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- PDB-4ivo: Structure of human protoporphyrinogen IX oxidase(R59Q) -

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Basic information

Entry
Database: PDB / ID: 4ivo
TitleStructure of human protoporphyrinogen IX oxidase(R59Q)
ComponentsProtoporphyrinogen oxidase
KeywordsOXIDOREDUCTASE / Oxidase / FAD Binding / Membrane
Function / homology
Function and homology information


phytoene dehydrogenase activity / protoporphyrinogen oxidase / oxygen-dependent protoporphyrinogen oxidase activity / carotenoid biosynthetic process / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / porphyrin-containing compound biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis ...phytoene dehydrogenase activity / protoporphyrinogen oxidase / oxygen-dependent protoporphyrinogen oxidase activity / carotenoid biosynthetic process / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / porphyrin-containing compound biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / mitochondrial membrane / mitochondrial intermembrane space / flavin adenine dinucleotide binding / mitochondrial inner membrane
Similarity search - Function
Protoporphyrinogen oxidase / 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
Similarity search - Domain/homology
Chem-ACJ / FLAVIN-ADENINE DINUCLEOTIDE / Protoporphyrinogen oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.597 Å
AuthorsXiaohong, Q. / Baifan, W.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Quantitative structural insight into human variegate porphyria disease.
Authors: Wang, B. / Wen, X. / Qin, X. / Wang, Z. / Tan, Y. / Shen, Y. / Xi, Z.
History
DepositionJan 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
B: Protoporphyrinogen oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9525
Polymers51,6211
Non-polymers1,3314
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protoporphyrinogen oxidase
hetero molecules

B: Protoporphyrinogen oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,90510
Polymers103,2422
Non-polymers2,6638
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_444x-y-1/3,-y-2/3,-z-2/31
Buried area7000 Å2
ΔGint-44 kcal/mol
Surface area37820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.809, 135.809, 158.338
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Protoporphyrinogen oxidase / / PPO


Mass: 51620.918 Da / Num. of mol.: 1 / Mutation: R59Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPOX / Plasmid: pTrcHis B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P50336, protoporphyrinogen oxidase
#2: Chemical ChemComp-ACJ / 5-[2-CHLORO-4-(TRIFLUOROMETHYL)PHENOXY]-2-NITROBENZOIC ACID / Acifluorfen


Mass: 361.657 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H7ClF3NO5
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10
Details: ammonium citrate dibasic, PEG3350, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 2, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 17528 / Num. obs: 16944 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.597→30.579 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 21.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 856 5.05 %
Rwork0.1771 --
obs0.1801 16944 96.54 %
all-17528 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.46 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1747 Å20 Å20 Å2
2---1.1747 Å2-0 Å2
3---2.3493 Å2
Refinement stepCycle: LAST / Resolution: 2.597→30.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3461 0 89 76 3626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083629
X-RAY DIFFRACTIONf_angle_d1.1414948
X-RAY DIFFRACTIONf_dihedral_angle_d17.3351366
X-RAY DIFFRACTIONf_chiral_restr0.064558
X-RAY DIFFRACTIONf_plane_restr0.005635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5965-2.75910.28091470.20712367X-RAY DIFFRACTION87
2.7591-2.9720.30961500.20932633X-RAY DIFFRACTION96
2.972-3.27080.23531500.18792674X-RAY DIFFRACTION98
3.2708-3.74330.23321380.1652749X-RAY DIFFRACTION99
3.7433-4.71340.20611420.1532784X-RAY DIFFRACTION99
4.7134-30.58070.22061290.17972881X-RAY DIFFRACTION100

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