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

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Entry
Database: PDB / ID: 2xto
TitleCrystal structure of GDP-bound human GIMAP2, amino acid residues 21- 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
GTPase GIMA/IAN/Toc / AIG1-type guanine nucleotide-binding (G) domain / AIG1 family / AIG1-type G domain profile. / P-loop containing nucleoside triphosphate hydrolase
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: 2.8 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. / Froehlich, 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)54,3686
Polymers53,4332
Non-polymers9354
Water00
1
A: GTPASE IMAP FAMILY MEMBER 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1843
Polymers26,7161
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTPASE IMAP FAMILY MEMBER 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1843
Polymers26,7161
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.680, 76.550, 101.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A21 - 256
2114B21 - 256

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Components

#1: Protein GTPASE IMAP FAMILY MEMBER 2 / IMMUNITY-ASSOCIATED PROTEIN 2 / HIMAP2 / GIMAP2


Mass: 26716.250 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-260
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: Chemical ChemComp-GDP / GUANOSINE-5'-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
Sequence detailsAMINO ACID RESIDUES 21-260 OF UNIPROT ENTRY Q9UG22 WERE CLONED, PURIFIED, AND CRYSTALLIZED

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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: 2.26 Å3/Da / Density % sol: 46.08 % / Description: NONE
Crystal growpH: 7.5 / Details: 19% 2-PROPANOL, 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: May 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 12565 / % possible obs: 98.2 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 8.5
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.89 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.8→12 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.861 / SU B: 40.192 / SU ML: 0.359 / Cross valid method: THROUGHOUT / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27565 591 4.9 %RANDOM
Rwork0.22941 ---
obs0.23176 11467 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.574 Å2
Baniso -1Baniso -2Baniso -3
1--2.52 Å20 Å20 Å2
2---0.97 Å20 Å2
3---3.49 Å2
Refinement stepCycle: LAST / Resolution: 2.8→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3469 0 58 0 3527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213589
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.971.9794837
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5285446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03824.907161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.11815663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5461519
X-RAY DIFFRACTIONr_chiral_restr0.0580.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022635
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_it0.0971.52202
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.20223516
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.35431387
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5914.51319
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 1708 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.320.5
2Bmedium positional0.320.5
1Amedium thermal0.152
2Bmedium thermal0.152
LS refinement shellResolution: 2.801→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 38 -
Rwork0.308 789 -
obs--95.61 %
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)
12.97970.22970.17352.41210.97032.14140.0546-0.1710.09080.0605-0.05240.0353-0.0743-0.2223-0.00220.0777-0.0093-0.01420.07820.02720.0471-11.9361-18.835610.7252
21.7166-2.35021.46813.3443-2.02431.2580.4760.3568-0.1203-0.8539-0.37760.08970.42960.2838-0.09840.4648-0.02180.08560.2769-0.07930.2525-5.5359-22.0567-8.9669
32.854-1.23-0.8352.1191-0.05090.8648-0.1297-0.02770.12330.14170.182-0.0760.0920.3515-0.05220.10620.048-0.06940.3132-0.00280.0842-0.1338-20.26038.2793
49.33081.15822.20777.1123-3.344518.5032-0.0867-0.47210.32740.41540.44960.5665-0.3872-0.8943-0.36290.21110.05030.05450.1727-0.05420.1284-15.1759-0.64415.276
52.423-0.0135-0.4791.56620.36052.7028-0.02630.1683-0.0364-0.09020.0591-0.0567-0.04450.0812-0.03280.0540.0082-0.0040.04370.00550.1239.304411.6713-4.621
63.8861-2.02433.94145.1491-3.02375.0749-0.1422-0.1369-0.18110.05670.17370.43560.04550.1077-0.03150.05410.05230.0780.13010.02550.19463.029621.04043.572
75.019-0.3631-0.98722.0047-0.07856.5788-0.04050.35270.09630.0045-0.05640.19510.0825-0.50570.09680.1404-0.0389-0.0660.06270.0030.1651-2.606610.1253-8.5707
89.3958-3.60575.638818.60171.065211.02740.14170.95860.5915-1.14-0.5203-1.1862-0.5670.51990.37860.3225-0.06440.09360.47340.150.28313.299117.2289-24.2756
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 145
2X-RAY DIFFRACTION2A146 - 171
3X-RAY DIFFRACTION3A172 - 223
4X-RAY DIFFRACTION4A235 - 256
5X-RAY DIFFRACTION5B21 - 160
6X-RAY DIFFRACTION6B161 - 189
7X-RAY DIFFRACTION7B190 - 235
8X-RAY DIFFRACTION8B236 - 254

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