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- PDB-1sp8: 4-Hydroxyphenylpyruvate Dioxygenase -

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Basic information

Entry
Database: PDB / ID: 1sp8
Title4-Hydroxyphenylpyruvate Dioxygenase
Components4-Hydroxyphenylpyruvate Dioxygenase
KeywordsOXIDOREDUCTASE
Function / homology2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Roll / Alpha Beta / :
Function and homology information
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2 Å
AuthorsFritze, I.M. / Linden, L. / Freigang, J. / Auerbach, G. / Huber, R. / Steinbacher, S.
CitationJournal: Plant physiol. / Year: 2004
Title: The crystal structures of Zea mays and Arabidopsis 4-Hydroxyphenylpyruvate Dioxygenase
Authors: Fritze, I.M. / Linden, L. / Freigang, J. / Auerbach, G. / Huber, R. / Steinbacher, S.
History
DepositionMar 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE The sequence of this protein does not match to any of the database sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-Hydroxyphenylpyruvate Dioxygenase
B: 4-Hydroxyphenylpyruvate Dioxygenase
C: 4-Hydroxyphenylpyruvate Dioxygenase
D: 4-Hydroxyphenylpyruvate Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,5608
Polymers179,3364
Non-polymers2234
Water15,259847
1
A: 4-Hydroxyphenylpyruvate Dioxygenase
B: 4-Hydroxyphenylpyruvate Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7804
Polymers89,6682
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-51 kcal/mol
Surface area30830 Å2
MethodPISA
2
C: 4-Hydroxyphenylpyruvate Dioxygenase
D: 4-Hydroxyphenylpyruvate Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7804
Polymers89,6682
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-51 kcal/mol
Surface area30700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89, 110.9, 174.8
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
4-Hydroxyphenylpyruvate Dioxygenase /


Mass: 44834.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 847 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.86 %

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→19.84 Å / Num. obs: 115602 / % possible obs: 98.6 %
Reflection shellResolution: 2→2.07 Å / % possible all: 98.6

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: SIRAS / Resolution: 2→19.84 Å
RfactorNum. reflection
Rfree0.324 -
Rwork0.275 -
obs-115214
Refinement stepCycle: LAST / Resolution: 2→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11809 0 4 847 12660

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