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- PDB-3lxx: Crystal structure of human GTPase IMAP family member 4 -

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Basic information

Entry
Database: PDB / ID: 3lxx
TitleCrystal structure of human GTPase IMAP family member 4
ComponentsGTPase IMAP family member 4
KeywordsIMMUNE SYSTEM / structural genomics consortium / SGC / Coiled coil / GTP-binding / Nucleotide-binding
Function / homology
Function and homology information


GTP binding / cytosol
Similarity search - Function
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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / sad / Resolution: 2.15 Å
AuthorsShen, Y. / Nedyalkova, L. / Tong, Y. / Tempel, W. / Mackenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. ...Shen, Y. / Nedyalkova, L. / 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 4
Authors: Shen, Y. / Nedyalkova, L. / Tong, Y. / Tempel, W. / Mackenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Andrews, D.W. / Park, H.
History
DepositionFeb 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTPase IMAP family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7955
Polymers27,3271
Non-polymers4684
Water30617
1
A: GTPase IMAP family member 4
hetero molecules

A: GTPase IMAP family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,58910
Polymers54,6542
Non-polymers9358
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2230 Å2
ΔGint-18 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.266, 102.663, 100.555
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein GTPase IMAP family member 4 / Immunity-associated protein 4 / Immunity-associated nucleotide 1 protein / IAN-1 / hIAN1


Mass: 27327.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GIMAP4, IAN1, IMAP4, MSTP062 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q9NUV9
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 1.95 Å3/Da / Density % sol: 36.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.8
Details: 25% PEG-3350, 0.25M sodium/potassium tartrate, 0.1M Hepes. 1:100 dispase was added, pH 7.8, VAPOR DIFFUSION, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B10.98013
SYNCHROTRONAPS 23-ID-B20.97948
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDNov 21, 2009
MARMOSAIC 300 mm CCD2CCDNov 19, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.980131
20.979481
ReflectionResolution: 2.15→20 Å / Num. obs: 11706 / % possible obs: 96.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.067 / Χ2: 1.916 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.15-2.192.80.3564391.50673
2.19-2.233.40.44841.4482.9
2.23-2.274.20.3835281.49489.3
2.27-2.324.60.3035701.48593.1
2.32-2.375.20.2725611.37397.4
2.37-2.425.50.2645991.35798.7
2.42-2.4860.2295771.35899.8
2.48-2.556.40.26071.41299.5
2.55-2.626.60.1665961.398100
2.62-2.7170.1495951.37100
2.71-2.87.10.1326041.364100
2.8-2.927.20.1035991.61100
2.92-3.057.20.0936031.763100
3.05-3.217.30.0756101.909100
3.21-3.417.20.0636032.017100
3.41-3.677.10.0536112.208100
3.67-4.047.10.0516182.733100
4.04-4.617.10.0466252.94100
4.61-5.796.90.0456262.793100
5.79-206.30.0416513.1697.3

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Phasing

PhasingMethod: sad

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.15→19.088 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.278 / WRfactor Rwork: 0.242 / SU B: 12.83 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.291 564 4.856 %RANDOM
Rwork0.252 ---
obs0.254 11614 96.864 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.778 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å20 Å2
2---0.467 Å20 Å2
3----0.763 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 31 17 1277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221274
X-RAY DIFFRACTIONr_bond_other_d0.0010.02825
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.9971731
X-RAY DIFFRACTIONr_angle_other_deg0.85432010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4415165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.79922.88945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0115197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3391510
X-RAY DIFFRACTIONr_chiral_restr0.0710.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021403
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02258
X-RAY DIFFRACTIONr_mcbond_it0.5741.5833
X-RAY DIFFRACTIONr_mcbond_other0.1151.5345
X-RAY DIFFRACTIONr_mcangle_it1.1121312
X-RAY DIFFRACTIONr_scbond_it1.8173441
X-RAY DIFFRACTIONr_scangle_it2.7784.5419
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 (%)
2.15-2.2050.481420.33663586478.356
2.205-2.2650.42450.30568183287.26
2.265-2.3290.415340.29873481594.233
2.329-2.40.371420.26875380698.635
2.4-2.4770.356490.2771076399.476
2.477-2.5630.252290.25571574799.598
2.563-2.6580.316430.253680723100
2.658-2.7640.374320.267687719100
2.764-2.8840.31290.254630659100
2.884-3.0210.291300.251610640100
3.021-3.180.339260.252594620100
3.18-3.3680.239230.256555578100
3.368-3.5920.253180.225537555100
3.592-3.8690.192290.223491520100
3.869-4.220.249220.21472494100
4.22-4.690.283240.193409433100
4.69-5.3620.216180.246378396100
5.362-6.4410.424130.286330343100
6.441-8.6310.35190.31527128299.291
8.631-19.0880.26370.317820192.04
Refinement TLS params.Method: refined / Origin x: 13.1023 Å / Origin y: 36.3916 Å / Origin z: 11.1784 Å
111213212223313233
T0.0679 Å2-0.0281 Å20.0254 Å2-0.0404 Å2-0.0147 Å2--0.0591 Å2
L2.4764 °2-0.4899 °20.7444 °2-3.0016 °20.0434 °2--5.0453 °2
S0.0047 Å °-0.0388 Å °-0.0838 Å °-0.1177 Å °-0.0751 Å °0.2505 Å °0.341 Å °-0.3253 Å °0.0704 Å °

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