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- PDB-3v70: Crystal Structure of Human GTPase IMAP family member 1 -

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Basic information

Entry
Database: PDB / ID: 3v70
TitleCrystal Structure of Human GTPase IMAP family member 1
ComponentsGTPase IMAP family member 1
KeywordsIMMUNE SYSTEM / immunity / structural genomics consortium / gtpase / immunity-associated protein / SGC
Function / homology
Function and homology information


membrane => GO:0016020 / Golgi membrane / endoplasmic reticulum membrane / GTP binding / endoplasmic reticulum
Similarity search - Function
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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.206 Å
AuthorsNedyalkova, L. / Shen, Y. / Tong, Y. / Tempel, W. / Mackenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. ...Nedyalkova, L. / Shen, Y. / Tong, Y. / Tempel, W. / 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 1
Authors: Nedyalkova, L. / Shen, Y. / Tong, Y. / Tempel, W. / Mackenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Andrews, D.W. / Park, H.
History
DepositionDec 20, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionJan 11, 2012ID: 3LXW
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: GTPase IMAP family member 1
B: GTPase IMAP family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3766
Polymers55,4412
Non-polymers9354
Water79344
1
A: GTPase IMAP family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1883
Polymers27,7201
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTPase IMAP family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1883
Polymers27,7201
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.348, 81.348, 178.934
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein GTPase IMAP family member 1 / Immunity-associated protein 1 / hIMAP1


Mass: 27720.316 Da / Num. of mol.: 2 / Fragment: UNP residues 25-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GIMAP1, IMAP1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q8WWP7
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.06 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 25% w/v PEG3350, 0.2M sodium chloride, 0.1M HEPES. GDP and 1:100 dispase were also added., pH 7.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97948 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 21552 / % possible obs: 97.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.098 / Χ2: 1.846 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.241.90.4228510.866175.6
2.24-2.282.10.4179281.088185
2.28-2.322.40.37910200.907190.6
2.32-2.372.80.37110710.907196
2.37-2.423.10.35310750.941198.1
2.42-2.483.50.32610870.955199.4
2.48-2.543.90.29811451.017199.9
2.54-2.614.30.28311130.9871100
2.61-2.694.50.25410981.0021100
2.69-2.774.60.22210901.031100
2.77-2.874.80.18111181.2211100
2.87-2.994.80.1511031.3251100
2.99-3.124.90.12811201.5021100
3.12-3.294.90.10710961.8251100
3.29-3.494.80.0911272.1651100
3.49-3.764.80.08510852.8651100
3.76-4.144.70.07911053.2221100
4.14-4.744.80.06711323.2491100
4.74-5.974.80.06510982.6631100
5.97-504.60.06510903.692197.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished model of GIMAP4. Related to PDB entry 3LXX.

3lxx


Resolution: 2.206→29.822 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.927 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED Programs PHENIX, ARP/WARP and COOT were also used during refinement, as was the MOLPROBITY server.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1045 4.851 %THIN SHELLS (SFTOOLS)
Rwork0.2125 ---
obs0.214 21544 96.818 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 86.22 Å2 / Biso mean: 32.343 Å2 / Biso min: 18.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.206→29.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3156 0 58 44 3258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193303
X-RAY DIFFRACTIONr_bond_other_d0.0050.022157
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9694501
X-RAY DIFFRACTIONr_angle_other_deg1.02335215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3835433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.8722.555137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12915494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1651534
X-RAY DIFFRACTIONr_chiral_restr0.0660.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023762
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02711
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 (%)
2.206-2.26300.321239165374.955
2.263-2.3250.354720.311352159589.279
2.325-2.3920.301870.2751413156395.969
2.392-2.4650.288820.2711411151098.874
2.465-2.5450.316980.2571339144199.722
2.545-2.6340.324780.2313361414100
2.634-2.7330.235820.2312711353100
2.733-2.8430.24490.22112701319100
2.843-2.9680.217440.22111881232100
2.968-3.1120.257490.24211801229100
3.112-3.2780.271600.22511041164100
3.278-3.4740.266600.23210181078100
3.474-3.7110.224760.2089391015100
3.711-4.0030.22180.18935953100
4.003-4.3770.183220.166851873100
4.377-4.880.201610.151724785100
4.88-5.610.227540.175657711100
5.61-6.8110.215170.224579596100
6.811-9.3910.26230.17944647199.575
9.391-29.8220.18130.17424728192.527
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)
14.04040.0989-0.86412.6494-0.24532.51590.09810.04260.02080.1603-0.0761-0.19740.0183-0.0646-0.02210.0926-0.0338-0.02320.04150.03590.040315.645117.7059120.5044
22.36150.07330.16774.5093-0.7743.22220.0817-0.08260.1912-0.0025-0.12490.0089-0.44120.12220.04320.1461-0.0365-0.0260.1047-0.02050.031118.071529.898990.9176
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 251
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION1A1 - 3
4X-RAY DIFFRACTION1A254 - 273
5X-RAY DIFFRACTION2B27 - 251
6X-RAY DIFFRACTION2B401 - 402
7X-RAY DIFFRACTION2B4 - 6
8X-RAY DIFFRACTION2B254 - 271

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