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- PDB-1a7j: PHOSPHORIBULOKINASE FROM RHODOBACTER SPHEROIDES -

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Basic information

Entry
Database: PDB / ID: 1a7j
TitlePHOSPHORIBULOKINASE FROM RHODOBACTER SPHEROIDES
ComponentsPHOSPHORIBULOKINASE
KeywordsTRANSFERASE / KINASE / CALVIN CYCLE
Function / homology
Function and homology information


phosphoribulokinase / phosphoribulokinase activity / reductive pentose-phosphate cycle / ATP binding
Similarity search - Function
Phosphoribulokinase signature. / Phosphoribulokinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoribulokinase 1
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsHarrison, D.H.T. / Runquist, J. / Holub, A. / Miziorko, H.
Citation
Journal: Biochemistry / Year: 1998
Title: The crystal structure of phosphoribulokinase from Rhodobacter sphaeroides reveals a fold similar to that of adenylate kinase.
Authors: Harrison, D.H. / Runquist, J.A. / Holub, A. / Miziorko, H.M.
#1: Journal: Biochemistry / Year: 1998
Title: Functional Evaluation of Invariant Arginines Situated in the Mobile Lid Domain of Phosphoribulokinase
Authors: Runquist, J.A. / Harrison, D.H. / Miziorko, H.M.
History
DepositionMar 16, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHORIBULOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8062
Polymers32,7101
Non-polymers961
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PHOSPHORIBULOKINASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)262,44816
Polymers261,6808
Non-polymers7698
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_566-x,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
Buried area22920 Å2
ΔGint-260 kcal/mol
Surface area93510 Å2
MethodPISA
3
A: PHOSPHORIBULOKINASE
hetero molecules

A: PHOSPHORIBULOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6124
Polymers65,4202
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)129.830, 129.830, 129.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

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Components

#1: Protein PHOSPHORIBULOKINASE /


Mass: 32709.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Cell line: BL21 / Gene: PRKA / Plasmid: PETBPRKWT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P12033, phosphoribulokinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growpH: 5
Details: PROTEIN WAS CRYSTALLIZED FROM AMMONIUM PHOSPHATE, pH 5.0
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.5 mg/mlprotein1drop
225 mMTris-HCl1drop
30.5 Mammonium sulfate1reservoir
40.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 10956 / % possible obs: 80.6 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.062
Reflection
*PLUS
Num. measured all: 42132

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→15 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.284 532 5 %RANDOM
Rwork0.213 ---
obs0.213 10828 80.1 %-
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 5 34 2226
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.337
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.64
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.292
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.298 45 5 %
Rwork0.298 916 -
obs--58.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.64
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.292
LS refinement shell
*PLUS
Rfactor obs: 0.298

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