIG1 family / AIG1-type G domain profile. / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTPase IMAP family member 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

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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
B: GTPASE IMAP FAMILY MEMBER 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9869
Polymers51,7742
Non-polymers1,2117
Water5,368298
1
A: GTPASE IMAP FAMILY MEMBER 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6316
Polymers25,8871
Non-polymers7445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTPASE IMAP FAMILY MEMBER 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3553
Polymers25,8871
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.890, 61.810, 185.310
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 / GIMAP2 / IMMUNITY-ASSOCIATED PROTEIN 2 / HIMAP2


Mass: 25887.150 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-234
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: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.35 Å3/Da / Density % sol: 48.15 % / Description: NONE
Crystal growpH: 7.5 / Details: 12.5% 2-PROPANOL, 30% GLYCEROL, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 54984 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.8
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→92.85 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.598 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2807 5.1 %RANDOM
Rwork0.181 ---
obs0.182 52141 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.7→92.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3059 0 76 298 3433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213270
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9854442
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2625438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44825134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15815580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5521515
X-RAY DIFFRACTIONr_chiral_restr0.0770.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022403
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_it0.6171.52052
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16623284
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.01531218
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2524.51140
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: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 200 -
Rwork0.223 3720 -
obs--97.2 %
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)
10.59370.0457-0.11421.0904-0.1521.05940.0169-0.05230.04040.0121-0.0508-0.1036-0.01860.08090.03380.0221-0.0008-0.02020.0117-0.00310.0524-12.788-3.3103-36.3018
20.45180.0020.13680.7306-0.14161.1637-0.0042-0.04130.0397-0.0190.00890.0319-0.0597-0.057-0.00470.02260.0042-0.010.0079-0.01190.0409-22.776-0.5122-36.461
30.8283-0.3338-0.04751.0876-0.5941.42450.0070.01510.0652-0.1359-0.00660.02480.0476-0.0381-0.00040.0603-0.0029-0.01370.00210.00090.0533-21.35116.5082-51.2746
40.93420.4414-0.45981.1084-0.54842.07760.0054-0.08540.1860.0668-0.0749-0.036-0.23260.03760.06960.0438-0.0036-0.01660.0114-0.02110.0917-16.278611.1415-34.7223
52.40170.71820.1579.93275.34264.80780.0921-0.5445-0.13350.274-0.117-0.0340.2085-0.03130.02490.0758-0.0225-0.01650.1550.01520.01783.2038-3.8344-8.7011
64.73261.5215-0.76953.2261.07061.5920.1787-1.0782-0.4110.684-0.1536-0.16410.30720.111-0.02510.2733-0.0438-0.07050.40.10420.0623.8812-7.5015-0.5675
74.67011.5851-0.59721.97860.25233.04730.1821-0.6402-0.12360.0311-0.0167-0.2148-0.01410.125-0.16540.06550.0237-0.03820.1857-0.04230.052711.7991-1.6986-8.9004
82.5805-0.0911-0.35881.78721.07361.41460.1244-0.44710.19360.1362-0.061-0.0693-0.04960.0429-0.06330.0619-0.03160.00240.1356-0.05730.02982.6913.4391-10.383
99.4094-0.5887-4.13557.9305-3.89895.28850.2449-0.28020.23630.4061-0.0780.432-0.3425-0.3214-0.16690.19920.01930.05410.3782-0.2450.223-12.10112.7438-2.4481
102.3230.0454-0.43811.14670.44320.9270.1078-0.3648-0.050.0877-0.10420.06230.0017-0.0508-0.00360.0368-0.0243-0.00160.1041-0.00130.0102-3.1143-3.625-13.2021
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 92
2X-RAY DIFFRACTION2A93 - 138
3X-RAY DIFFRACTION3A139 - 184
4X-RAY DIFFRACTION4A185 - 227
5X-RAY DIFFRACTION5B21 - 31
6X-RAY DIFFRACTION6B32 - 68
7X-RAY DIFFRACTION7B69 - 96
8X-RAY DIFFRACTION8B97 - 150
9X-RAY DIFFRACTION9B151 - 167
10X-RAY DIFFRACTION10B168 - 226

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