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- PDB-3i6d: Crystal structure of PPO from bacillus subtilis with AF -

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Basic information

Entry
Database: PDB / ID: 3i6d
TitleCrystal structure of PPO from bacillus subtilis with AF
ComponentsProtoporphyrinogen oxidase
KeywordsOXIDOREDUCTASE / Protein-inhibitor complex / FAD / Flavoprotein / Porphyrin biosynthesis
Function / homology
Function and homology information


coproporphyrinogen III oxidase (coproporphyrin-forming) / oxygen-dependent protoporphyrinogen oxidase activity / heme biosynthetic process / oxidoreductase activity / 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
Chem-ACJ / FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Coproporphyrinogen III oxidase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement combined with SAD / Resolution: 2.9 Å
AuthorsShen, Y.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Structural insight into unique properties of protoporphyrinogen oxidase from Bacillus subtilis
Authors: Qin, X. / Sun, L. / Wen, X. / Yang, X. / Tan, Y. / Jin, H. / Cao, Q. / Zhou, W. / Xi, Z. / Shen, Y.
History
DepositionJul 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Protoporphyrinogen oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,0248
Polymers102,5402
Non-polymers2,4846
Water19811
1
A: Protoporphyrinogen oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5124
Polymers51,2701
Non-polymers1,2423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protoporphyrinogen oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5124
Polymers51,2701
Non-polymers1,2423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.175, 96.175, 299.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Protoporphyrinogen oxidase / / PPO / protoporphyrinogen IX oxidase


Mass: 51269.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: P32397, protoporphyrinogen oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-ACJ / 5-[2-CHLORO-4-(TRIFLUOROMETHYL)PHENOXY]-2-NITROBENZOIC ACID / Acifluorfen


Mass: 361.657 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H7ClF3NO5
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ammonium phosphate dibasic, Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.9796
SYNCHROTRONBSRF 3W1A20.9791
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDMay 27, 2009
MAR CCD 130 mm2CCDJan 3, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GraphiteSINGLE WAVELENGTHMx-ray1
2GraphiteSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97911
ReflectionResolution: 2.8→30 Å / Num. obs: 35093 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9 % / Biso Wilson estimate: 1.4 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 25.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 1.95 / Num. unique all: 3003 / % possible all: 85.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement combined with SAD
Resolution: 2.9→29.92 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 94037.84 / 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
Rfree0.293 1513 4.9 %RANDOM
Rwork0.272 ---
obs0.272 30881 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.5353 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 77.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.71 Å20 Å20 Å2
2--4.71 Å20 Å2
3----9.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6350 0 164 11 6525
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d2.13
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scbond_it1.252
X-RAY DIFFRACTIONc_scangle_it2.072.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.404 227 4.9 %
Rwork0.381 4363 -
obs--87.4 %
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 DIFFRACTION5po4.parampo4.top

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