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- PDB-1vm7: Crystal structure of Ribokinase (TM0960) from Thermotoga maritima... -

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Basic information

Entry
Database: PDB / ID: 1vm7
TitleCrystal structure of Ribokinase (TM0960) from Thermotoga maritima at 2.15 A resolution
Componentsribokinase
KeywordsTRANSFERASE / TM0960 / RIBOKINASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


ribokinase / ribokinase activity / D-ribose catabolic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / 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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Ribokinase (TM0960) from Thermotoga maritima at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ribokinase
B: ribokinase


Theoretical massNumber of molelcules
Total (without water)68,3002
Polymers68,3002
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-17 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.142, 45.265, 77.260
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-354-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
12A
22B
32A
42B
52A
62B

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNGLYGLYAA12 - 4024 - 52
211ASNASNGLYGLYBB12 - 4024 - 52
321GLYGLYPROPROAA92 - 110104 - 122
421GLYGLYPROPROBB92 - 110104 - 122
112METMETSERSERAA1 - 1113 - 23
212PHEPHESERSERBB2 - 1114 - 23
322LYSLYSTHRTHRAA41 - 9153 - 103
422LYSLYSTHRTHRBB41 - 9153 - 103
532GLYGLYLEULEUAA111 - 299123 - 311
632GLYGLYASNASNBB111 - 298123 - 310

NCS ensembles :
ID
1
2

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Components

#1: Protein ribokinase /


Mass: 34149.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0960 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X055, ribokinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.34 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 0.4M (NH4)2Tartrate, 0.4% PEG-3350, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Feb 11, 2004
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→60.4 Å / Num. obs: 39375 / % possible obs: 92.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 37.9 Å2 / Rsym value: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 1884 / Rsym value: 0.682 / % possible all: 61.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gqt

1gqt


Resolution: 2.15→60.4 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.629 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Hydrogens have been added in the riding positions. There is some unexplained density at the 2-fold near B235-B236 main chain.
RfactorNum. reflection% reflectionSelection details
Rfree0.23539 1676 5 %RANDOM
Rwork0.18954 ---
obs0.19189 32122 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.282 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å20.85 Å2
2---1.2 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.15→60.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4537 0 0 279 4816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224616
X-RAY DIFFRACTIONr_bond_other_d0.0030.024267
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9686254
X-RAY DIFFRACTIONr_angle_other_deg0.86239937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0235594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21625.758198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15815787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3551514
X-RAY DIFFRACTIONr_chiral_restr0.0810.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025174
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02886
X-RAY DIFFRACTIONr_nbd_refined0.2020.2983
X-RAY DIFFRACTIONr_nbd_other0.1770.24503
X-RAY DIFFRACTIONr_nbtor_other0.0870.22937
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1860.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.29
X-RAY DIFFRACTIONr_mcbond_it0.551.53053
X-RAY DIFFRACTIONr_mcbond_other0.161.51222
X-RAY DIFFRACTIONr_mcangle_it0.83924757
X-RAY DIFFRACTIONr_scbond_it1.55931765
X-RAY DIFFRACTIONr_scangle_it2.3764.51497
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22332
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0590.21
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
1280tight positional0.10.05
1452medium positional0.570.5
1280tight thermal0.150.5
1452medium thermal0.582
21466tight positional0.080.05
22151medium positional0.470.5
21466tight thermal0.140.5
22151medium thermal0.472
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 102 4.85 %
Rwork0.238 2001 -
obs--83.72 %
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)
11.4097-0.19890.13645.3338-1.9082.34130.00770.01410.02730.1811-0.0842-0.3560.02280.30080.0765-0.2314-0.0269-0.0092-0.1512-0.0454-0.1361118.12588.197330.3153
22.27080.1257-0.57733.37751.313.9110.09620.2396-0.1662-0.68210.0196-0.2459-0.45510.1916-0.1157-0.0623-0.00030.0584-0.1675-0.0598-0.1186119.969824.623210.3268
31.7284-0.479-1.61962.46652.17724.8066-0.04060.07650.0013-0.0761-0.03690.05640.1516-0.19630.0776-0.2046-0.0150.0196-0.197-0.0395-0.1624108.57274.089630.333
42.5380.7870.66843.7947-0.52692.93460.2518-0.3016-0.16080.4269-0.0861-0.05690.1483-0.2322-0.1657-0.1548-0.0267-0.0241-0.0935-0.0762-0.1765103.0448-0.68754.1135
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA12 - 4024 - 52
21AA92 - 110104 - 122
32AA1 - 1113 - 23
42AA41 - 9153 - 103
52AA111 - 299123 - 311
63BB12 - 4024 - 52
73BB92 - 110104 - 122
84BB2 - 1114 - 23
94BB41 - 9153 - 103
104BB111 - 298123 - 310

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