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- PDB-3d7j: SCO6650, a 6-pyruvoyltetrahydropterin synthase homolog from Strep... -

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Basic information

Entry
Database: PDB / ID: 3d7j
TitleSCO6650, a 6-pyruvoyltetrahydropterin synthase homolog from Streptomyces coelicolor
ComponentsUncharacterized protein SCO6650
KeywordsUNKNOWN FUNCTION / T-fold
Function / homology
Function and homology information


6-carboxytetrahydropterin synthase / 6-carboxy-5,6,7,8-tetrahydropterin synthase activity / metal ion binding
Similarity search - Function
6-pyruvoyl tetrahydropterin synthase/QueD / 6-pyruvoyl tetrahydropterin synthase/QueD family / 6-pyruvoyl tetrahydropterin synthase/QueD superfamily / 6-pyruvoyl tetrahydropterin synthase / Tetrahydropterin Synthase; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
6-carboxy-5,6,7,8-tetrahydropterin synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsSpoonamore, J.E. / Roberts, S.A. / Heroux, A. / Bandarian, V.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of a 6-pyruvoyltetrahydropterin synthase homolog from Streptomyces coelicolor.
Authors: Spoonamore, J.E. / Roberts, S.A. / Heroux, A. / Bandarian, V.
History
DepositionMay 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein SCO6650
B: Uncharacterized protein SCO6650
C: Uncharacterized protein SCO6650
D: Uncharacterized protein SCO6650
E: Uncharacterized protein SCO6650
F: Uncharacterized protein SCO6650
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,25811
Polymers100,1066
Non-polymers1525
Water12,196677
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15440 Å2
ΔGint-126.6 kcal/mol
Surface area29740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.400, 88.000, 120.900
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
Uncharacterized protein SCO6650


Mass: 16684.355 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A(3)2 / Gene: SCO6650 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O86696
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 677 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2 M NaCl, 10% PEG6000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X26C10.9777, 0.9600, 0.9787
SYNCHROTRONNSLS X26C20.9771
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 5, 2005
ADSC QUANTUM 42CCDApr 5, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si crystal (111)MADMx-ray1
2Si crystal (111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97771
20.961
30.97871
40.97711
ReflectionResolution: 1.45→41.34 Å / Num. all: 141171 / Num. obs: 140447 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 44
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7012 / % possible all: 72

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→41.34 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.313 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGEN ATOMS HAVE BEEN ADDED IN RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 7022 5 %RANDOM
Rwork0.206 ---
all0.207 140447 --
obs0.207 133425 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.396 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2---0.21 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.45→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6206 0 5 677 6888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0216471
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9328789
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835830
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59423.028327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.425151022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3331563
X-RAY DIFFRACTIONr_chiral_restr0.0880.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025053
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.23152
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24533
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2549
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1450.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1640.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7061.54058
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24926475
X-RAY DIFFRACTIONr_scbond_it1.94732455
X-RAY DIFFRACTIONr_scangle_it3.0724.52311
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.485 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 368 -
Rwork0.305 7199 -
obs--70.36 %

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