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- PDB-6z3e: Crystal structure of GDP-bound human GIMAP5, amino acid residues 1-276 -

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Basic information

Entry
Database: PDB / ID: 6z3e
TitleCrystal structure of GDP-bound human GIMAP5, amino acid residues 1-276
ComponentsGTPase IMAP family member 5
KeywordsHYDROLASE / GTPase / immunity
Function / homology
Function and homology information


multivesicular body membrane / membrane => GO:0016020 / lysosomal membrane / GTP binding
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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.80038678769 Å
AuthorsSchwefel, D. / Daumke, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: Crystal structure of GDP-bound human GIMAP5
Authors: Schwefel, D. / Daumke, O.
History
DepositionMay 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTPase IMAP family member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6073
Polymers31,1391
Non-polymers4682
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-18 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.280, 57.230, 106.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein GTPase IMAP family member 5 / Immune-associated nucleotide-binding protein 5 / Immunity-associated nucleotide 4-like 1 protein / ...Immune-associated nucleotide-binding protein 5 / Immunity-associated nucleotide 4-like 1 protein / Immunity-associated nucleotide 5 protein / hIAN5 / Immunity-associated protein 3


Mass: 31139.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GIMAP5, IAN4L1, IAN5, IMAP3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96F15
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 16% 2-propanol 50 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 6579 / % possible obs: 98 % / Redundancy: 4.7 % / Biso Wilson estimate: 25.6825591945 Å2 / Rmerge(I) obs: 0.0166 / Net I/σ(I): 9.37
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.475 / Num. unique obs: 595

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xtp

2xtp


Resolution: 2.80038678769→39.0355231003 Å / SU ML: 0.367330651165 / Cross valid method: FREE R-VALUE / σ(F): 1.99501071312 / Phase error: 25.3287354556
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.268149989389 309 4.6967624259 %
Rwork0.215153938036 6270 -
obs0.217666000947 6579 99.0514905149 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.7779106911 Å2
Refinement stepCycle: LAST / Resolution: 2.80038678769→39.0355231003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 29 14 1915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003918529067091966
X-RAY DIFFRACTIONf_angle_d0.8193415186612662
X-RAY DIFFRACTIONf_chiral_restr0.0452000291228294
X-RAY DIFFRACTIONf_plane_restr0.0052578644946346
X-RAY DIFFRACTIONf_dihedral_angle_d14.29061451261630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8004-2.90040.389409300673310.281011119735595X-RAY DIFFRACTION95.865237366
2.9004-3.01650.414787683567320.259735350036603X-RAY DIFFRACTION98.9096573209
3.0165-3.15380.261874424713230.226378875194623X-RAY DIFFRACTION99.0797546012
3.1538-3.320.309648180709290.224105775997605X-RAY DIFFRACTION99.3730407524
3.32-3.52780.249402451446270.230129136357623X-RAY DIFFRACTION99.0853658537
3.5278-3.80.262066270501290.202460228285633X-RAY DIFFRACTION99.5488721805
3.8-4.1820.283699716613310.192669429453631X-RAY DIFFRACTION99.6987951807
4.182-4.78620.219549530579250.178472180032635X-RAY DIFFRACTION100
4.7862-6.02660.27517024657370.2055956971641X-RAY DIFFRACTION99.5594713656
6.0266-390.204964808956450.218593340949681X-RAY DIFFRACTION99.316005472
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)
11.99718763149-0.45955894891-0.3263959044361.96565076036-0.3132272524243.769937222070.07364539313120.202625075066-0.545254118038-0.0311967522988-0.1116083696560.2232394538790.1017312996950.03833939190460.08044782953070.0743948746959-0.04423303293620.01999168813370.111127672982-0.06470358027060.13752575205816.1379746315-0.42252582238720.2385783104
21.777978922280.48951618693-0.1244512073382.43177184503-0.8952326260990.7087989984410.209185717421-0.12315650947-0.3202169162750.106464149115-0.273329732431-0.110247976735-0.009552025795480.2268876075010.1057211813350.1429054553490.01144593152620.002385105109790.1657918986760.006630141056190.17348800447920.21415140066.5725016698519.5580336896
31.879812074910.4567786825660.1573000395551.590714530650.4463584966941.15165963854-0.191180763323-0.1874057731780.140694671683-0.1453199535410.1674518756970.3425067407180.0860880259829-0.1926648403470.007195089675310.1027431572450.0345184767709-0.05079670050680.147109653483-0.007107452188110.2071115091482.754543394886.90292024517.1487922524
40.429886568363-0.131038500740.1874749165121.52965768607-0.614012349010.746964462801-0.001026961412780.151502192848-0.150366847425-0.4256157321910.02081775690360.141303668490.27795879194-0.05586609527530.06721626401180.241201090801-0.05389804892340.04027256046450.101814035596-0.03940133163170.34307984274310.2106392732-0.3080172839089.59591765612
55.46112018060.302142797792-1.73355295341.52349104547-0.1952178362132.220246492370.6211710967320.6352244707850.797434031958-0.44995096772-0.4272019692120.0189177323387-0.396775501110.274951436058-0.141626166040.467292343688-0.1094965796890.09482740297760.2616930193670.005517824120430.21209168837124.117354167321.25410094139.56682699361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 27:56)
2X-RAY DIFFRACTION2(chain A and resseq 57:108)
3X-RAY DIFFRACTION3(chain A and resseq 109:180)
4X-RAY DIFFRACTION4(chain A and resseq 181:231)
5X-RAY DIFFRACTION5(chain A and resseq 232:263)

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