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- PDB-6hzl: Crystal structure of redox-inhibited phosphoribulokinase from Syn... -

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Basic information

Entry
Database: PDB / ID: 6hzl
TitleCrystal structure of redox-inhibited phosphoribulokinase from Synechococcus sp. (strain PCC 6301), osmate derivative
ComponentsPhosphoribulokinase
KeywordsTRANSFERASE / Phosphoribulokinase / Calvin cycle
Function / homology
Function and homology information


phosphoribulokinase / phosphoribulokinase activity / carbohydrate metabolic process / phosphorylation / ATP binding
Similarity search - Function
Phosphoribulokinase signature. / Phosphoribulokinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
OSMIUM ION / Phosphoribulokinase
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 6301 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.77 Å
AuthorsWilson, R.H. / Bracher, A. / Hartl, F.U. / Hayer-Hartl, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structure of phosphoribulokinase from Synechococcus sp. strain PCC 6301.
Authors: Wilson, R.H. / Hayer-Hartl, M. / Bracher, A.
History
DepositionOct 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribulokinase
B: Phosphoribulokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9024
Polymers75,5222
Non-polymers3802
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-9 kcal/mol
Surface area28830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.432, 141.432, 206.563
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 332
2010B4 - 332

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Components

#1: Protein Phosphoribulokinase /


Mass: 37760.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 6301 (bacteria)
Gene: prk, syc0567_d / Plasmid: pHUE-prk4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3K6J7, phosphoribulokinase
#2: Chemical ChemComp-OS / OSMIUM ION / Osmium


Mass: 190.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Os
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8 / Details: 20 % PEG-3350, 200 mM ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.13937 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13937 Å / Relative weight: 1
ReflectionResolution: 2.77→49.33 Å / Num. obs: 20468 / % possible obs: 100 % / Redundancy: 51.9 % / Biso Wilson estimate: 75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.03 / Rrim(I) all: 0.228 / Net I/σ(I): 17.4 / Num. measured all: 1062487 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.77-2.9223.32.4656832629380.7060.5022.5171.7100
8.76-49.33550.094388307060.9990.0130.09453.999.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
REFMACrefinement
XDSVERSION Nov 1, 2016data reduction
Aimless0.5.28data scaling
HKL2Mapphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.77→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2532 / WRfactor Rwork: 0.2279 / FOM work R set: 0.7785 / SU B: 38.101 / SU ML: 0.33 / SU R Cruickshank DPI: 0.3879 / SU Rfree: 0.3686 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 1017 5 %RANDOM
Rwork0.2352 ---
obs0.2363 19429 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 281.89 Å2 / Biso mean: 114.536 Å2 / Biso min: 52.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å2-0 Å2
2--0.07 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 2.77→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4954 0 2 1 4957
Biso mean--174.65 58.43 -
Num. residues----624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0195061
X-RAY DIFFRACTIONr_bond_other_d0.0020.024800
X-RAY DIFFRACTIONr_angle_refined_deg0.8971.9736861
X-RAY DIFFRACTIONr_angle_other_deg0.687311038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.575620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02423.806247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36215860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2681541
X-RAY DIFFRACTIONr_chiral_restr0.050.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215717
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021146
Refine LS restraints NCS

Ens-ID: 1 / Number: 18265 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.77→2.842 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 66 -
Rwork0.338 1409 -
all-1475 -
obs--99.93 %
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)
12.79371.58170.11412.8611-0.79121.1381-0.00390.0240.30530.0563-0.1710.1396-0.1605-0.11120.17490.2270.0083-0.02210.29140.05390.095668.8923-13.594117.2147
23.1530.3846-0.33683.18861.00833.01210.2290.02470.923-0.09820.1228-1.2665-0.9291.2806-0.35180.7346-0.46740.01831.09880.28321.2072115.04912.677219.0507
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 332
2X-RAY DIFFRACTION2B4 - 332

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