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- PDB-1rkx: Crystal Structure at 1.8 Angstrom of CDP-D-glucose 4,6-dehydratas... -

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Basic information

Entry
Database: PDB / ID: 1rkx
TitleCrystal Structure at 1.8 Angstrom of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis
ComponentsCDP-glucose-4,6-dehydratase
KeywordsLYASE / Dehydratase / SDR / CDP Glucose dehydratase
Function / homology
Function and homology information


CDP-glucose 4,6-dehydratase / CDP-glucose 4,6-dehydratase activity / nucleotide binding
Similarity search - Function
CDP-glucose 4,6-dehydratase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / CDP-D-glucose-4,6-dehydratase
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MIR / Resolution: 1.8 Å
AuthorsVogan, E.M. / Bellamacina, C. / He, X. / Liu, H.W. / Ringe, D. / Petsko, G.A.
Citation
Journal: Biochemistry / Year: 2004
Title: Crystal Structure at 1.8 A Resolution of CDP-d-Glucose 4,6-Dehydratase from Yersinia pseudotuberculosis
Authors: Vogan, E.M. / Bellamacina, C. / He, X. / Liu, H.W. / Ringe, D. / Petsko, G.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Purification, crystallization and molecular symmetry of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis.
Authors: Vogan, E.M. / Bellamacina, C.R. / He, X. / Liu, H.-W. / Ringe, D. / Petsko, G.A.
#2: Journal: To be Published
Title: The X-ray crystal structure of CDP-D-glucose 4,6-dehydratase from Yersinia pseduotuberculosis.
History
DepositionNov 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: CDP-glucose-4,6-dehydratase
B: CDP-glucose-4,6-dehydratase
C: CDP-glucose-4,6-dehydratase
D: CDP-glucose-4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,9158
Polymers161,2614
Non-polymers2,6544
Water15,529862
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12650 Å2
ΔGint-85 kcal/mol
Surface area48620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.900, 115.870, 126.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a 222 tetramer. All molecules all included explicitly.

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Components

#1: Protein
CDP-glucose-4,6-dehydratase


Mass: 40315.230 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: ascB / Plasmid: pJT8 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q57329, CDP-glucose 4,6-dehydratase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 862 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, PEG 4000, potassium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.0704 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 1999
RadiationMonochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0704 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 136502 / Num. obs: 133360 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.066 / Net I/σ(I): 18.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 13502 / Rsym value: 0.35 / % possible all: 93.4

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD, MIR
Starting model: NONE

Resolution: 1.8→36.25 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4589 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 5025 3.8 %SHELLS
Rwork0.229 ---
all0.229 133248 --
obs0.229 133248 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.66 Å2 / ksol: 0.367491 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1-8.04 Å20 Å20 Å2
2---3.89 Å20 Å2
3----4.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.8→36.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11121 0 176 862 12159
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.221.5
X-RAY DIFFRACTIONc_mcangle_it3.232
X-RAY DIFFRACTIONc_scbond_it3.12
X-RAY DIFFRACTIONc_scangle_it5.172.5
Refine LS restraints NCSNCS model details: RESTR
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.8-1.860.3383352.70.307122100.0181254592.7
1.86-1.940.4776700.3951318797.8
1.94-2.030.313350.2581345399.4
2.03-2.130.2596700.2251349199.6
2.13-2.270.2743350.2921338798.7
2.27-2.440.2936700.2351347099
2.44-2.690.2493690.2091360699.8
2.69-3.080.2476360.221363199.9
3.08-3.880.2313350.2071234489.6
3.88-5000.2096700.1841413499.7
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NAD.PARNAD.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM

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