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- PDB-6kex: Crystal structure of reduced phosphoribulokinase from Arabidopsis... -

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Basic information

Entry
Database: PDB / ID: 6kex
TitleCrystal structure of reduced phosphoribulokinase from Arabidopsis thaliana
ComponentsPhosphoribulokinase
KeywordsTRANSFERASE / phosphoribulokinase reduced
Function / homology
Function and homology information


phosphoribulokinase / phosphoribulokinase activity / supramolecular complex / stromule / apoplast / reductive pentose-phosphate cycle / chloroplast envelope / thylakoid / chloroplast stroma / chloroplast thylakoid membrane ...phosphoribulokinase / phosphoribulokinase activity / supramolecular complex / stromule / apoplast / reductive pentose-phosphate cycle / chloroplast envelope / thylakoid / chloroplast stroma / chloroplast thylakoid membrane / response to cold / chloroplast / disordered domain specific binding / phosphorylation / protein homodimerization activity / ATP binding / nucleus
Similarity search - Function
Phosphoribulokinase signature. / Phosphoribulokinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Phosphoribulokinase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYu, A. / Xie, Y. / Li, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31770778 China
CitationJournal: Plant Cell / Year: 2020
Title: Photosynthetic Phosphoribulokinase Structures: Enzymatic Mechanisms and the Redox Regulation of the Calvin-Benson-Bassham Cycle.
Authors: Yu, A. / Xie, Y. / Pan, X. / Zhang, H. / Cao, P. / Su, X. / Chang, W. / Li, M.
History
DepositionJul 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribulokinase
B: Phosphoribulokinase
C: Phosphoribulokinase
D: Phosphoribulokinase


Theoretical massNumber of molelcules
Total (without water)162,0084
Polymers162,0084
Non-polymers00
Water3,171176
1
A: Phosphoribulokinase
C: Phosphoribulokinase


Theoretical massNumber of molelcules
Total (without water)81,0042
Polymers81,0042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoribulokinase

D: Phosphoribulokinase


Theoretical massNumber of molelcules
Total (without water)81,0042
Polymers81,0042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Unit cell
Length a, b, c (Å)49.835, 80.359, 103.087
Angle α, β, γ (deg.)70.100, 82.260, 89.850
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Phosphoribulokinase / / PRKase / Phosphopentokinase


Mass: 40501.918 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g32060, T12O21.4 / Production host: Escherichia coli (E. coli) / References: UniProt: P25697, phosphoribulokinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 4% v/v Tacsimate pH5.0, 12% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→49.33 Å / Num. obs: 50674 / % possible obs: 95.27 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 10.9
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 0.763 / Num. unique obs: 2506

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.33 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2563 --
Rwork0.2107 --
obs-49034 94.53 %
Refinement stepCycle: LAST / Resolution: 2.5→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10938 0 0 178 11116
LS refinement shellResolution: 2.5→2.589 Å
RfactorNum. reflection% reflection
Rfree0.3608 --
Rwork0.2648 --
obs-4839 94.53 %
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)
13.16072.2120.87898.80231.71522.0149-0.35130.3640.75340.39490.10910.8349-0.85260.20040.23610.5686-0.0139-0.18210.48260.1450.516-15.515819.4864-23.5565
21.03710.09990.5911.2431-0.61212.6454-0.11410.18290.1323-0.02770.0433-0.037-0.26160.15130.06640.2641-0.03130.00290.2787-0.00060.3353-19.429615.6643-21.6632
32.15581.55912.85434.29560.07285.031-0.19890.07180.51820.73520.1541-0.0229-0.810.22850.04360.7967-0.1699-0.0560.35520.03470.437-39.418658.4651-24.411
43.2597-1.0410.03261.502-1.71172.6699-0.03780.27560.33420.1198-0.1966-0.1376-0.29690.17490.21940.5315-0.0541-0.05810.3094-0.01260.2978-43.31560.0685-36.5166
53.2461-4.3178-2.06935.74722.58936.2706-0.2678-0.11870.04060.39740.49930.0952-0.55760.0023-0.22620.5058-0.00120.06340.41590.00830.4799-61.311762.1251-21.4546
60.8031-0.17960.25911.0157-0.67411.5029-0.0192-0.05140.07780.16570.04160.1119-0.1369-0.0735-0.02580.3868-0.0014-0.02990.214-0.01140.3885-46.163948.2818-10.0556
73.0092-0.3271-0.77243.17281.21067.22420.08860.01990.1443-0.3126-0.0061-0.1205-0.76320.446-0.08440.3718-0.059-0.06120.27090.07660.313-36.825451.3203-12.7401
82.94960.10340.49016.24362.11718.09610.08920.0285-0.6312-0.5311-0.07640.03250.5341-0.3811-0.0050.5790.0825-0.02060.33890.01150.363-28.405928.2813-69.6962
92.971-0.06421.58861.1534-1.74913.4710.10830.0268-0.2802-0.0852-0.05140.00160.3299-0.0441-0.0520.44360.05110.00350.2553-0.05710.3007-33.824926.7927-59.4871
101.09080.1594-0.65740.933-0.71622.2717-0.08390.0029-0.0813-0.02430.07270.02460.313-0.13870.00350.47080.0647-0.05470.2859-0.01990.4218-39.715134.762-80.3993
113.35370.36721.30753.85460.79986.95760.1120.1441-0.16730.25580.095-0.11350.67250.6626-0.2110.35110.09860.05710.34780.05920.3112-25.755235.3465-81.5745
122.3285-1.75350.35578.75241.28172.0114-0.224-0.5285-0.6364-0.39530.28650.27481.01720.1122-0.06990.52270.0150.11840.46520.03150.4516-3.869167.5639-70.2464
133.7272-0.11491.32062.7012-0.78283.2833-0.0183-0.6437-0.50860.4525-0.09180.03910.3353-0.21440.11650.4468-0.00040.04120.38690.060.3155-7.402466.9685-57.7361
142.71130.65180.58752.2498-0.41782.4240.0276-0.1943-0.19720.05940.08860.57430.3046-0.1563-0.13650.40440.06620.01390.3778-0.03280.5256-22.337869.6891-74.7949
151.9341-0.21270.0642.79480.33674.2965-0.04220.06080.0086-0.1437-0.01360.00370.34530.23770.05180.24350.01240.01580.25450.04930.2958-5.095676.2066-87.0423
164.57690.11171.78712.74370.38734.0250.1062-0.48520.08570.1375-0.0383-0.70340.06190.4828-0.05840.31730.0360.03470.46110.05990.43468.110576.3616-71.3464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 353 )
3X-RAY DIFFRACTION3chain 'B' and (resid 5 through 30 )
4X-RAY DIFFRACTION4chain 'B' and (resid 31 through 149 )
5X-RAY DIFFRACTION5chain 'B' and (resid 150 through 186 )
6X-RAY DIFFRACTION6chain 'B' and (resid 187 through 255 )
7X-RAY DIFFRACTION7chain 'B' and (resid 256 through 347 )
8X-RAY DIFFRACTION8chain 'C' and (resid 5 through 30 )
9X-RAY DIFFRACTION9chain 'C' and (resid 31 through 160 )
10X-RAY DIFFRACTION10chain 'C' and (resid 161 through 255 )
11X-RAY DIFFRACTION11chain 'C' and (resid 256 through 347 )
12X-RAY DIFFRACTION12chain 'D' and (resid 5 through 30 )
13X-RAY DIFFRACTION13chain 'D' and (resid 31 through 149 )
14X-RAY DIFFRACTION14chain 'D' and (resid 150 through 214 )
15X-RAY DIFFRACTION15chain 'D' and (resid 215 through 318 )
16X-RAY DIFFRACTION16chain 'D' and (resid 319 through 351 )

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