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- PDB-2v78: Crystal structure of Sulfolobus solfataricus 2-keto-3-deoxyglucon... -

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Basic information

Entry
Database: PDB / ID: 2v78
TitleCrystal structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase
ComponentsFRUCTOKINASE
KeywordsTRANSFERASE / KINASE / PFKB FAMILY CARBOHYDRATE KINASE / 2-KETO-3-DEOXYGLUCONATE KINASE
Function / homology
Function and homology information


2-dehydro-3-deoxyglucono/galactono-kinase / 2-dehydro-3-deoxygalactonokinase activity / 2-dehydro-3-deoxygluconokinase activity / phosphorylation / nucleotide binding / ATP binding
Similarity search - Function
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
2-dehydro-3-deoxygluconokinase/2-dehydro-3-deoxygalactonokinase
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPotter, J.A. / Theodossis, A. / Kerou, M. / Lamble, H.J. / Bull, S.D. / Hough, D.W. / Danson, M.J. / Taylor, G.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: The Structure of Sulfolobus Solfataricus 2-Keto-3-Deoxygluconate Kinase.
Authors: Potter, J.A. / Kerou, M. / Lamble, H.J. / Bull, S.D. / Hough, D.W. / Danson, M.J. / Taylor, G.L.
History
DepositionJul 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FRUCTOKINASE
B: FRUCTOKINASE
C: FRUCTOKINASE


Theoretical massNumber of molelcules
Total (without water)104,7563
Polymers104,7563
Non-polymers00
Water8,323462
1
A: FRUCTOKINASE
B: FRUCTOKINASE
C: FRUCTOKINASE

A: FRUCTOKINASE
B: FRUCTOKINASE
C: FRUCTOKINASE


Theoretical massNumber of molelcules
Total (without water)209,5126
Polymers209,5126
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area16110 Å2
ΔGint-85.53 kcal/mol
Surface area62750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.865, 104.865, 422.502
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A2 - 311
2114B2 - 311
3114C2 - 311

NCS oper:
IDCodeMatrixVector
1given(-0.499, 0.357, 0.79), (0.314, -0.775, 0.548), (0.808, 0.521, 0.275)-74.49928, 15.89086, 40.03625
2given(-0.508, -0.359, -0.783), (0.322, 0.764, -0.559), (0.799, -0.536, -0.272)-74.70044, 16.36462, 39.8315

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Components

#1: Protein FRUCTOKINASE / / 2-KETO-3-DEOXYGLUCONATE KINASE


Mass: 34918.715 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q97U29, fructokinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.09 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→76.3 Å / Num. obs: 91205 / % possible obs: 97 % / Observed criterion σ(I): 7.2 / Redundancy: 12.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 7.2 / % possible all: 81.4

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.98 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.536 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 4554 5 %RANDOM
Rwork0.162 ---
obs0.164 86496 96.9 %-
Displacement parametersBiso mean: 21.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7335 0 0 462 7797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0227819
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.97610642
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08951016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02224.494356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.572151416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.951547
X-RAY DIFFRACTIONr_chiral_restr0.1390.21200
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025948
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.23536
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.25520
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2484
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.2100
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1461.55017
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72527881
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.03533201
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4364.52737
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

Ens-ID: 1 / Number: 2228 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.320.5
2Bmedium positional0.290.5
3Cmedium positional0.280.5
1Amedium thermal1.432
2Bmedium thermal1.452
3Cmedium thermal1.422
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 260
Rwork0.177 4785
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)
10.15150.1048-0.04150.39760.00770.22830.0141-0.0104-0.0119-0.02310.0006-0.0246-0.02760.0245-0.01480.0172-0.02320.0071-0.0334-0.0054-0.0263-26.801220.37294.8145
20.14130.1553-0.06520.25860.00680.25180.0216-0.032-0.01180.0048-0.0269-0.0310.0073-0.00380.00530.008-0.0238-0.0027-0.0165-0.0006-0.0269-50.1125-5.662830.2916
30.1260.00750.10520.5713-0.06280.1615-0.0116-0.00270.01340.03510.01790.0592-0.0414-0.0411-0.00640.01210.0190.0131-0.02890.0052-0.0034-72.099120.55716.1924
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 312
2X-RAY DIFFRACTION2B2 - 312
3X-RAY DIFFRACTION3C2 - 312

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