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- PDB-2c4e: Crystal Structure of Methanocaldococcus jannaschii Nucleoside Kin... -

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Basic information

Entry
Database: PDB / ID: 2c4e
TitleCrystal Structure of Methanocaldococcus jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family
ComponentsSUGAR KINASE MJ0406
KeywordsTRANSFERASE / NUCLEOSIDE KINASE / HYPERTHERMOPHILE / RIBOKINASE FAMILY / RIBOKINASE FOLD
Function / homology
Function and homology information


cytidine kinase / nucleoside kinase activity / guanosine kinase activity / inosine kinase / inosine kinase activity / cytidine kinase activity / phosphorylation / magnesium ion binding / ATP binding
Similarity search - Function
Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMETHANOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsArnfors, L. / Hansen, T. / Meining, W. / Schoenheit, P. / Ladenstein, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of Methanocaldococcus Jannaschii Nucleoside Kinase: An Archaeal Member of the Ribokinase Family.
Authors: Arnfors, L. / Hansen, T. / Schoenheit, P. / Ladenstein, R. / Meining, W.
History
DepositionOct 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUGAR KINASE MJ0406
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9872
Polymers33,9631
Non-polymers241
Water2,036113
1
A: SUGAR KINASE MJ0406
hetero molecules

A: SUGAR KINASE MJ0406
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9744
Polymers67,9252
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2390 Å2
ΔGint-24.7 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.123, 148.081, 41.122
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein SUGAR KINASE MJ0406 / NUCLEOSIDE KINASE


Mass: 33962.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCOCCUS JANNASCHII (archaea) / Description: METHANOCALDOCOCCUS JANNASCHII / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57849
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growDetails: 10% PEG3500, 0.15 M MGAC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.134
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.134 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 44110 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 15.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 41.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→74.54 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.317 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2221 5 %RANDOM
Rwork0.234 ---
obs0.235 41803 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.99 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20 Å2
2---1.1 Å20 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 1.7→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 0 1 113 2472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212429
X-RAY DIFFRACTIONr_bond_other_d0.0040.022134
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.9583295
X-RAY DIFFRACTIONr_angle_other_deg0.75135014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1725301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022708
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02476
X-RAY DIFFRACTIONr_nbd_refined0.2060.2433
X-RAY DIFFRACTIONr_nbd_other0.2330.22293
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.080.21397
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3150.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6371.51491
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.13422399
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.573938
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.514.5895
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.301 157
Rwork0.296 3026
Refinement TLS params.Method: refined / Origin x: 5.7438 Å / Origin y: 22.7869 Å / Origin z: 17.7216 Å
111213212223313233
T0.0868 Å2-0.008 Å20.0392 Å2-0.0537 Å2-0.0685 Å2--0.0997 Å2
L2.5048 °2-0.273 °20.3425 °2-1.8693 °2-0.2107 °2--1.3316 °2
S-0.028 Å °0.1417 Å °-0.4903 Å °-0.0359 Å °-0.0139 Å °0.0195 Å °0.1474 Å °0.0328 Å °0.0419 Å °

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