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- PDB-9qkn: Structure of the cyanobacteria specific PRK from Gloeocapsa PCC 73106 -

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Basic information

Entry
Database: PDB / ID: 9qkn
TitleStructure of the cyanobacteria specific PRK from Gloeocapsa PCC 73106
ComponentsUridine kinase
KeywordsPHOTOSYNTHESIS / carbon fixation / sugar kinase
Function / homology:
Function and homology information
Biological speciesGloeocapsa sp. PCC 73106 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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: Uridine kinase


Theoretical massNumber of molelcules
Total (without water)36,3271
Polymers36,3271
Non-polymers00
Water00
1
A: Uridine kinase

A: Uridine kinase

A: Uridine kinase

A: Uridine kinase


Theoretical massNumber of molelcules
Total (without water)145,3064
Polymers145,3064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
Unit cell
Length a, b, c (Å)57.430, 103.470, 140.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Uridine kinase / Phosphoribulokinase


Mass: 36326.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Phosphoribulokinase / Source: (gene. exp.) Gloeocapsa sp. PCC 73106 (bacteria) / Gene: GLO73106DRAFT_00009540 / Production host: Escherichia coli KRX (bacteria) / Strain (production host): KRX / References: UniProt: L8LPL6
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: 2.87 Å3/Da / Density % sol: 57.09 %
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99988 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 3.2→53.14 Å / Num. obs: 7197 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 115.99 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.047 / Rrim(I) all: 0.115 / Net I/σ(I): 9.7
Reflection shellResolution: 3.2→3.26 Å / Rmerge(I) obs: 1.275 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 343 / CC1/2: 0.673 / Rpim(I) all: 0.66 / Rrim(I) all: 1.442 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→42.59 Å / SU ML: 0.5416 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 41.3317
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3161 328 4.58 %
Rwork0.2562 6836 -
obs0.259 7164 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 146.39 Å2
Refinement stepCycle: LAST / Resolution: 3.2→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 0 0 2478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00332525
X-RAY DIFFRACTIONf_angle_d0.70883429
X-RAY DIFFRACTIONf_chiral_restr0.0467395
X-RAY DIFFRACTIONf_plane_restr0.0067444
X-RAY DIFFRACTIONf_dihedral_angle_d6.0915344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-4.030.40211510.32833341X-RAY DIFFRACTION99.06
4.03-42.590.29361770.23563495X-RAY DIFFRACTION99.67
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)
15.68620597833.693178568820.1981699392094.30541212799-0.578817099077.589063381830.7609346225941.355413876790.0725387532285-0.7332959467380.184938688290.261358899776-1.67471067466-0.223890626912-0.684477159910.9631167712630.165755998248-0.1974950747931.036670173290.01878576253550.881842346186-7.87631932247-15.9438005018-13.8972710049
20.116228299958-0.3535226082190.4045578101833.393348529430.7178411897973.23112018050.5728820356370.5776258691370.618350504369-0.584675879153-0.01978754108320.7920871507540.23037793978-0.0348096897024-0.3163525387971.23005056639-0.0316385924546-0.2204092758721.25480204395-0.04210358724751.34839765625-12.0063580408-16.952454515-20.9610572174
31.405518180740.803504406804-0.6073978021441.462162161311.404583798692.80935788450.6122915551581.77347081493-0.380601677553-2.006197098370.7026068695420.0211674907327-0.1300346742241.19612783261-0.6496821266641.727167396910.1994553838280.1895194487671.94975167069-0.3001622878471.1826454246910.7016398523-11.544184188-27.8927880865
44.75366961272.270554599030.9070700805476.16652598091-0.3344986077421.377871779590.3461878526340.705151007063-0.0940610787967-1.323116920010.05063685904970.0708386979428-0.514478583002-0.566598633351-0.4664500601251.354525421370.00923194337705-0.02436786352891.145704060140.022883335980.865076163018-3.25568372201-8.23138222018-19.3061435992
50.0709251941134-0.593710486338-0.4401289586492.21180571848-0.1587380865331.74956154855-0.4252390790890.2737050018570.0890960083315-0.376624881650.304138214658-0.3226998068060.5520888292110.3043648383190.25987578561.56482594722-0.132211886168-0.04871205255411.14952280199-0.2306631081231.15379382938-0.682853878828-25.148832044-24.5291192379
61.73917419722-0.571791932043-1.173594671090.3817512362230.6607954411031.03511799361-0.803984664093-0.191253815556-0.5513070349150.377872232660.521058395514-0.7608298354981.15274272129-1.305566012930.2582807452251.568358915270.111478399931-0.02553141918571.40693067918-0.04139293886181.2768534350510.4714208863-27.1778264595-30.4745497401
76.22899477064-0.500891524487-1.256866766554.13569517458-0.1113258154231.256515460180.387199216159-0.16351748064-0.7479441519451.10686543123-0.444472766339-0.2991357182281.29012400991-0.4996292068790.1325165577661.90944215242-0.0862482257904-0.234080136461.18210894488-0.01463568565261.16868260479-5.54701131245-36.4463582909-12.3358043757
83.68738350418-3.021556320731.909913060276.95376141260.8292512382276.917295405750.524167177958-0.966990588648-2.129678730950.879525362020.5690930451811.017142151641.10848099528-0.337340571311-1.075919962532.12003957759-0.09231144100920.0498442252021.059999657460.1318654804061.41551744288-14.3091911396-37.8370993208-9.7766527078
93.38699393314-2.149143133320.6044518594195.79487552481-0.03399096322533.75107195766-0.207745601652-0.106113207573-1.18780556684-1.48177652651-0.7633512010071.46434195840.501042044725-1.39204398163-0.3287054322721.80982877034-0.333644241937-0.1654883066071.603709441070.1153042936391.6361900097-22.4916650616-28.7995196757-19.0799679026
104.31282296076-1.43768423714-1.773504071091.98303536747-0.5264532589152.881076451450.490523345118-1.15235620833-0.7865767576430.9767624962841.190342090250.63866321913-2.0322348382-1.40455997621-0.2501812806612.21899689272-0.36458853889-0.02187189160321.24286877162-0.07689839675571.23913950818-15.8847010795-23.6409060659-7.97646591831
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 1 through 17 )1 - 171 - 17
22chain 'A' and (resid 18 through 41 )18 - 4118 - 41
33chain 'A' and (resid 42 through 64 )42 - 6442 - 64
44chain 'A' and (resid 65 through 115 )65 - 11565 - 115
55chain 'A' and (resid 116 through 150 )116 - 150116 - 150
66chain 'A' and (resid 151 through 168 )151 - 168151 - 168
77chain 'A' and (resid 169 through 232 )169 - 232169 - 228
88chain 'A' and (resid 233 through 259 )233 - 259229 - 255
99chain 'A' and (resid 260 through 290 )260 - 290256 - 286
1010chain 'A' and (resid 291 through 314 )291 - 314287 - 310

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