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- PDB-2cgk: Crystal Structure of L-rhamnulose kinase from Escherichia coli in... -

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Basic information

Entry
Database: PDB / ID: 2cgk
TitleCrystal Structure of L-rhamnulose kinase from Escherichia coli in an open uncomplexed conformation.
ComponentsL-RHAMNULOSE KINASE
KeywordsTRANSFERASE / L-RHAMNULOSE KINASE / RHAMNOSE DEGRADATION / HEXOKINASE-HSP70- ACTIN SUPERFAMILY / INDUCED FIT / IN-LINE PHOSPHORYL TRANSFER / KINASE / RHAMNOSE METABOLISM
Function / homology
Function and homology information


rhamnulokinase / rhamnulokinase activity / rhamnose catabolic process / glycerol kinase activity / glycerol metabolic process / ATP binding / cytosol
Similarity search - Function
Rhamnulokinase / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L-Rhamnulokinase / Rhamnulokinase
Similarity search - Component
Biological speciesESCHERICHIA COLI BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsGrueninger, D. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure and Reaction Mechanism of L-Rhamnulose Kinase from Escherichia Coli.
Authors: Grueninger, D. / Schulz, G.E.
History
DepositionMar 9, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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: L-RHAMNULOSE KINASE
B: L-RHAMNULOSE KINASE


Theoretical massNumber of molelcules
Total (without water)107,9092
Polymers107,9092
Non-polymers00
Water1,69394
1
A: L-RHAMNULOSE KINASE


Theoretical massNumber of molelcules
Total (without water)53,9551
Polymers53,9551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: L-RHAMNULOSE KINASE


Theoretical massNumber of molelcules
Total (without water)53,9551
Polymers53,9551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.259, 164.933, 51.570
Angle α, β, γ (deg.)90.00, 93.45, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99999, 0.00391, -0.00275), (0.00385, -0.99977, -0.02121), (-0.00285, 0.0212, -0.99977)
Vector: -25.94741, 71.07143, 24.19212)

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Components

#1: Protein L-RHAMNULOSE KINASE / RHAMNULOKINASE / RHAMNULOSE KINASE


Mass: 53954.715 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI BL21(DE3) (bacteria) / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105
References: UniProt: Q8X899, UniProt: P32171*PLUS, rhamnulokinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 69 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 70 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLU 69 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 70 TO ALA ENGINEERED RESIDUE IN CHAIN A, ARG 73 TO ALA
Has protein modificationY
Sequence detailsTHE SEQUENCE DISCREPANCIES ARE BECAUSE THE DATABASE SEQUENCE IS FROM E.COLI STRAIN O157-H7. THE ...THE SEQUENCE DISCREPANCIES ARE BECAUSE THE DATABASE SEQUENCE IS FROM E.COLI STRAIN O157-H7. THE GENE WHICH WAS USED FOR PROTEIN EXPRESSION AND STRUCTURE DETERMINATION WAS ISOLATED FROM E.COLI BL21 (DE3).

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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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growDetails: 17 % PEG 8000, 120 MM LICL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 26, 2005
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.46→52 Å / Num. obs: 29856 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.3
Reflection shellResolution: 2.46→2.54 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.6 / % possible all: 97.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
CCP4phasing
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CGL

2cgl


Resolution: 2.46→44 Å / Data cutoff high absF: 10000 / Cross valid method: RMSD / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
Details: THE STRUCTURE WAS REFINED USING STRICT NCS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 1792 5.7 %RANDOM
Rwork0.2382 ---
obs0.2382 29856 94.7 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 28.1832 Å2 / ksol: 0.340036 e/Å3
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.214 Å20 Å2-0.188 Å2
2--0.932 Å20 Å2
3----8.146 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.46→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7404 0 0 94 7498
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.37
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.46→2.55 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.338 173 6 %
Rwork0.303 2714 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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