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- PDB-2c49: Crystal Structure of Methanocaldococcus jannaschii Nucleoside Kin... -

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Basic information

Entry
Database: PDB / ID: 2c49
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 / inosine kinase / inosine kinase activity / guanosine 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
ADENOSINE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Nucleoside kinase
Similarity search - Component
Biological speciesMETHANOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 17, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUGAR KINASE MJ0406
B: SUGAR KINASE MJ0406
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,56910
Polymers67,9252
Non-polymers1,6448
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.006, 83.131, 146.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUALAALAAA6 - 156 - 15
21GLUGLUALAALABB6 - 156 - 15
12GLYGLYPROPROAA42 - 9742 - 97
22GLYGLYPROPROBB42 - 9742 - 97
13TRPTRPLEULEUAA115 - 297115 - 297
23TRPTRPLEULEUBB115 - 297115 - 297

NCS oper: (Code: given
Matrix: (-0.99608, 0.032971, 0.08207), (0.023822, 0.99364, -0.11006), (-0.085177, -0.10767, -0.99053)
Vector: 130.16, -1.7879, 70.508)

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Components

#1: Protein SUGAR KINASE MJ0406 / NUCLEOSIDE KINASE


Mass: 33962.613 Da / Num. of mol.: 2
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-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 15% PEG4000, 0.10 M MGCL2, 0.1 M TRIS-HCL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8098
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8098 Å / Relative weight: 1
ReflectionResolution: 1.93→20 Å / Num. obs: 58526 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 13.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→72.55 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.891 / SU B: 3.803 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2955 5.1 %RANDOM
Rwork0.243 ---
obs0.245 55509 97.1 %-
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: 21.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--1.26 Å20 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.92→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4731 0 104 162 4997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214982
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.71.9886777
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5385596
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_restr0.1160.2727
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023749
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.22331
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2219
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7581.52971
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26424782
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.07232011
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9894.51988
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1924 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.440.5
medium thermal1.152
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.336 193
Rwork0.296 3739
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)
12.454-0.6070.46651.86790.27692.96870.02320.11630.0207-0.0744-0.09540.0044-0.06850.12820.07220.01940.0081-0.00770.01050.01780.065571.350622.858160.61
20.3299-0.0792-0.23423.3372-1.20375.4807-0.03670.23610.3473-0.0043-0.0586-0.3196-0.59420.4290.09520.2009-0.02-0.04270.15180.04350.178371.345730.073939.1974
31.7338-0.16580.31881.8826-0.88492.1245-0.004-0.16070.1099-0.0860.05690.1399-0.0371-0.0957-0.05290.09130.0067-0.00520.0335-0.03520.097858.82823.943812.0094
41.62120.63960.6431.51161.56396.1729-0.09630.15940.32410.0615-0.00250.1671-0.5116-0.48660.09880.24950.0793-0.02340.11680.02180.151659.51830.836638.0425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 15
2X-RAY DIFFRACTION1A41 - 98
3X-RAY DIFFRACTION1A114 - 301
4X-RAY DIFFRACTION2A16 - 40
5X-RAY DIFFRACTION2A99 - 113
6X-RAY DIFFRACTION3B3 - 15
7X-RAY DIFFRACTION3B41 - 98
8X-RAY DIFFRACTION3B114 - 300
9X-RAY DIFFRACTION4B16 - 40
10X-RAY DIFFRACTION4B99 - 113

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