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- PDB-9qkp: Structure of the cyanobacteria specific PRK from Chroococcidiopsi... -

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Basic information

Entry
Database: PDB / ID: 9qkp
TitleStructure of the cyanobacteria specific PRK from Chroococcidiopsis (Hyella disjuncta) PCC 6712 (P41212 crystal form)
Componentscyanobacteria specific phosphoribulokinase from Chroococcidiopsis PCC 6712
KeywordsPHOTOSYNTHESIS / carbon fixation / sugar kinase
Function / homologyADENOSINE-5'-DIPHOSPHATE / RIBULOSE-1,5-DIPHOSPHATE
Function and homology information
Biological species[Chroococcidiopsis] sp. PCC 6712 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsTufail, F. / Yang, L. / Murray, J.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Imperial College London United Kingdom
CitationJournal: To Be Published
Title: A cyanobacteria specific class of phosphoribulokinase
Authors: Tufail, F. / Yang, L. / Murray, J.W.
History
DepositionMar 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cyanobacteria specific phosphoribulokinase from Chroococcidiopsis PCC 6712
B: cyanobacteria specific phosphoribulokinase from Chroococcidiopsis PCC 6712
C: cyanobacteria specific phosphoribulokinase from Chroococcidiopsis PCC 6712
D: cyanobacteria specific phosphoribulokinase from Chroococcidiopsis PCC 6712
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,52017
Polymers140,8324
Non-polymers3,68813
Water27015
1
A: cyanobacteria specific phosphoribulokinase from Chroococcidiopsis PCC 6712
hetero molecules

A: cyanobacteria specific phosphoribulokinase from Chroococcidiopsis PCC 6712
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0838
Polymers70,4162
Non-polymers1,6676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
2
B: cyanobacteria specific phosphoribulokinase from Chroococcidiopsis PCC 6712
C: cyanobacteria specific phosphoribulokinase from Chroococcidiopsis PCC 6712
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4379
Polymers70,4162
Non-polymers2,0217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: cyanobacteria specific phosphoribulokinase from Chroococcidiopsis PCC 6712
hetero molecules

D: cyanobacteria specific phosphoribulokinase from Chroococcidiopsis PCC 6712
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0838
Polymers70,4162
Non-polymers1,6676
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)92.752, 92.752, 407.667
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 4 and (name N or name...
d_2ens_1(chain "B" and ((resid 4 and (name N or name...
d_3ens_1(chain "C" and ((resid 4 and (name N or name...
d_4ens_1(chain "D" and (resid 4 through 215 or (resid 220...

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_11ARGARGTHRTHRAA4 - 2054 - 205
d_12LEULEUSERSERAA211 - 311211 - 311
d_13SO4SO4SO4SO4AE1001
d_14ADPADPADPADPAF1002
d_15RUBRUBRUBRUBAG1003
d_21ARGARGTHRTHRBB4 - 2054 - 205
d_22LEULEULEULEUBB211 - 215211 - 215
d_23ASNASNSERSERBB220 - 311220 - 311
d_24SO4SO4SO4SO4BI402
d_25ADPADPADPADPBJ403
d_26RUBRUBRUBRUBBK404
d_31ARGARGTHRTHRCC4 - 2054 - 205
d_32LEULEUSERSERCC211 - 311211 - 311
d_33SO4SO4SO4SO4CL1001
d_34ADPADPADPADPCM1002
d_35RUBRUBRUBRUBCN1003
d_41ARGARGSERSERDD4 - 3114 - 311
d_42SO4SO4SO4SO4DO1001
d_43ADPADPADPADPDP1002
d_44RUBRUBRUBRUBDQ1003

NCS oper:
IDCodeMatrixVector
1given(0.786593211338, 0.344576026949, -0.512385091048), (-0.155131852995, -0.692914477245, -0.704133251175), (-0.597666485645, 0.633353683873, -0.491587106281)53.8751894511, 75.840414937, 85.1696207452
2given(-0.337806807823, -0.798900650847, 0.497638735093), (0.671617109445, 0.165816039206, 0.722104908889), (-0.6594065657, 0.578154642997, 0.480541558966)-49.1146150406, -69.447407685, -13.9596598209
3given(-0.498192323032, 0.510676831929, 0.700723613562), (-0.495531926836, 0.495479854472, -0.713405791467), (-0.711514243539, -0.702644210923, 0.00621241480168)-56.3176223626, 88.1791328718, -0.803266348871

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
cyanobacteria specific phosphoribulokinase from Chroococcidiopsis PCC 6712


Mass: 35207.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Chroococcidiopsis] sp. PCC 6712 (bacteria)
Gene: Chr6712_000348 / Production host: Escherichia coli KRX (bacteria) / References: phosphoribulokinase
#4: Sugar
ChemComp-RUB / RIBULOSE-1,5-DIPHOSPHATE


Type: saccharide / Mass: 310.090 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C5H12O11P2 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 24 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C16H34O8 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.11 Å3/Da / Density % sol: 60.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8
Details: 0.1M Tris-HCl pH 8.0, 28% (w/v) PEG 5000 MME, 0.28 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.43→84.42 Å / Num. obs: 68603 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 74.15 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.074 / Net I/σ(I): 16.6
Reflection shellResolution: 2.43→2.47 Å / Redundancy: 7.1 % / Rmerge(I) obs: 2.004 / Num. unique obs: 3310 / CC1/2: 0.396 / Rpim(I) all: 0.802 / Rrim(I) all: 2.162 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→65.59 Å / SU ML: 0.4889 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.2972
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2682 2023 2.96 %
Rwork0.2325 66329 -
obs0.2335 68352 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 135.59 Å2
Refinement stepCycle: LAST / Resolution: 2.43→65.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9479 0 219 15 9713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00529892
X-RAY DIFFRACTIONf_angle_d0.910913474
X-RAY DIFFRACTIONf_chiral_restr0.05291517
X-RAY DIFFRACTIONf_plane_restr0.00841733
X-RAY DIFFRACTIONf_dihedral_angle_d13.08311432
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.364745029843
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.33987203305
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.305117371373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.490.37961370.35834538X-RAY DIFFRACTION97.97
2.49-2.560.38761480.3434647X-RAY DIFFRACTION99.9
2.56-2.630.41631400.38394656X-RAY DIFFRACTION99.73
2.63-2.720.49581360.44644679X-RAY DIFFRACTION99.71
2.72-2.820.38321440.36384659X-RAY DIFFRACTION99.9
2.82-2.930.32711550.28884662X-RAY DIFFRACTION99.94
2.93-3.060.32491340.27274689X-RAY DIFFRACTION99.83
3.06-3.220.30251380.29344730X-RAY DIFFRACTION99.96
3.22-3.420.36011600.30064694X-RAY DIFFRACTION99.88
3.42-3.690.27711470.22524738X-RAY DIFFRACTION99.98
3.69-4.060.21941540.20184764X-RAY DIFFRACTION99.98
4.06-4.650.19571250.17414843X-RAY DIFFRACTION100
4.65-5.850.22141690.19434843X-RAY DIFFRACTION100
5.85-65.590.25921360.21195187X-RAY DIFFRACTION99.78
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)
14.92539198234-1.009980503560.9165382393574.64068780738-0.8390994729512.2169215202-0.234565801068-0.021997553844-0.865785573586-0.2185055308030.04752744541050.3113149048480.40102793989-0.1961155702080.0167707177040.8680882126240.04847922529210.1924253908750.4991391286530.02576390435010.52746019341.04263047338-6.447016073883.7988237329
21.754648491850.3340724774120.2746653838021.221103784320.5548583458626.96102780443-0.179043196622-0.1022437823390.24514375209-0.07304233661260.06069110295220.133027009424-0.695035343211-0.518912381710.1297883022410.6381009452170.1258644701590.05450097783740.4824013825770.06862910958590.487204108321-0.2503589625764.2813238676283.0140416727
33.320913836681.431965712774.714263524984.988877040592.367475036227.26402791655-0.594560822893-0.259060756779-1.38467060304-0.4325690547620.392699598552-0.1487986844840.561327404616-0.80046033689-0.1205409197860.765201471684-0.101134867660.1708567780740.691747336709-0.03751120179430.871078531594.54312801357-12.380905668463.1343867052
48.69011293808-0.8272453822031.213891186813.87355733087-0.2455059187955.09878411940.392592865191-0.152650523778-0.748655000271-0.089624751266-0.1538655228940.7181216846451.03048372597-0.972522083637-0.1931756776150.962246496789-0.26482978953-0.02325183200990.6202695509090.008848916038730.571564010724-4.59641831687-13.595786136266.4381881751
52.27840332402-1.296315878741.924128801577.95535674694-0.7434967728379.13297652057-0.385598999276-0.500455754869-0.2440684410650.2967952051990.4563693906320.9755907748140.317203032898-1.3376971935-0.165527450390.627362660108-0.1383836935790.1328270881320.7375882700150.009864086999070.657242634328-9.60394728505-8.0021932699172.4688884489
62.102363441041.65626505566-0.3465659807744.28043864214-0.08028114037912.43769334851-0.08365865232190.08038305705790.158556484628-0.09685565911670.1848137612890.08188695447260.067026700478-0.25738381672-0.05087733230580.643089647327-0.03870192342070.0321012910140.3965913498820.01167580178960.53799694201512.491281403514.86726294946.7492229231
74.877437599781.44446746153-1.973693915745.21612880249-0.5027712449276.395557799530.09650840324530.4341421580250.6766230873730.2364764934730.1356741389850.0987617559134-0.374222477541-0.316728674393-0.2388160192230.760648052312-0.03368575191040.06943024101650.4138262431460.02549392009970.74725537757620.883571462638.858775121445.3789754082
85.515021347780.290928039088-0.6259052821169.032998365092.027142062525.154873349080.03936319462790.4438669402121.47701025307-0.371174213790.1005784790371.28332319864-0.586076296488-1.47947268183-0.1662971159130.7601430649410.07351801537370.06768874075160.6092196327880.08974806075681.168148201725.5934041976935.430324572948.548182178
94.469427261551.20412726211-0.0242794202556.315905451582.660930896115.29485535136-0.4926758396880.589380270784-0.132091068648-0.6016917669150.5986908578070.1787992978830.945187927103-0.957279331929-0.03389743781911.30154811774-0.580440681759-0.1328908523151.079297673330.1600949862160.616402487962-7.48396612035-6.8815561308330.2004054962
102.727339569111.654925563021.909219490092.940312671572.298009700222.10387263256-0.7468986967230.5034341435850.044166502146-0.9171234046320.7331931047510.3995964936081.23817031455-0.990542972976-0.09158696799871.35746312241-0.693801846928-0.1635179677691.136690421140.1089081500780.668888938641-6.93951296406-6.7430943070229.2287885821
110.209676584059-0.629995891692-0.2484549939523.060471669311.406770460481.67287539152-0.712954053940.0682062211373-0.362351666924-0.1348241226870.05720899712862.047728486970.884348225826-1.954255721870.7727933770162.02307070055-1.63268756993-0.5171375669911.998663752320.01409706956771.00531700837-20.2980021807-14.952087095124.094954752
121.542132310250.0179203036611-0.3194013661820.324462158027-0.2171317346660.222665557701-0.3684151194971.0351597936-0.633407819981-0.1181557668430.1090853255240.158070323140.897216171684-0.1254773111410.1046498715772.40003260627-0.780083781011-0.2443949638741.7816121997-0.006996474621490.831534864036-5.98593224478-23.44033267996.63487531215
133.007978503970.02297355107510.9831702496461.4919727219-0.8483270193042.29551212889-0.596587968510.539537563662-0.1110380752850.0450842612281-0.0632038575333-0.1396481563270.487026065994-0.359935930331-0.1078591633472.61504753372-2.37953837736-0.02803644161651.45128792695-0.04404200158970.848467981523-15.1890781715-21.97293188048.96158477719
147.101411711360.9909769185410.4384693937251.78448481730.2200036865124.17863610254-0.6302543020130.833103577715-0.534495363661-0.6888746572790.674342561855-1.477892655651.156577926970.1979272118820.4598324571742.34598431645-0.5454144008040.4025647725871.28719064891-0.2632639430352.330402509933.33138389026-29.567955483514.8834249182
156.446911169660.0911833147145-1.248569600628.98163562167-0.826094086137.002701894770.01612729358390.0315938876272-0.626255573386-0.721967269838-0.363998882375-0.6241226875270.06870385849080.9365118968820.6388954182322.45127554578-0.814301201546-0.006298195833181.2035139745-0.1001006444371.07470056663-3.60720378833-24.957116116522.8208094138
163.54241957423-1.703767186090.1367420388224.942564741280.8193851522191.20611921129-0.5437755517741.167397846480.268542998341-0.1992262702320.532872229386-0.4686142595570.329836137746-0.509591787484-0.1661371605712.61660711496-0.6410614187530.1634957006032.595797957570.1337436535941.995446743066.3115445868124.8729629485-1.0429315223
178.30338971872.31587195827-2.655537992698.668642504332.234856464484.026753364410.353516763153-0.5132445557850.237767599773-0.520746361183-0.3395354939682.08764268992-0.567769993922-0.0500465034507-0.1172413415342.382457230060.12497685747-0.1148023476262.209827143890.1103604969112.67665075523-0.16503861807440.9595671291-6.51667691944
184.66361078127-0.6227250986640.8796865197172.926974577882.388264959322.355525616230.6759194029490.529321398539-0.483256173048-0.656481952989-1.24494533689-0.859674188324-0.214380360218-0.340938171090.6690646716432.8649700895-0.06203378480020.3603053671342.59175982885-0.318996303262.65180305354-20.743792766936.52005055465.41026980648
196.832762041853.196753214170.63157532748.525333390430.8573747424887.184069731750.5792053126410.0664819590456-1.643733889231.27909217509-1.262977828881.1864869481.2000618725-0.3670556532221.026449064662.6478067941-0.245309179470.5557886638211.69149505653-0.082818643412.73483408561-9.5540964605836.646364090611.7929277912
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 17 )AA2 - 171 - 16
22chain 'A' and (resid 18 through 202 )AA18 - 20217 - 201
33chain 'A' and (resid 203 through 233 )AA203 - 233202 - 228
44chain 'A' and (resid 234 through 270 )AA234 - 270229 - 265
55chain 'A' and (resid 271 through 311 )AA271 - 311266 - 306
66chain 'B' and (resid 3 through 202 )BG3 - 2021 - 200
77chain 'B' and (resid 203 through 248 )BG203 - 248201 - 246
88chain 'B' and (resid 249 through 311 )BG249 - 311247 - 309
99chain 'C' and (resid 2 through 64 )CK2 - 641 - 63
1010chain 'C' and (resid 65 through 150 )CK65 - 15064 - 149
1111chain 'C' and (resid 151 through 202 )CK151 - 202150 - 201
1212chain 'C' and (resid 203 through 225 )CK203 - 225202 - 220
1313chain 'C' and (resid 226 through 248 )CK226 - 248221 - 243
1414chain 'C' and (resid 249 through 270 )CK249 - 270244 - 265
1515chain 'C' and (resid 271 through 311 )CK271 - 311266 - 306
1616chain 'D' and (resid 4 through 131 )DO4 - 1311 - 128
1717chain 'D' and (resid 132 through 202 )DO132 - 202129 - 199
1818chain 'D' and (resid 203 through 233 )DO203 - 233200 - 221
1919chain 'D' and (resid 234 through 311 )DO234 - 311222 - 299

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