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- PDB-2ive: Structure of protoporphyrinogen oxidase from Myxococcus xanthus -

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Basic information

Entry
Database: PDB / ID: 2ive
TitleStructure of protoporphyrinogen oxidase from Myxococcus xanthus
ComponentsPROTOPORPHYRINOGEN OXIDASE
KeywordsOXIDOREDUCTASE / PROTOPORPHYRINOGEN OXIDASE / PORPHYRIN BIOSYNTHESIS / CHLOROPHYLL BIOSYNTHESIS / FAD / PORPHYRIA / FLAVOPROTEIN / HEME BIOSYNTHESIS / HAEM BIOSYNTHESIS
Function / homology
Function and homology information


protoporphyrinogen oxidase / oxygen-dependent protoporphyrinogen oxidase activity / protoporphyrinogen IX biosynthetic process / plasma membrane / cytoplasm
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-TWN / Protoporphyrinogen oxidase
Similarity search - Component
Biological speciesMYXOCOCCUS XANTHUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCorradi, H.R. / Corrigall, A.V. / Boix, E. / Mohan, C.G. / Sturrock, E.D. / Meissner, P.N. / Acharya, K.R.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of Protoporphyrinogen Oxidase from Myxococcus Xanthus and its Complex with the Inhibitor Acifluorfen.
Authors: Corradi, H.R. / Corrigall, A.V. / Boix, E. / Mohan, C.G. / Sturrock, E.D. / Meissner, P.N. / Acharya, K.R.
History
DepositionJun 13, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTOPORPHYRINOGEN OXIDASE
B: PROTOPORPHYRINOGEN OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,98013
Polymers100,7932
Non-polymers3,18711
Water2,630146
1
A: PROTOPORPHYRINOGEN OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8136
Polymers50,3971
Non-polymers1,4165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROTOPORPHYRINOGEN OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1687
Polymers50,3971
Non-polymers1,7716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)148.566, 148.566, 132.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-2052-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.68436, 0.72908, 0.01024), (0.72915, 0.68432, 0.0069), (-0.00197, 0.01219, -0.99992)
Vector: 24.68063, -53.83945, 111.49263)

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Components

#1: Protein PROTOPORPHYRINOGEN OXIDASE / PPO / PPOX


Mass: 50396.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYXOCOCCUS XANTHUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P56601
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TWN / (3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL LAURATE


Mass: 354.567 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H42O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPROTOPORPHYRINOGEN OXIDASE IS RESPONSIBLE FOR THE CATALYTIC OXIDATION OF PROTOPORPHYRINOGEN IX.
Sequence detailsTHE FIRST MET IN THE PPOX SEQUENCE WAS REPLACED BY THE HIS TAG IN THE CONSTRUCT, BUT THIS RESIDUE ...THE FIRST MET IN THE PPOX SEQUENCE WAS REPLACED BY THE HIS TAG IN THE CONSTRUCT, BUT THIS RESIDUE WAS NOT OBSERVED IN THE STRUCTURE

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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: 3.74 Å3/Da / Density % sol: 66.85 %
Crystal growpH: 7.5
Details: 0.1M TRIS/HCL PH 7.5, 1.5M AMMONIUM SULPHATE, 20% GLYCEROL, 1% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.7→74.3 Å / Num. obs: 41382 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.7
Reflection shellResolution: 2.7→2.85 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
MOLREPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SEZ

1sez


Resolution: 2.7→74.33 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.849 / SU B: 12.894 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.496 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 87-93 IN BOTH MOLECULES COULD NOT BE MODELLED VERY ACCURATELY DUE TO LOTS OF NOISE IN THE MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 857 2.1 %RANDOM
Rwork0.247 ---
obs0.248 40498 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.7→74.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6648 0 217 146 7011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0216920
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1222.0059399
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8285897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.38521.852270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.243151007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5141574
X-RAY DIFFRACTIONr_chiral_restr0.0680.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025194
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.23062
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.24622
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2691.54543
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.48426992
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.43132673
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.7644.52407
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.335 79
Rwork0.329 2914

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