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- PDB-1sez: Crystal Structure of Protoporphyrinogen IX Oxidase -

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Basic information

Entry
Database: PDB / ID: 1sez
TitleCrystal Structure of Protoporphyrinogen IX Oxidase
ComponentsProtoporphyrinogen oxidase, mitochondrial
KeywordsOXIDOREDUCTASE / FAD-binding / Para-hydroxy-benzoate-hydroxylase fold (PHBH-fold) / monotopic membrane-binding domain
Function / homology
Function and homology information


protoporphyrinogen oxidase / oxygen-dependent protoporphyrinogen oxidase activity / protoporphyrinogen IX biosynthetic process / chloroplast / oxidoreductase activity / mitochondrion
Similarity search - Function
protoporphyrinogen ix oxidase, domain 3 / protoporphyrinogen ix oxidase, domain 3 / Protoporphyrinogen oxidase, mitochondrial; domain 2 / Protoporphyrinogen oxidase / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...protoporphyrinogen ix oxidase, domain 3 / protoporphyrinogen ix oxidase, domain 3 / Protoporphyrinogen oxidase, mitochondrial; domain 2 / Protoporphyrinogen oxidase / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-OMN / Chem-TON / Protoporphyrinogen oxidase, mitochondrial
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsKoch, M. / Breithaupt, C. / Kiefersauer, R. / Freigang, J. / Huber, R. / Messerschmidt, A.
CitationJournal: Embo J. / Year: 2004
Title: Crystal structure of protoporphyrinogen IX oxidase: a key enzyme in haem and chlorophyll biosynthesis.
Authors: Koch, M. / Breithaupt, C. / Kiefersauer, R. / Freigang, J. / Huber, R. / Messerschmidt, A.
History
DepositionFeb 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protoporphyrinogen oxidase, mitochondrial
B: Protoporphyrinogen oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7678
Polymers111,8042
Non-polymers2,9636
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-30 kcal/mol
Surface area39110 Å2
MethodPISA
2
A: Protoporphyrinogen oxidase, mitochondrial
B: Protoporphyrinogen oxidase, mitochondrial
hetero molecules

A: Protoporphyrinogen oxidase, mitochondrial
B: Protoporphyrinogen oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,53416
Polymers223,6084
Non-polymers5,92612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area16050 Å2
ΔGint-77 kcal/mol
Surface area76310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.090, 147.250, 127.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second subunit of the biological assembly is generated by the two fold axis: x, -y, -z+1

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Components

#1: Protein Protoporphyrinogen oxidase, mitochondrial / PPO II / Protoporphyrinogen IX oxidase isozyme II / PPX II / PX-2


Mass: 55902.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: PPXII, PPOX2 / Plasmid: pET32a-PPO2NT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O24164, protoporphyrinogen oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-OMN / 4-BROMO-3-(5'-CARBOXY-4'-CHLORO-2'-FLUOROPHENYL)-1-METHYL-5-TRIFLUOROMETHYL-PYRAZOL


Mass: 401.539 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H6BrClF4N2O2
#4: Chemical ChemComp-TON / 2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL


Mass: 294.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H30O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.78 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: PEG 1000, sodium citrate, sodium chloride, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2003 / Details: Si-monochromator
RadiationMonochromator: Si-mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→19.73 Å / Num. all: 25016 / Num. obs: 24891 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 83 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 11.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2083 / Rsym value: 0.528 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.9→19.73 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2.5 / σ(I): 2.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1187 -RANDOM
Rwork0.227 ---
all0.267 25019 --
obs0.25 24421 97.6 %-
Displacement parametersBiso mean: 66.3 Å2
Baniso -1Baniso -2Baniso -3
1--9.798 Å28.01 Å21.788 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.418 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6960 0 192 143 7295
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 2.9→2.94 Å
RfactorNum. reflection% reflection
Rfree0.4824 57 -
Rwork0.3872 --
obs-1034 100 %

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