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- PDB-6yc7: Structure of adenylylated C. glutamicum GlnK -

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Basic information

Entry
Database: PDB / ID: 6yc7
TitleStructure of adenylylated C. glutamicum GlnK
ComponentsPII protein
KeywordsSIGNALING PROTEIN / PII / Corynebacteria / Nitrogen regulation / Post-translational modification / Adenylylation
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity
Similarity search - Function
Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII / P-II protein family profile. / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal
Similarity search - Domain/homology
ADENINE ARABINOSE-5'-PHOSPHATE / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / PII protein
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGrau, F.C. / Muller, Y.A.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Crystal structures of adenylylated and unadenylylated P II protein GlnK from Corynebacterium glutamicum.
Authors: Grau, F.C. / Burkovski, A. / Muller, Y.A.
History
DepositionMar 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PII protein
B: PII protein
C: PII protein
D: PII protein
E: PII protein
F: PII protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,38811
Polymers73,5726
Non-polymers1,8165
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19320 Å2
ΔGint-71 kcal/mol
Surface area24120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.444, 53.444, 179.951
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein
PII protein


Mass: 12262.013 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Corynebacterium glutamicum (bacteria) / References: UniProt: H7C694
#2: Chemical ChemComp-A5O / ADENINE ARABINOSE-5'-PHOSPHATE / Vidarabine phosphate


Type: RNA linking / Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: antineoplastic, antivirus*YM
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.06 M MgCl2, 0.06 M CaCl2, 0:1M MOPS pH 7.1, 0.1M HEPES pH 7.1, 15% (v/v) MPD, 15% (w/v) PEG 1000 and 15% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→22.97 Å / Num. obs: 53142 / % possible obs: 99.57 % / Redundancy: 5.1 % / Biso Wilson estimate: 30.05 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05774 / Net I/σ(I): 17.54
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 1.079 / Num. unique obs: 5326 / CC1/2: 0.634 / CC star: 0.881

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.17.1_3660refinement
Cootmodel building
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CY6
Resolution: 1.8→22.97 Å / SU ML: 0.191 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.0505
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2225 1288 2.43 %
Rwork0.1879 51808 -
obs0.1888 53096 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.23 Å2
Refinement stepCycle: LAST / Resolution: 1.8→22.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 0 116 278 5052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00944825
X-RAY DIFFRACTIONf_angle_d0.9776533
X-RAY DIFFRACTIONf_chiral_restr0.0676812
X-RAY DIFFRACTIONf_plane_restr0.0055805
X-RAY DIFFRACTIONf_dihedral_angle_d22.51631775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.29511390.27515772X-RAY DIFFRACTION99.75
1.87-1.960.26481440.23195774X-RAY DIFFRACTION99.53
1.96-2.060.30931350.20955791X-RAY DIFFRACTION99.41
2.06-2.190.22511380.20185706X-RAY DIFFRACTION99.4
2.19-2.360.2141440.18955752X-RAY DIFFRACTION99.92
2.36-2.590.21971380.20015770X-RAY DIFFRACTION99.92
2.6-2.970.25361500.2035827X-RAY DIFFRACTION99.97
2.97-3.740.24131500.18155672X-RAY DIFFRACTION99.22
3.74-22.970.18151500.16485744X-RAY DIFFRACTION99.39
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.2660123555430.166837637780.2201364394570.4484430399140.2449796453480.139679553198-0.00492944302984-0.129362629333-0.02418414772550.1039863902030.116075083171-0.0426232562240.05588269474810.2673705003430.0003973448781860.2558400551720.02026644824190.0224412370940.272055410387-0.005246866322790.239117119858-11.6134791713-12.888587278614.7017896512
20.440540733488-0.09571911441420.1873069722392.492797461630.3471626199910.149213637473-0.443986121186-0.8761165858320.2564739467050.9434706156110.399294521814-0.5836313174950.4964421416671.318515875240.2065670872350.4390182438790.134701135801-0.1219315837380.616096391707-0.007555602530620.393195776925-2.91058553007-15.732716966323.9703462723
30.5921288905750.0392627309353-0.8326563245410.0679789541256-0.1162007403811.29789446722-0.03494563558640.1483093516950.2633610412621.067239236870.660502065628-0.516966525984-1.522761277630.4074939899720.0185894306230.493185261549-0.03808875095140.04039235901260.7007413266920.0229522826280.529598921982-0.544495467286-9.5633691254716.8426540311
40.145753142523-0.140628225068-0.01030924235290.3305684963510.07949610211330.0814837751212-0.200449721479-0.5211891023370.2091950294080.06896756913460.103610166641-0.04688349827290.7033655518790.2153926494920.001196261674460.370442989579-0.01115716484210.0416407602610.412648490739-0.02275308799660.262866646365-15.689912943-7.3049894203524.626116036
50.5112980259650.364204842463-0.4542631577850.262118634341-0.2566903858240.412080353756-0.374057196055-0.168578205251-0.580855026681-0.131128372488-0.1101790133350.3949125568050.812073267358-1.04667880725-0.005417315679230.4966215744260.04576463611940.1156067115360.884496407764-0.01293394344480.845705646971-35.6971641788-7.2771854931332.141425617
60.2829314158-0.189616715111-0.02872609474390.4957486643830.4157776417760.124501006183-0.012119972646-0.335879968919-0.1806724498920.117546943017-0.1112151338760.03274931356410.09690480810460.395034557526-0.0003173833980640.3116190542010.06207426396690.03206520556530.361339810961-0.008539709538830.241733868691-11.6779791468-10.89873292318.8109166957
71.316089213160.4180920502680.5015506501380.8025752215720.5447201959340.58876597029-0.127272487426-0.0486188284799-0.221766419609-0.0444794162914-0.0342413013048-0.0951959370190.2648752567570.417461531634-0.05678026568560.2347109860690.1049328539660.01069375658540.2679569721870.01306141718670.241511290824-5.56832043937-19.753480782413.0754795184
80.4126315551140.2074071314980.03638839747190.2141047464540.2515209843170.7899592773040.198988230048-0.102158654376-0.2284182648540.615913179429-0.2044861066570.5922114967260.3407392193630.533686502769-0.02327236748140.5846982911090.06392910661620.09535128939840.334886808440.1254019538170.438832384176-15.5488081306-24.629879705525.1836157884
90.000667600300460.07171767703590.05585195110270.02772344894340.09064532275530.0880016607933-0.0769091561455-0.132721711919-0.0255151479911-0.228014555110.2007929510240.2195153139950.41914139524-0.04295460715744.12674035936E-50.2385667176010.01049875990330.05534367297280.255512517898-0.003967549454590.250958766871-14.8436478605-14.417001225910.5940531812
101.01701440819-0.6329705183550.2324062665530.6806031485340.2319619724732.556559854670.154793541491-0.0033779712217-0.120930784357-0.1271426137360.288768113732-0.410968102135-0.1475813602740.2842814194530.4436591360590.219369946152-0.02141839736270.05349353533760.265900901346-0.07945532383140.312882254843-1.89490294379-0.1386304508095.39666097913
111.81353197630.222225383816-1.219845301010.727580382859-0.9108797447041.591346381060.219618827921-0.2308809784560.2788303556590.134057186180.01707090708090.0597304963887-0.397373262359-0.3605580665750.2244688114940.3257566975660.0699367450541-0.002040531068640.211128217608-0.07916697256780.277980643888-14.24816623568.2749154850314.0932714701
120.4247829783470.168341085725-0.2686134596640.00162711477637-0.09447929874330.1503227328430.6008114793210.5072522813960.0836509865820.202765684596-0.297261933849-0.1156228624080.365259432150.8234400223110.01348531215860.6941329138530.208069867596-0.1191625857080.821930154892-0.002635344509210.642397278374-0.461770010651-11.005705536333.1143893151
131.19311427848-0.481537425526-1.264033470751.280810514880.2851093483651.33796138440.183545953079-0.07990330696950.214985684111-0.09927378576570.0262538131669-0.191986332582-0.2914000677860.07419245856070.00360879251780.270061107582-0.01472420681640.02886180568150.219308688353-0.03184628347340.308735114166-9.823441237445.307943973489.29774143389
140.4399429879310.06274546879750.06168626679070.405644114865-0.1725939309450.5001696918550.07973316516540.3550815573170.1484596656-0.197053591705-0.02921478145210.0902288969984-0.121297939811-0.306012817312-0.00439016747410.2606019848480.0965719625327-0.03260074081690.413760222512-0.02014883851090.343108129275-30.99439810431.214441317984.45972682575
151.63667655640.1852298749541.064947356941.861487104540.3681888022361.084069756930.0248010696976-0.1203526405260.04755560720420.143214970667-0.1167056179440.08445873581530.0787059597364-0.321066214007-0.002886132444750.175057602640.0009415387548510.03115431180950.323038850868-0.05002257373280.261367101871-29.7684969118-5.4130135323615.9730298645
160.4301183884230.1558114583570.14581276290.3543259920660.3803476909080.3297199156630.1073525740770.0171835592937-0.249257416834-0.456362883134-0.244819185550.05175444110560.573583240109-0.06211179002790.0002473283949680.310005005924-0.01609069482370.01902330985230.2386266067250.003911294047120.381909661117-17.9843309479-23.338737381212.4346169308
170.5124131573160.398558660101-0.1691757906132.078841271371.290417920.8307745403970.02770250401210.182030231329-0.0339747792462-0.2729733918180.111928221477-0.108482131316-0.1024325039730.2978568154390.01841318111980.229900299268-0.05088543591340.03603338512150.3582809868360.003801263181590.184459267215-7.38413753512.599166373539.2732626444
180.0696718760304-0.0191757697695-0.03906571193440.03884465999440.127453113415-0.0315767760889-0.3293786290130.382083966051-0.24953070730.3158235306740.514593004638-0.683853479252-0.714300338786-0.702014746290.003579404427250.4525101571540.05915522066480.007556962871430.8916485973480.1632123346470.9500595041-33.04351203198.6507357477727.2929170158
190.923493069732-0.5700280803460.07263460013820.9769888220030.5012571609760.5568326669450.009169194682760.1557854401890.0892320363912-0.172209053433-0.0107924226543-0.05976884790950.04520446501020.2329158872190.005061000022770.249657150948-0.100015220712-0.011646687350.292522951651-0.001749559910610.21619876844-8.167203248515.966087968644.4749690727
200.621904771232-0.131772699553-0.5847562258380.1691315967710.4460825046821.506518339660.1688926786720.369233516120.426405563022-0.483632343446-0.1794158964570.995193000075-0.7408758210510.507342665452-0.2787598931650.610660877613-0.0872679946373-0.1621276815020.2823502805830.1478377118660.50128542514-15.559719432324.587078598534.8435110395
210.4106865158770.5211386138330.6625858833791.425940135041.152595448811.121012445070.0541594510880.145682643937-0.1144658330610.06796119381660.172499770355-0.09392064826480.08470184833210.115722653680.05281867570220.1868092534390.0107354307372-0.02332439411120.256881546895-0.0413739296080.243282192865-5.58632939324.1916617151653.0800209194
221.931321459980.0469959457140.7822291049811.10699906417-1.10480323782.161574029010.1553680466340.31915202375-0.286836930652-0.161513952010.05310922615180.06541886239490.477074345943-0.3724414432620.5590064757260.330526858405-0.076719218296-0.008612832884140.230713646754-0.08971936499550.29215737349-14.1744158328-8.2576247611345.8903815899
230.202366862753-0.05276756227180.1079600400750.0171185208846-0.1110959760630.1180888460170.257675648298-0.578595822657-0.3045090067150.208696880678-0.574137307024-0.860965253773-0.9479247364671.04753094793-0.002337892786660.647985219007-0.1716803049430.07971402407360.875148858207-0.04576155502070.647548123845-0.90605278527711.632789155726.7131860534
241.01164371610.4567490263651.287780226540.5699566495250.0195440962011.611357025260.2095558032620.0528342061224-0.2000710963820.06473765425660.0352318920051-0.1084336480020.2876938450170.07766195315850.01220618928990.2918965639190.0105341055894-0.02707791691380.210988432432-0.04240621600890.285811928012-9.8495418188-5.3305071310950.8909117031
250.37142586991-0.106365701893-0.2204588064830.248627273613-0.1397721491340.7734198380950.0353990132569-0.530850666292-0.04263224639590.206766492379-0.05817300220410.04091692839140.14290643193-0.349713771314-0.002035191726280.263138562228-0.09817401935520.03114348596540.3824327370120.000467553051350.324796311789-31.0106319659-1.2411914732755.514117591
260.991343158221-0.536800990307-0.6492869123670.384588459381-0.09379956042120.6848045847960.06558533494030.1988953596830.0332220399722-0.116240718428-0.2143836030660.183937351792-0.076244752659-0.3008948946653.37080671252E-60.2470747625040.0176357712219-0.05741482525650.350616460195-0.07147633407830.285444693659-31.61719529887.9139545702841.7771391283
270.1946672878280.08940733336850.1596118922670.05619690113040.08758950617180.169790961446-0.1259683890711.362641344670.210532909015-0.6263036121860.1842091185830.0736813915013-0.914343032405-0.160147692195-0.003396981055590.5725354762650.0929741203798-0.08879604692220.4746542190920.006196815685930.564059334623-30.890905401416.63426582641.7165171612
280.82176068088-0.0868928447764-0.5082882781810.1408423590830.3220268184750.628300211123-0.1478379267950.709247265093-0.554727716482-0.0159000518235-0.3041502979060.324244844272-0.587554595331-0.658702799524-0.03897186030240.3299296504770.0244174171371-0.009394522475660.440970233628-0.1539177593760.341038261813-22.3654160892-2.1423743863437.8378027436
290.6356086489950.445696249433-1.21806274490.198935180451-0.1141259537860.435014678232-0.1928827594870.06522034953590.0741035837997-0.417626053582-0.01476835619810.216235795888-0.228876763034-0.140845446628-0.00934375818620.2355079519990.0186280763593-0.03478630395540.365328715835-0.06631555737760.362804948529-25.71154637495.8321318136242.8596099495
300.5210552803850.04604588997570.4409266117981.146249306980.230283637650.9389528072630.272733567757-0.111983215836-0.07944846506740.283463633763-0.1649637156710.1666693743580.131837970086-0.3565887571420.01375715322420.2215516240330.02567655450710.01729655984130.492016008023-0.06225930152070.32023624465-34.375445862910.134587130650.1319098994
310.0069869727148-0.00472612370479-0.01745511623920.11121316965-0.1008374129940.035809946423-0.0900746724672-0.447966664694-1.09023551316-0.4624836653590.3157403009440.1784359157910.0268261019575-0.4894936436730.0006461687593830.2894733602-0.0849180314376-0.006059809376320.544912926375-0.1485557997780.591384277165-36.8273529352-5.0750840133444.3295006454
32-0.0150617910801-0.0197744372925-0.009798720315550.006681470334240.01988202013510.09412491963810.07240435139450.1470773166790.3120384030810.318304056169-0.01638572644620.2054718447680.2445651402590.231788612514-0.00016055728670.24442691853-0.0226911825903-0.02647618506250.246344112953-0.05176000777780.243230405808-24.72314360645.3472826129952.2812458433
330.5880369572690.2649641026610.08818836572670.4210280975320.5626352286050.4273154820390.138323881719-0.1133684927450.3186930283480.153643608109-0.2524629449280.196174073403-0.332012690412-0.04128622002031.81958834127E-50.3101173508410.00277235201619-0.03180943630040.2291324975630.003717306214190.351716763427-18.137989829623.351200206447.4967964998
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 9 )
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 23 )
3X-RAY DIFFRACTION3chain 'A' and (resid 24 through 28 )
4X-RAY DIFFRACTION4chain 'A' and (resid 29 through 35 )
5X-RAY DIFFRACTION5chain 'A' and (resid 36 through 55 )
6X-RAY DIFFRACTION6chain 'A' and (resid 56 through 66 )
7X-RAY DIFFRACTION7chain 'A' and (resid 67 through 81 )
8X-RAY DIFFRACTION8chain 'A' and (resid 82 through 89 )
9X-RAY DIFFRACTION9chain 'A' and (resid 90 through 95 )
10X-RAY DIFFRACTION10chain 'A' and (resid 96 through 112 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 35 )
12X-RAY DIFFRACTION12chain 'B' and (resid 36 through 55 )
13X-RAY DIFFRACTION13chain 'B' and (resid 56 through 95 )
14X-RAY DIFFRACTION14chain 'B' and (resid 96 through 112 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 95 )
16X-RAY DIFFRACTION16chain 'C' and (resid 96 through 112 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 35 )
18X-RAY DIFFRACTION18chain 'D' and (resid 36 through 55 )
19X-RAY DIFFRACTION19chain 'D' and (resid 56 through 81 )
20X-RAY DIFFRACTION20chain 'D' and (resid 82 through 89 )
21X-RAY DIFFRACTION21chain 'D' and (resid 90 through 112 )
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 35 )
23X-RAY DIFFRACTION23chain 'E' and (resid 36 through 55 )
24X-RAY DIFFRACTION24chain 'E' and (resid 56 through 95 )
25X-RAY DIFFRACTION25chain 'E' and (resid 96 through 112 )
26X-RAY DIFFRACTION26chain 'F' and (resid 1 through 22 )
27X-RAY DIFFRACTION27chain 'F' and (resid 23 through 28 )
28X-RAY DIFFRACTION28chain 'F' and (resid 29 through 55 )
29X-RAY DIFFRACTION29chain 'F' and (resid 56 through 66 )
30X-RAY DIFFRACTION30chain 'F' and (resid 67 through 81 )
31X-RAY DIFFRACTION31chain 'F' and (resid 82 through 89 )
32X-RAY DIFFRACTION32chain 'F' and (resid 90 through 95 )
33X-RAY DIFFRACTION33chain 'F' and (resid 96 through 112 )

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