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- PDB-1v1a: 2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOU... -

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Basic information

Entry
Database: PDB / ID: 1v1a
Title2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP
Components2-KETO-3-DEOXYGLUCONATE KINASE
KeywordsTRANSFERASE / 2-KETO-3-DEOXYGLUCONATE KINASE / ATP / THERMUS THERMOPHILUS / STRUCTURAL GENOMICS / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI
Function / homology
Function and homology information


2-dehydro-3-deoxygluconokinase / 2-dehydro-3-deoxygluconokinase activity / phosphorylation / nucleotide binding / ATP binding
Similarity search - Function
: / 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
ADENOSINE-5'-DIPHOSPHATE / 2-KETO-3-DEOXYGLUCONATE / 2-dehydro-3-deoxygluconokinase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTahirov, T.H. / Inagaki, E.
Citation
Journal: J. Mol. Biol. / Year: 2004
Title: Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate.
Authors: Ohshima, N. / Inagaki, E. / Yasuike, K. / Takio, K. / Tahirov, T.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and Preliminary Crystallographic Analysis of 2-Keto-3-Deoxygluconate Kinase from Thermus Thermophilus.
Authors: Inagaki, E. / Ukita, Y. / Kumei, M. / Kajihara, Y. / Tahirov, T.H.
History
DepositionApr 12, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 1, 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_initial_refinement_model / struct_site
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 / _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: 2-KETO-3-DEOXYGLUCONATE KINASE
B: 2-KETO-3-DEOXYGLUCONATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1516
Polymers66,9402
Non-polymers1,2114
Water3,801211
1
A: 2-KETO-3-DEOXYGLUCONATE KINASE
B: 2-KETO-3-DEOXYGLUCONATE KINASE
hetero molecules

A: 2-KETO-3-DEOXYGLUCONATE KINASE
B: 2-KETO-3-DEOXYGLUCONATE KINASE
hetero molecules

A: 2-KETO-3-DEOXYGLUCONATE KINASE
B: 2-KETO-3-DEOXYGLUCONATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,45318
Polymers200,8216
Non-polymers3,63212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.321, 84.321, 168.701
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 33470.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53W83*PLUS
#2: Chemical ChemComp-KDG / 2-KETO-3-DEOXYGLUCONATE


Mass: 178.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O6
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.53 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: VAPOUR-DIFFUSION SITTING DROP AT 298 K. 10.0 MG/ML OF PROTEIN SOLUTION CONTAINING 5 MM KDG AND 5 MM AMP-PNP WAS MIXED WITH RESERVOIR SOLUTION CONTAINING 0.35 M AMMONIUM SULFATE AND 0.1 M ...Details: VAPOUR-DIFFUSION SITTING DROP AT 298 K. 10.0 MG/ML OF PROTEIN SOLUTION CONTAINING 5 MM KDG AND 5 MM AMP-PNP WAS MIXED WITH RESERVOIR SOLUTION CONTAINING 0.35 M AMMONIUM SULFATE AND 0.1 M TRIS-HCL BUFFER, PH 8.5. BEFORE THE DATA COLLECTION THE CRYSTAL WAS SOAKED IN SOLUTION CONTAINING 0.35 M MAGNESIUM CHLORIDE INSTEAD OF AMMONIUM SULFATE. THE CRYOPROTECTANT CONTAINED 33% OF ETHYLENE GLYCOL IN ADDITION TO MAGNESIUM CHLORIDE, BUFFER AND LIGANDS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1
DetectorType: RIGAKU IMAGE PLATE R-AXISV / Detector: IMAGE PLATE / Date: Mar 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 38730 / % possible obs: 97.9 % / Observed criterion σ(I): -0.4 / Redundancy: 4.58 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 19.6
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.68 / % possible all: 96.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY V19

Resolution: 2.1→29.82 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1289180.4 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: CRYSTAL IS WITH HEMIHEDRAL TWINNING, TWINNING OPERATOR IS "H, -H-K, -L", TWINNING FRACTION IS 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.2677 1852 4.7 %RANDOM
Rwork0.1798 ---
obs0.1798 37822 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 85.7706 Å2 / ksol: 0.355934 e/Å3
Displacement parametersBiso mean: 51.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.709 Å2-3.064 Å20 Å2
2---3.709 Å20 Å2
3---7.417 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4594 0 78 211 4883
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.941.5
X-RAY DIFFRACTIONc_mcangle_it8.462
X-RAY DIFFRACTIONc_scbond_it8.642
X-RAY DIFFRACTIONc_scangle_it11.512.5
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3657 212 5.36 %
Rwork0.2938 3387 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3DHA.PARDHA.TOP

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