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- PDB-2dj6: Crystal structure of 6-pyruvoyl tetrahydrobiopterin synthase from... -

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Basic information

Entry
Database: PDB / ID: 2dj6
TitleCrystal structure of 6-pyruvoyl tetrahydrobiopterin synthase from Pyrococcus horikoshii OT3
Componentshypothetical protein PH0634
KeywordsLYASE / 6-pyruvoyl tetrahydrobiopterin synthase (PTPS) / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


lyase 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
: / Uncharacterized protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsBagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of 6-pyruvoyl tetrahydrobiopterin synthase from Pyrococcus horikoshii OT3
Authors: Bagautdinov, B. / Kunishima, N.
History
DepositionMar 31, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: hypothetical protein PH0634
B: hypothetical protein PH0634
C: hypothetical protein PH0634


Theoretical massNumber of molelcules
Total (without water)40,5973
Polymers40,5973
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-10 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.831, 95.708, 105.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTrimer (A,B and C) in the assymmetric unit represents a biological unit

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Components

#1: Protein hypothetical protein PH0634 / 6-pyruvoyl tetrahydrobiopterin synthase


Mass: 13532.464 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0634 / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL
References: GenBank: 3257041, UniProt: O58368*PLUS, 6-pyruvoyltetrahydropterin synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 291 K / Method: microbathch / pH: 6.25
Details: 16.5% PEG 20000, 0.1M Acetate, NAOH pH 6.25, microbathch, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONSPring-8 BL26B120.97945, 0.97970, 0.96500
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDMar 15, 2006mirrors
MARRESEARCH2CCDMay 15, 2005mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979451
30.97971
40.9651
ReflectionResolution: 2.1→47.85 Å / Num. all: 21576 / Num. obs: 21534 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 66.05 Å2 / Rmerge(I) obs: 0.276 / Rsym value: 0.262 / Net I/σ(I): 9.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 3.07 / Num. unique all: 2094 / Rsym value: 0.262 / % possible all: 98.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNS1.1refinement
HKL-2000data reduction
CNS1.1phasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→33.56 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 1086 -RANDOM
Rwork0.2005 ---
all0.205 21534 --
obs0.2005 21534 95.9 %-
Displacement parametersBiso mean: 39.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å20 Å20 Å2
2---7.42 Å20 Å2
3---5.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→33.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 0 219 2923
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.028
RfactorNum. reflection% reflection
Rfree0.288 109 -
Rwork0.246 --
obs-2094 98.5 %

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