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- PDB-3p1j: Crystal structure of human GTPase IMAP family member 2 in the nuc... -

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Basic information

Entry
Database: PDB / ID: 3p1j
TitleCrystal structure of human GTPase IMAP family member 2 in the nucleotide-free state
ComponentsGTPase IMAP family member 2
KeywordsHYDROLASE / immunity / structural genomics consortium / gtpase / immunity-associated protein / SGC
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
GTPase IMAP family member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsShen, L. / Tempel, W. / Tong, Y. / Guan, X. / Nedyalkova, L. / Wernimont, A.K. / Mackenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Shen, L. / Tempel, W. / Tong, Y. / Guan, X. / Nedyalkova, L. / Wernimont, A.K. / Mackenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Andrews, D.W. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of human GTPase IMAP family member 2 in the nucleotide-free state
Authors: Shen, L. / Tempel, W. / Tong, Y. / Guan, X. / Nedyalkova, L. / Wernimont, A.K. / Mackenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Andrews, D.W. / Park, H.
History
DepositionSep 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: GTPase IMAP family member 2
D: GTPase IMAP family member 2


Theoretical massNumber of molelcules
Total (without water)92,72123
Polymers92,7214
Non-polymers019
Water00
1
A: GTPase IMAP family member 2
D: GTPase IMAP family member 2


Theoretical massNumber of molelcules
Total (without water)46,36016
Polymers46,3602
Non-polymers014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-15 kcal/mol
Surface area16370 Å2
MethodPISA
2
B: GTPase IMAP family member 2
C: GTPase IMAP family member 2


Theoretical massNumber of molelcules
Total (without water)46,3607
Polymers46,3602
Non-polymers05
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-15 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.472, 132.472, 84.161
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
GTPase IMAP family member 2 / Immunity-associated protein 2 / hIMAP2


Mass: 23180.244 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GIMAP2, IMAP2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q9UG22
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 19 / Source method: obtained synthetically

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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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 5-fold molar excess of GDP was added to protein stock solution. 1.4M sodium citrate, 0.1M HEPES, pH 7.6, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97895 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.58→40 Å / Num. obs: 26603 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.077 / Χ2: 1.966 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.58-2.6750.99326352.057100
2.67-2.785.70.78926312.039100
2.78-2.916.10.52326772.092100
2.91-3.066.30.3826202.051100
3.06-3.256.30.22926552.093100
3.25-3.56.40.13326552.033100
3.5-3.856.30.08326522.089100
3.85-4.416.30.06226722.372100
4.41-5.556.30.0426791.586100
5.55-406.20.02527271.29799.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
MOLREPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3LXW

3lxw
PDB Unreleased entry


Resolution: 2.58→30 Å / Cor.coef. Fo:Fc: 0.9317 / Cor.coef. Fo:Fc free: 0.9084 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 1005 3.78 %thin shells (sftools)
Rwork0.2053 ---
obs0.2062 26556 100 %-
Displacement parametersBiso max: 163.4 Å2 / Biso mean: 69.4552 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--7.4279 Å20 Å20 Å2
2---7.4279 Å20 Å2
3---14.8558 Å2
Refine analyzeLuzzati coordinate error obs: 0.397 Å
Refinement stepCycle: LAST / Resolution: 2.58→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5380 0 19 0 5399
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d17832
X-RAY DIFFRACTIONt_trig_c_planes1142
X-RAY DIFFRACTIONt_gen_planes8225
X-RAY DIFFRACTIONt_it545320
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion7695
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact63314
X-RAY DIFFRACTIONt_bond_d545320.01
X-RAY DIFFRACTIONt_angle_deg738621.06
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion17.73
LS refinement shellResolution: 2.58→2.69 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3199 83 2.8 %
Rwork0.2525 2884 -
all0.2548 2967 -
obs--100 %
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)
11.7280.11610.68373.4441-0.03182.05630.0632-0.11970.18950.2452-0.19440.3813-0.037-0.11570.1312-0.0476-0.01910.1024-0.1393-0.0649-0.0873-59.5132-11.4107-1.7754
22.1497-1.79050.09165.28091.63082.9203-0.18580.08230.0513-0.0514-0.17390.1023-0.3467-0.41530.35970.001-0.0217-0.0705-0.2474-0.0298-0.1399-96.5506-14.007-26.395
33.5719-0.18312.47444.11921.25986.9890.0613-0.13010.2058-0.2299-0.2410.38310.5411-0.34560.1797-0.08170.0305-0.1095-0.2798-0.1232-0.1232-92.49252.60335.8582
42.7891-0.7903-0.51863.44470.75972.62230.08540.3688-0.2736-0.1095-0.0947-0.15560.1531-0.00250.0094-0.08550.0457-0.0165-0.0839-0.0738-0.1032-53.2768-31.1747-31.8415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A21 - 225
2X-RAY DIFFRACTION2{ B|* }B21 - 224
3X-RAY DIFFRACTION3{ C|* }C21 - 226
4X-RAY DIFFRACTION4{ D|* }D21 - 225

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