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- PDB-7zhk: GPN-loop GTPase from Sulfolobus acidocaldarius open state (GDP) -

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Basic information

Entry
Database: PDB / ID: 7zhk
TitleGPN-loop GTPase from Sulfolobus acidocaldarius open state (GDP)
ComponentsGTPase
KeywordsUNKNOWN FUNCTION / GPN-loop / self-activating / GTPase / homodimer
Function / homologyGPN-loop GTPase / Conserved hypothetical ATP binding protein / hydrolase activity / nucleotide binding / P-loop containing nucleoside triphosphate hydrolase / GUANOSINE-5'-DIPHOSPHATE / GTPase
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
B: GTPase
C: GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9829
Polymers92,5793
Non-polymers1,4036
Water5,999333
1
A: GTPase
C: GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6556
Polymers61,7202
Non-polymers9354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTPase
hetero molecules

B: GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6556
Polymers61,7202
Non-polymers9354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Unit cell
Length a, b, c (Å)117.689, 141.878, 100.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 182 or resid 184 through 187 or resid 189 through 240))
d_2ens_1(chain "B" and (resid 1 through 182 or resid 184 through 187 or resid 189 through 240))
d_3ens_1(chain "C" and (resid 1 through 182 or resid 184 through 187 or resid 189 through 240))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERMETMETAA1 - 18220 - 201
d_12SERSERGLUGLUAA184 - 187203 - 206
d_13GLYGLYALAALAAA189 - 240208 - 259
d_21SERSERMETMETBB1 - 18220 - 201
d_22SERSERGLUGLUBB184 - 187203 - 206
d_23GLYGLYALAALABB189 - 240208 - 259
d_31SERSERMETMETCC1 - 18220 - 201
d_32SERSERGLUGLUCC184 - 187203 - 206
d_33GLYGLYALAALACC189 - 240208 - 259

NCS oper:
IDCodeMatrixVector
1given(-0.999975258167, -0.00637431440834, -0.00297509152563), (-0.00164946574825, -0.19866616708, 0.980065831116), (-0.00683829777851, 0.980046489802, 0.198650737501)-39.0377640863, 0.0288543295816, -0.122732248273
2given(-0.999905266357, -0.00844423480792, 0.010869830311), (0.00364272690943, -0.923892263665, -0.382635356025), (0.0132736149237, -0.382559511761, 0.923835500026)-77.9443907223, -49.334967838, -9.26276308226

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Components

#1: Protein GTPase


Mass: 30859.830 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: ATY89_00095, ATZ20_03140 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U2WWJ1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M MgCl2, 0.1 M MES pH=5.5, 40% (v/v) PEG400

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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: Nov 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→45.29 Å / Num. obs: 30856 / % possible obs: 93.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 52.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.05 / Rrim(I) all: 0.083 / Χ2: 1.02 / Net I/σ(I): 10.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 6660 / CC1/2: 0.325 / Rpim(I) all: 1.063 / Rrim(I) all: 1.628 / Χ2: 1.02 / % possible all: 67.3

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
xia2data reduction
PHASERphasing
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZHF

7zhf


Resolution: 2.4→45.29 Å / SU ML: 0.2698 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1522
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2469 1283 5.04 %
Rwork0.1879 24182 -
obs0.1909 25465 76.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.36 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5653 0 87 333 6073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225888
X-RAY DIFFRACTIONf_angle_d0.5458020
X-RAY DIFFRACTIONf_chiral_restr0.0418950
X-RAY DIFFRACTIONf_plane_restr0.00361003
X-RAY DIFFRACTIONf_dihedral_angle_d14.50072171
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.596935861527
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.763930193554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50.3322360.2549680X-RAY DIFFRACTION19.68
2.5-2.610.2769680.24961281X-RAY DIFFRACTION37.18
2.61-2.750.32131100.25632192X-RAY DIFFRACTION63.47
2.75-2.920.27521650.2312770X-RAY DIFFRACTION80.28
2.92-3.140.30591750.20963188X-RAY DIFFRACTION91.78
3.14-3.460.24712010.20753455X-RAY DIFFRACTION99.13
3.46-3.960.25631590.16563486X-RAY DIFFRACTION99.26
3.96-4.990.21261840.14743523X-RAY DIFFRACTION99.7
4.99-45.290.2351850.20353607X-RAY DIFFRACTION98.26
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)
13.66640991375-0.5240867979661.052899958765.15424010907-0.3795275478725.22504230020.05732954146950.563977043539-0.229693532682-0.9606178844790.06987801386970.2413470755180.209452479246-0.00796775657636-0.1693347569320.403955811442-0.0534673069904-4.84897154683E-50.3740587192890.02651739335960.286799259595-25.4614314937-27.6201724679-16.7013695491
25.147595712750.3783021817370.4728392967045.281020414633.751467339247.746978676620.567406784387-0.084907292583-1.52578745482-0.747206534851-0.212703556514-0.05690910510110.8281250135520.0263430675329-0.285503114670.571214813979-0.0122521313142-0.08296078972430.360002851241-0.07881285856060.687372804702-20.6857508653-35.6101570513-15.7301310045
34.518493323860.1187336225870.1358246897672.474108851220.2561941807033.14626012467-0.062615225811-0.165365956811-0.881065605863-0.066580843942-0.006648185621060.2939211991290.511460196129-0.2084255989350.08438189991370.257098829664-0.0895535207715-0.05479180991140.3074031592090.06624011400120.392531577229-30.3027617852-26.5364295564-1.89644148566
45.403904000952.02571833365-1.851496119335.57760314597-0.5296356258265.006410562-0.0962006217555-0.624252078195-0.149675786370.738589279934-0.04450912483510.366844278487-0.125137588435-0.5053518031630.115584168610.385752137905-0.0244070446283-0.05673867135570.5663822050810.1031154871480.382233149687-30.3390763-17.295049878611.3350716047
56.41114172765-0.7839861255273.044011971336.90922905859-0.6027240814184.83924606690.108865681389-0.6618438574120.007929158696521.774291174550.156665026969-2.35265371729-0.323661607869-0.363340131645-0.07328949603210.362308330703-0.00540656451802-0.08764767978330.5020305651610.06469045367220.397455836-14.3471329804-28.53908486592.60287566023
67.95924603991-0.6324714008920.3968868797612.900248306460.5390685209972.99188221891-0.1381179847950.596360143544-0.494725037273-0.09645832857250.02272969713120.6163868148650.257958535883-0.4336917919160.02695996266170.467135000473-0.1244257564120.06322752259550.472890392374-0.06131974410560.361585442731-21.7847006312-3.51735914056-27.5425857083
76.33056521284-0.471699503269-1.804070812624.31424576145-1.482244091687.32941545118-0.209344263817-0.399672695176-0.715433886112-0.4312703656770.08097360374560.006163588726140.6643946372370.2321893181180.1491410483820.568133099829-0.1460044533150.1150762160920.467702067673-0.004143717937260.429223177084-15.9416342392-14.0424583098-28.4793535761
85.92769715097-0.721223295667-0.5461866824580.519046933478-1.442555736456.100257851750.3521332273330.452604045685-0.749445923428-0.474318036302-0.071894609248-0.06280924059571.706190654210.270361853718-0.1370290225360.9117951032360.02716065253040.226261925070.633073494905-0.1665498490260.550646037693-2.41070929222-17.7312845878-33.9494594212
92.12718730189-0.2742116127791.303868724146.410106128583.245328514092.77621438569-0.4704013288061.17081579298-0.244921107742-0.864346756259-0.268082235180.7010363918150.162587288110.3466797130210.510980001840.644708821768-0.08263955006320.1160843592450.847214816597-0.02305236319430.535030146366-18.0709736549-8.15911454434-38.1302279446
103.553708760510.147557818139-1.727133233912.53319485717-0.6970098915171.92658909204-0.07580028736450.4743971182870.247910490992-0.5730051416750.186402118036-0.134142051951-0.173849463125-0.19088467956-0.09297184294110.399617201647-0.053661170930.1194863238830.3630785482790.005760034163910.297659494543-7.138840910543.18265920281-27.8377873676
113.372529964130.9416947403720.4108929435764.226573310941.082675124070.274596760367-0.0002109812903610.2216041779460.51374176262-0.214590432304-0.192413514783-0.358139297901-0.4622373766821.077651641610.05975884148430.3327783832830.04103319323090.1455445669060.4017170457250.02911595023980.347211423097-13.75847002794.69881026792-20.9941996628
127.346039802951.62772087523-6.348302997316.31947953033-1.182254741817.634251048050.7014020467050.0830195494280.8165311815370.704458967558-0.100397714005-0.63356147838-1.00014228020.720610489659-0.6901118121990.4366182726290.02434807156660.1306153020170.495789631384-0.02624609519830.532742842063-7.8466550486616.1142020091-10.0231252819
135.165870969552.39185684983-2.13826420373.91537019260.556682182717.355275065180.712543443580.4686573378691.54057351448-0.5393584014770.166244109696-0.605815559907-1.662795324790.996765277916-0.591110479450.664537652089-0.08066974551780.2629082646530.414381542687-0.03403610629760.8244198902810.4231741012920.4476390336-20.5274216216
148.924564702153.17102436889-0.8234272583018.582863147171.615128497294.946728139150.1044831843430.6521958469620.630507964711.026211977190.3079610165310.632108142116-0.399898356466-0.37877834371-0.3066238738090.28717821009-0.0203785138380.0558834497380.4448368737080.009498755841860.354608260211-19.00912288176.38116188049-17.5697894599
155.71183302352-1.888819857562.02131390644.52081293842-4.589156764014.85454112415-0.385625600095-0.3471032796330.107680970010.2438029720610.7549065313950.25768758067-0.800210712581-2.09394881470.08568197182820.6735034358240.1019355574790.07150909145420.5831268471010.04026994162910.449532434874-24.41250950658.23829179066-27.3665292196
165.592882652891.334464776330.9339102899463.383213071450.09133937677112.55748878026-0.222355505740.233168801095-0.113632296113-0.4202031872470.2263190555191.146186472430.358337625271-1.26099323511-0.03180002448890.372705013755-0.0536681997191-0.174583338940.886702390433-0.01341033036620.818629645623-59.0070317122-20.8686334938-10.7808904607
179.44172393219-3.17529480507-4.430661517896.122665336561.4198811537.636072767660.7794400366131.247188223270.162029115042-1.31794638384-0.0825329638411-0.287250308894-0.406877722114-0.480747349814-0.7379820844170.986294655594-0.182881023667-0.08414181359410.6037709792410.135007767150.513248492173-42.4981932924-12.3532223074-24.0541076783
188.42161901065-3.93943096779-4.846113991045.566706685291.69211835957.474102716850.638731044618-0.3329023808071.31355163982-1.129832444520.2660622276310.330047324957-1.20570805033-0.146044798907-0.9160153050580.730300916016-0.123777758321-0.125972367040.519641735433-0.1355415166930.965305180057-47.4036785875-8.7419058208-14.6104046156
195.70389074694-1.124206264771.536359516053.129624353680.8063304433015.244998404990.03498858742790.3212731346330.102768581017-0.2303469007440.2061634848111.10210979528-0.000480580872548-0.957127366307-0.03640041840710.310385484323-0.0745356480877-0.1146200644860.4745324548560.2442029319470.68546290665-51.2824302742-16.8481964844-7.61174449906
203.629970320592.09151560367-2.152169002131.21379571773-1.293234880439.461857174320.2359283154610.03173215833641.341559450250.023561876796-0.108506844094-0.994478222751-1.34488982837-0.7170634917460.1555566089730.7339912074460.0311626113415-0.09175548432530.293445418551-0.1176817181251.10196871156-49.4416879336-8.25895931792-3.54688057444
213.41391768591-1.14050276354-0.3012822568671.60048193170.08262050914115.39197690575-0.0537907943382-0.608667429251-0.8163673924990.08475405354440.0642378030390.5702873371930.746363088442-0.5169709359930.09521383252620.312856296523-0.09986353139340.01542580352530.5565949297450.1443094667050.664329172021-48.982655015-32.75015188991.73604692297
227.430488586320.762808213073.674657828552.704775111830.4432454112554.67749914034-0.0472565613211-0.78277019938-1.0189537680.321892534298-0.0796374565020.4700547535591.09895537386-0.255470540261-0.07547691284350.646329859937-0.06594672388130.1699837258960.7409376717720.3065650637140.768480887244-45.5040015412-35.60836048377.89981419866
230.7858560728011.47962986039-1.3883396446.531784097691.140696580686.206473172060.172148622487-0.363597613667-0.1826963978970.858581813146-0.4643448343250.859721338058-0.159955608637-0.9311315679350.4012972800910.479167987361-0.03370167717040.09589543745470.9015702657870.1807448629571.16227232193-63.2709673-24.06779723153.89854110596
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 82 )AA0 - 821 - 83
22chain 'A' and (resid 83 through 106 )AA83 - 10684 - 107
33chain 'A' and (resid 107 through 175 )AA107 - 175108 - 176
44chain 'A' and (resid 176 through 227 )AA176 - 227177 - 228
55chain 'A' and (resid 228 through 240 )AA228 - 240229 - 241
66chain 'B' and (resid 1 through 36 )BB1 - 361 - 36
77chain 'B' and (resid 37 through 51 )BB37 - 5137 - 51
88chain 'B' and (resid 52 through 82 )BB52 - 8252 - 82
99chain 'B' and (resid 83 through 106 )BB83 - 10683 - 106
1010chain 'B' and (resid 107 through 159 )BB107 - 159107 - 159
1111chain 'B' and (resid 160 through 175 )BB160 - 175160 - 175
1212chain 'B' and (resid 176 through 199 )BB176 - 199176 - 199
1313chain 'B' and (resid 200 through 212 )BB200 - 212200 - 212
1414chain 'B' and (resid 213 through 227 )BB213 - 227213 - 227
1515chain 'B' and (resid 228 through 240 )BB228 - 240228 - 240
1616chain 'C' and (resid 1 through 51 )CC1 - 511 - 51
1717chain 'C' and (resid 52 through 68 )CC52 - 6852 - 68
1818chain 'C' and (resid 69 through 93 )CC69 - 9369 - 93
1919chain 'C' and (resid 94 through 113 )CC94 - 11394 - 113
2020chain 'C' and (resid 114 through 127 )CC114 - 127114 - 127
2121chain 'C' and (resid 128 through 188 )CC128 - 188128 - 188
2222chain 'C' and (resid 189 through 227 )CC189 - 227189 - 227
2323chain 'C' and (resid 228 through 240 )CC228 - 240228 - 240

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