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- PDB-3nks: Structure of human protoporphyrinogen IX oxidase -

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Basic information

Entry
Database: PDB / ID: 3nks
TitleStructure of human protoporphyrinogen IX oxidase
ComponentsProtoporphyrinogen oxidase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / FAD containing protein / PPO / variegate porphyria disease / VP / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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: 1.9 Å
AuthorsShen, Y.
CitationJournal: Faseb J. / Year: 2011
Title: Structural insight into human variegate porphyria disease
Authors: Qin, X. / Tan, Y. / Wang, L. / Wang, Z. / Wang, B. / Wen, X. / Yang, G. / Xi, Z. / Shen, Y.
History
DepositionJun 21, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Protoporphyrinogen oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1535
Polymers50,8211
Non-polymers1,3314
Water4,846269
1


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

A: Protoporphyrinogen oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,30510
Polymers101,6422
Non-polymers2,6638
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_445-x-2/3,-x+y-1/3,-z+2/31
Buried area1710 Å2
ΔGint-13 kcal/mol
Surface area39620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.702, 136.702, 158.877
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 / / protoporphyrinogen IX oxidase / PPO


Mass: 50821.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPOX / 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.: 269 / 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: 2.81 Å3/Da / Density % sol: 56.24 %
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: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 44210 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 25.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3927 / Rsym value: 0.458 / % possible all: 88.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IVE

2ive


Resolution: 1.9→29.71 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 97002.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2120 5 %RANDOM
Rwork0.206 ---
obs0.206 42448 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.79 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.84 Å20 Å20 Å2
2---2.84 Å20 Å2
3---5.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3460 0 89 269 3818
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d2.11
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 294 5 %
Rwork0.259 5587 -
obs--79.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3fad.paramfad.top
X-RAY DIFFRACTION4acj.paramacj.top
X-RAY DIFFRACTION5gol.paramgol.top

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