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- PDB-7zhf: GPN-loop GTPase from Sulfolobus acidocaldarius closed state (GppNHp) -

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Basic information

Entry
Database: PDB / ID: 7zhf
TitleGPN-loop GTPase from Sulfolobus acidocaldarius closed state (GppNHp)
ComponentsGTPase
KeywordsUNKNOWN FUNCTION / GPN-loop / self-activating / GTPase / homodimer
Function / homologyGPN-loop GTPase / Conserved hypothetical ATP binding protein / GTPase activity / GTP binding / P-loop containing nucleoside triphosphate hydrolase / metal ion binding / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKorf, L. / Essen, L.-O.
Funding support Germany, 1items
OrganizationGrant numberCountry
Volkswagen Foundation Germany
CitationJournal: Mbio / Year: 2023
Title: Archaeal GPN-loop GTPases involve a lock-switch-rock mechanism for GTP hydrolysis.
Authors: Korf, L. / Ye, X. / Vogt, M.S. / Steinchen, W. / Watad, M. / van der Does, C. / Tourte, M. / Sivabalasarma, S. / Albers, S.-V. / Essen, L.-O.
History
DepositionApr 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5345
Polymers30,8601
Non-polymers6744
Water3,477193
1
A: GTPase
hetero molecules

A: GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,06810
Polymers61,7202
Non-polymers1,3488
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6830 Å2
ΔGint-78 kcal/mol
Surface area20930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.305, 84.950, 75.322
Angle α, β, γ (deg.)90.000, 95.618, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

21A-530-

HOH

31A-592-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GTPase


Mass: 30859.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: ATY89_00095, ATZ20_03140 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0U2WWJ1

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Non-polymers , 5 types, 197 molecules

#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.018 M CaCl2, 0.09M Sodium acetate pH=4.6, 27% (v/v) MPD, 10% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2020 / Details: flexible two-stage focusing X-ray optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→41.09 Å / Num. obs: 24163 / % possible obs: 90.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 41.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.027 / Rrim(I) all: 0.038 / Χ2: 0.71 / Net I/σ(I): 9.1
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 24086 / CC1/2: 0.92 / Rpim(I) all: 0.385 / Rrim(I) all: 0.573 / Χ2: 1.07 / % possible all: 54.9

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
xia2data scaling
BALBESphasing
xia2data reduction
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YR7

1yr7


Resolution: 1.8→41.09 Å / SU ML: 0.1564 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.3241
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.204 795 3.3 %
Rwork0.1725 23286 -
obs0.1735 24081 89.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.72 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 40 193 2194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062117
X-RAY DIFFRACTIONf_angle_d0.8122899
X-RAY DIFFRACTIONf_chiral_restr0.0536340
X-RAY DIFFRACTIONf_plane_restr0.006367
X-RAY DIFFRACTIONf_dihedral_angle_d13.9358775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.910.2886960.2732757X-RAY DIFFRACTION64.07
1.91-2.060.2821460.23294084X-RAY DIFFRACTION94.44
2.06-2.270.22541390.20124097X-RAY DIFFRACTION95.53
2.27-2.60.20431310.1954103X-RAY DIFFRACTION94.19
2.6-3.270.23751460.20284204X-RAY DIFFRACTION96.84
3.27-41.090.18011370.14724041X-RAY DIFFRACTION91.97
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)
10.9257772658480.2406293931221.45654163231.861137218910.8071201130972.3926042494-0.103161604786-0.19998476506-0.1221968136490.631338431618-0.03731208365870.2872791323031.17360543684-0.6576050538890.1829641360510.694516626139-0.004460126881120.07767643743630.4291024653720.02839921107290.45316835261514.892923364638.242967273464.7083800376
24.27781521421-0.6395786103390.9262310907153.81064480433-1.629513706436.21026019624-0.207653700808-0.31601402587-0.3154117482550.7654113610770.235563213112-0.03361822288771.104273620580.463488245961-0.04388412224890.7402557813380.177432654245-0.01716851866460.4464852937550.04603702025920.41375129752124.962171065633.64720662157.6921252916
37.88857124078-2.036405315994.572105864793.08379387027-1.265372875044.741071908730.002548085621751.22481040833-2.216660443-0.1609087949710.8829815277720.3852311295591.98541348457-0.792834198672-0.8662377940591.10529101379-0.4424563001650.02987540535750.724524705075-0.1028537507930.97972054457510.387341367626.048928652241.3399791547
42.667248319860.6456568708980.2094175131212.50083263784-2.437975634958.138245017-0.730878477059-0.597442515471-1.263349381930.316017385578-0.009070242066650.393064594092.06379404457-1.421240921680.626060490860.748618470233-0.1825673208580.1985915156910.6637711392260.1487203655640.7455121506638.4632095315132.644638007449.941887166
52.92312922278-0.1160897994470.03329691523.6850642873-0.9962618071446.87527451145-0.032463052874-0.1378427572970.1450639193950.2462814912830.2087963075070.130534132006-0.103818581169-0.102776324906-0.1996101215170.2513490612910.02779933755860.006129244136020.241489894431-0.008876516013290.27380255212321.411179650846.243943635548.6884464801
66.08387135374-0.3796850866332.556934214755.14070594827-0.8439614656043.222314414240.1569006886940.285874289281.0775486867-0.2158863440540.0149135260599-0.349854159542-0.7956669834270.910481150035-0.177725725240.719722936334-0.2291990648290.2449264061090.677050709705-0.1126106293090.74395023036133.06893349560.502129076139.5616251101
77.072295191591.61623394145-5.2350290164.01381361340.8188321733527.517339927940.219071169853-1.001374631950.4317979279080.7384523221170.245721796064-0.371291879468-0.6165129632241.41999779518-0.437539657920.483190810006-0.0976237914704-0.1117973822940.737535269284-0.08934198104510.37908365191530.961196041249.067965370357.8526657813
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -9 through 13 )-9 - 131 - 23
22chain 'A' and (resid 14 through 51 )14 - 5124 - 61
33chain 'A' and (resid 52 through 68 )52 - 6862 - 78
44chain 'A' and (resid 69 through 93 )69 - 9379 - 103
55chain 'A' and (resid 94 through 175 )94 - 175104 - 185
66chain 'A' and (resid 176 through 212 )176 - 212186 - 222
77chain 'A' and (resid 213 through 240 )213 - 240223 - 250

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