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- PDB-3h6e: The crystal structure of a carbohydrate kinase from Novosphingobi... -

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Basic information

Entry
Database: PDB / ID: 3h6e
TitleThe crystal structure of a carbohydrate kinase from Novosphingobium aromaticivorans
ComponentsCarbohydrate kinase, FGGY
KeywordsTRANSFERASE / carbohydrate kinase / Novosphingobium aromaticivorans / strain DSM 12444 / SGX / 11200i / Kinase / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


kinase activity / carbohydrate metabolic process
Similarity search - Function
: / Carbohydrate kinase FGGY, C-terminal domain / : / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Carbohydrate kinase, FGGY
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of carbohydrate kinase from Novosphingobium aromaticivorans
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionApr 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbohydrate kinase, FGGY
B: Carbohydrate kinase, FGGY


Theoretical massNumber of molelcules
Total (without water)106,6262
Polymers106,6262
Non-polymers00
Water5,783321
1
A: Carbohydrate kinase, FGGY


Theoretical massNumber of molelcules
Total (without water)53,3131
Polymers53,3131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbohydrate kinase, FGGY


Theoretical massNumber of molelcules
Total (without water)53,3131
Polymers53,3131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.614, 81.198, 229.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbohydrate kinase, FGGY


Mass: 53312.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: Saro_1051 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-codon+RIL - Stratagene / References: UniProt: Q2G9H7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Magnesesium chloride hexahydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→114.71 Å / Num. obs: 35006 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 38.41 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 29.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 11.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→51.279 Å / SU ML: 0.37 / Isotropic thermal model: isotropic / σ(F): 1.14 / Phase error: 26.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2736 1755 5.03 %
Rwork0.2199 --
obs0.2226 34918 99.91 %
all-35006 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.755 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 27.29 Å2
Baniso -1Baniso -2Baniso -3
1--6.4113 Å2-0 Å20 Å2
2---0.3504 Å2-0 Å2
3---6.7617 Å2
Refinement stepCycle: LAST / Resolution: 2.5→51.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7148 0 0 321 7469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047318
X-RAY DIFFRACTIONf_angle_d0.83310004
X-RAY DIFFRACTIONf_dihedral_angle_d16.7212630
X-RAY DIFFRACTIONf_chiral_restr0.0571125
X-RAY DIFFRACTIONf_plane_restr0.0031313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.56760.28921420.21982462X-RAY DIFFRACTION100
2.5676-2.64320.32111310.24012532X-RAY DIFFRACTION100
2.6432-2.72850.33211260.24812511X-RAY DIFFRACTION100
2.7285-2.8260.31551160.24442543X-RAY DIFFRACTION100
2.826-2.93920.30151180.23812544X-RAY DIFFRACTION100
2.9392-3.07290.31321250.24052502X-RAY DIFFRACTION100
3.0729-3.23490.30321580.23262519X-RAY DIFFRACTION100
3.2349-3.43750.25531790.22212479X-RAY DIFFRACTION100
3.4375-3.70290.26031300.20732570X-RAY DIFFRACTION100
3.7029-4.07540.24751390.19222561X-RAY DIFFRACTION100
4.0754-4.66470.22721320.17642548X-RAY DIFFRACTION100
4.6647-5.87570.25931320.19152638X-RAY DIFFRACTION100
5.8757-51.29030.24161270.23022754X-RAY DIFFRACTION99

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