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

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Basic information

Entry
Database: PDB / ID: 9qko
TitleStructure of the cyanobacteria specific PRK from Chroococcidiopsis (Hyella disjuncta) PCC 6712 (P1 crystal form)
Componentscyanobacteria specific phoshoribulokinase from Hyella disjuncta PCC 6712
KeywordsPHOTOSYNTHESIS / carbon fixation / sugar kinase
Function / homologyADENOSINE-5'-DIPHOSPHATE / RIBULOSE-1,5-DIPHOSPHATE
Function and homology information
Biological speciesChroococcidiopsis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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.
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

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Assembly

Deposited unit
B: cyanobacteria specific phoshoribulokinase from Hyella disjuncta PCC 6712
A: cyanobacteria specific phoshoribulokinase from Hyella disjuncta PCC 6712
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0838
Polymers70,4162
Non-polymers1,6676
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-80 kcal/mol
Surface area25500 Å2
Unit cell
Length a, b, c (Å)46.572, 53.080, 64.367
Angle α, β, γ (deg.)92.947, 101.841, 103.238
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

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_11GLUGLUGLUGLUAB3 - 3083 - 308
d_12SO4SO4SO4SO4AF1001
d_13ADPADPADPADPAG1002
d_14RUBRUBRUBRUBAH1003
d_21GLUGLUGLUGLUBA3 - 3083 - 308
d_22SO4SO4SO4SO4BC1001
d_23ADPADPADPADPBD1002
d_24RUBRUBRUBRUBBE1003

NCS oper: (Code: givenMatrix: (0.532065169074, 0.387527232786, -0.752814253124), (0.397602761096, -0.899338437087, -0.18194070448), (-0.74754177156, -0.202516713944, -0.632588555339)Vector: 6. ...NCS oper: (Code: given
Matrix: (0.532065169074, 0.387527232786, -0.752814253124), (0.397602761096, -0.899338437087, -0.18194070448), (-0.74754177156, -0.202516713944, -0.632588555339)
Vector: 6.79330428502, 13.5885512298, 20.6240697094)

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Components

#1: Protein cyanobacteria specific phoshoribulokinase from Hyella disjuncta PCC 6712


Mass: 35207.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis (bacteria) / Gene: PCC 6712 / Production host: Escherichia coli KRX (bacteria) / References: phosphoribulokinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Sugar ChemComp-RUB / RIBULOSE-1,5-DIPHOSPHATE


Type: saccharide / Mass: 310.090 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O11P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M MES-NaOH pH 6.5, 30 % PEG MME 5000, 0.2 M Ammonium sulfate monohydrate

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Data collection

DiffractionMean temperature: 199 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.619904 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.619904 Å / Relative weight: 1
ReflectionResolution: 2.597→62.66 Å / Num. obs: 17524 / % possible obs: 97.3 % / Redundancy: 1.8 % / Biso Wilson estimate: 60.05 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.11 / Net I/σ(I): 2.8
Reflection shellResolution: 2.597→2.642 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 1 / Num. unique obs: 698 / CC1/2: 0.37 / Rrim(I) all: 1.3 / % possible all: 78.6

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→38.49 Å / SU ML: 0.3986 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.7214
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.275 843 4.89 %
Rwork0.2352 16407 -
obs0.2371 17250 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.6 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 100 0 4918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00425018
X-RAY DIFFRACTIONf_angle_d0.81036826
X-RAY DIFFRACTIONf_chiral_restr0.0496760
X-RAY DIFFRACTIONf_plane_restr0.0071878
X-RAY DIFFRACTIONf_dihedral_angle_d12.0969708
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.400911340763 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.760.37831250.34292316X-RAY DIFFRACTION81.89
2.76-2.970.3041360.3072807X-RAY DIFFRACTION97.74
2.97-3.270.33331470.2972821X-RAY DIFFRACTION98.93
3.27-3.750.29621450.26262816X-RAY DIFFRACTION98.44
3.75-4.720.26991620.20772825X-RAY DIFFRACTION99.2
4.72-38.490.22431280.19732822X-RAY DIFFRACTION98.43
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)
15.0800925534-5.482154091594.9487573369210.0351982096-8.197048281619.725002403650.09347543395240.15621254387-0.6529272240620.2034764562420.1598485119090.8219227640140.008770464870290.604032302744-0.2068714117610.254163328737-0.1334404082230.05771196578260.303114299784-0.162566598110.388857051128-2.8418571570313.0880901323-4.424020783
27.37432759679-1.347977616263.436013706863.071022853540.2859232358696.064054990990.903411636033-0.7944527256960.1731203775590.698126146893-0.3376604454741.21987790258-1.62415792836-0.09439377446780.02815842204820.7637626697450.2284878635860.4267593881740.5235841260870.0125070962341.04083368127-17.938176807428.4232285226-12.9827295198
36.58938050491-2.346947126141.561998094136.45407715596-3.10832513964.89000707911-0.973577235142-0.599726177481-0.2453501426532.855708502960.8225966321630.555335826439-3.40907669657-0.3101775782910.05410764326441.459952828370.1246797757670.08562604411250.4999049070590.06913995535850.800135582492-15.039961880132.0290507292-6.66842358806
45.29142865119-4.623890925692.796118628547.18274526099-3.66467374887.810742922040.3124022508980.190767341555-0.8157584633440.1446651778450.1849581905170.881983418534-0.1277431602490.459466487866-0.4935263717780.4027895459540.03728800000040.04491935615120.360417767756-0.03362324486960.42092066227911.0290006111-7.5047550909420.6914650158
54.49524718503-4.864292966574.06202179594.40444871652-2.938947749715.86307683005-0.692605602879-0.2804352205020.06737383639681.529757089570.6707298118530.23589547956-1.181535383050.1942319307280.001138101187240.8433913755810.008287378598420.03773296820580.484561865717-0.01933471495420.3209431862128.871354384054.2429250251319.7807209311
65.5437999137-0.3791749226892.197312942048.45319966255-3.20760423373.57947906763-1.03178954431.071152802891.399241250443.306189909960.198238213687-1.68831879397-2.615100457180.1039261156860.467641430841.359544296910.0808939035421-0.2082808904130.8941110946310.1547423381250.54415713177522.15368320853.7935359633330.1766505454
76.65531808136-1.46132445517-0.8184904008672.90726508741-0.8670300407059.334793511920.01792987254341.34510257877-0.7078702332121.133453923190.3323348698370.269702061622-0.450212753417-0.502507705222-0.1007413670680.9392233544530.03515782803650.04054900159460.7311660441960.07252908783760.83530422276817.8888370793-16.11888467337.1551155439
86.561145776593.059659952821.059535866473.34821716852-1.792062595373.46358066857-0.167405871867-0.201575992966-1.790561408312.898976132610.7484441047871.48197692097-0.910131684388-0.703293586118-0.3880664442611.309406111270.3153793752790.3042170927510.5753765531260.3596598619890.71470970346915.1286887778-15.733870721842.3675596303
95.147180672672.374110821281.857474892471.02359932341.090869530728.619753606640.08359453227020.0172208167125-2.53348086611-3.729310659410.3582068938332.75520609632.381376979170.500263610449-2.722171873471.716180988670.0557786051619-1.272163913770.524150561805-0.3785467665862.4123133926212.9656587652-27.166911381225.6480173871
104.27656623471-1.97268498551-1.066317910557.61479317149-1.522402236964.023446540931.20209087942.956980069070.000258202546182-2.2210208550.332954596182.02290057797-0.3308612521410.156955800444-0.4953769094930.1465292782630.01205438873860.1904731538451.068033012460.02927675835760.77545649270818.9228901689-16.968891650824.9370462062
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 3 through 183 )BA3 - 1831 - 181
22chain 'B' and (resid 184 through 221 )BA184 - 221182 - 215
33chain 'B' and (resid 222 through 308 )BA222 - 308216 - 302
44chain 'A' and (resid 3 through 42 )AE3 - 421 - 40
55chain 'A' and (resid 43 through 131 )AE43 - 13141 - 129
66chain 'A' and (resid 132 through 183 )AE132 - 183130 - 181
77chain 'A' and (resid 184 through 221 )AE184 - 221182 - 215
88chain 'A' and (resid 222 through 248 )AE222 - 248216 - 242
99chain 'A' and (resid 249 through 272 )AE249 - 272243 - 266
1010chain 'A' and (resid 273 through 308 )AE273 - 308267 - 302

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