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- PDB-5b3f: Crystal structure of phosphoribulokinase from Methanospirillum hu... -

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Basic information

Entry
Database: PDB / ID: 5b3f
TitleCrystal structure of phosphoribulokinase from Methanospirillum hungatei
ComponentsPhosphoribulokinase/uridine kinase
KeywordsTRANSFERASE / Archaea / Kinase
Function / homologyphosphoribulokinase / phosphoribulokinase activity / Phosphoribulokinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / reductive pentose-phosphate cycle / P-loop containing nucleoside triphosphate hydrolase / ATP binding / phosphoribulokinase
Function and homology information
Biological speciesMethanospirillum hungatei JF-1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsMatsumura, H. / Ashida, H.
CitationJournal: Nat Commun / Year: 2017
Title: A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea
Authors: Kono, T. / Mehrotra, S. / Endo, C. / Kizu, N. / Matusda, M. / Kimura, H. / Mizohata, E. / Inoue, T. / Hasunuma, T. / Yokota, A. / Matsumura, H. / Ashida, H.
History
DepositionFeb 22, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribulokinase/uridine kinase
B: Phosphoribulokinase/uridine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7446
Polymers79,3602
Non-polymers3844
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-89 kcal/mol
Surface area27560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.414, 93.822, 99.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphoribulokinase/uridine kinase


Mass: 39679.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanospirillum hungatei JF-1 (archaea)
Strain: JF-1 / Gene: Mhun_0794 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FUB5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.8 / Details: PEG4000, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→34.02 Å / Num. obs: 24121 / % possible obs: 92.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 34.8 Å2 / Net I/σ(I): 13.5
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.274 / % possible all: 90

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→34.02 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 269892.21 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1095 4.8 %RANDOM
Rwork0.223 ---
obs0.223 23005 88.1 %-
Solvent computationBsol: 40.3927 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 45.5 Å2
Baniso -1Baniso -2Baniso -3
1--8.69 Å20 Å20 Å2
2--24.05 Å20 Å2
3----15.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.4 Å
Refinement stepCycle: 1 / Resolution: 2.5→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4979 0 20 148 5147
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 164 4.7 %
Rwork0.317 3350 -
obs--82.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION3CNS_TOPPAR/ion.paramCNS_TOPPAR/ion.top
X-RAY DIFFRACTION4CNS_TOPPAR/dna-rna_rep.param

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