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- PDB-8e83: Structure of 2-hydroxyisoflavanone synthase from Medicago truncatula -

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Basic information

Entry
Database: PDB / ID: 8.0E+83
TitleStructure of 2-hydroxyisoflavanone synthase from Medicago truncatula
ComponentsIsoflavone synthase 1
KeywordsOXIDOREDUCTASE / cytochrome P450 / isoflavonoid / aryl-ring migration / hydroxylation
Function / homology
Function and homology information


2-hydroxyisoflavanone synthase / 2-hydroxyisoflavanone synthase activity / iron ion binding / heme binding / membrane
Similarity search - Function
Cytochrome P450, E-class, group I / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Isoflavone synthase 1
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPan, H. / Wang, X.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Commun Biol / Year: 2022
Title: The protein conformational basis of isoflavone biosynthesis.
Authors: Wang, X. / Pan, H. / Sagurthi, S. / Paris, V. / Zhuo, C. / Dixon, R.A.
History
DepositionAug 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoflavone synthase 1
B: Isoflavone synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,91110
Polymers114,1022
Non-polymers1,8098
Water8,341463
1
A: Isoflavone synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9565
Polymers57,0511
Non-polymers9054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoflavone synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9565
Polymers57,0511
Non-polymers9054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.119, 73.787, 148.671
Angle α, β, γ (deg.)90.000, 93.476, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Isoflavone synthase 1 / Putative 2-hydroxyisoflavanone synthase


Mass: 57050.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MtrunA17_Chr4g0046351 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q49BZ0, 2-hydroxyisoflavanone synthase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.2 M (NH4)2SO4, 0.2 M ammonium tartrate dibasic, 0.05 M imidazole, 30% (w/v)PEG3350 and 0.1M K2HPO4/NaH2PO4 (pH6.8)

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→42.7 Å / Num. obs: 71558 / % possible obs: 98 % / Redundancy: 3.4 % / Biso Wilson estimate: 29.5055778015 Å2 / CC1/2: 0.82 / Rmerge(I) obs: 0.069 / Net I/σ(I): 17.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6584 / CC1/2: 0.78 / % possible all: 87.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet protein structure

Resolution: 2→42.7 Å / SU ML: 0.226254793945 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.724302692
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2277 3588 5.01418449628 %
Rwork0.1916 67969 -
obs0.1934 71557 98.0044922892 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44 Å2
Refinement stepCycle: LAST / Resolution: 2→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7139 0 116 463 7718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002567492046347411
X-RAY DIFFRACTIONf_angle_d0.52521763348510065
X-RAY DIFFRACTIONf_chiral_restr0.03971576757491122
X-RAY DIFFRACTIONf_plane_restr0.005459058682561275
X-RAY DIFFRACTIONf_dihedral_angle_d11.50122322752744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02870.2937644708331130.2603483295262125X-RAY DIFFRACTION80.8234019502
2.0287-2.05650.3114478370831480.2400436090832396X-RAY DIFFRACTION91.3793103448
2.0565-2.08590.2883253329321290.2286812945652489X-RAY DIFFRACTION93.6002860207
2.0859-2.1170.258369012241140.2198781977982522X-RAY DIFFRACTION94.683908046
2.117-2.15010.2528591748751400.2167353785952562X-RAY DIFFRACTION96.6726296959
2.1501-2.18540.2616473807191390.2184503040242612X-RAY DIFFRACTION97.3805309735
2.1854-2.2230.2464178148721290.2089332096512602X-RAY DIFFRACTION97.6054324518
2.223-2.26350.2729350540241300.2044684539092590X-RAY DIFFRACTION98.2304080896
2.2635-2.3070.2501016326291390.2014170654662643X-RAY DIFFRACTION99.1800356506
2.307-2.35410.2321547516061460.2005171508372613X-RAY DIFFRACTION99.6748554913
2.3541-2.40530.2696694895671350.1977581364922699X-RAY DIFFRACTION99.8942544942
2.4053-2.46120.2777491566691370.2027382911342623X-RAY DIFFRACTION100
2.4612-2.52280.2193877591491550.2024626348542658X-RAY DIFFRACTION99.9644633973
2.5228-2.5910.2616302593291320.2030706052762645X-RAY DIFFRACTION99.9640028798
2.591-2.66720.2445100351451450.2046537952582691X-RAY DIFFRACTION99.9295278365
2.6672-2.75330.2244691887221380.2107517501952660X-RAY DIFFRACTION100
2.7533-2.85160.2480417225541430.2031604067352652X-RAY DIFFRACTION100
2.8516-2.96580.2783873732551400.2164074888772699X-RAY DIFFRACTION100
2.9658-3.10070.2752839706011370.2038039289252652X-RAY DIFFRACTION100
3.1007-3.26420.2740518954131350.2077458656272646X-RAY DIFFRACTION100
3.2642-3.46860.2089450102541500.1921475763082681X-RAY DIFFRACTION100
3.4686-3.73620.1993516226481370.1807866844892682X-RAY DIFFRACTION99.8936924167
3.7362-4.1120.178755769821430.1633089067762690X-RAY DIFFRACTION99.9647141849
4.112-4.70630.1984457652181400.1507726499132691X-RAY DIFFRACTION99.9646892655
4.7063-5.9270.1742400302321490.1818915167422705X-RAY DIFFRACTION99.9649737303
5.927-42.696780.21838558241450.183796970432741X-RAY DIFFRACTION99.141188595
Refinement TLS params.Method: refined / Origin x: 14.7647587292 Å / Origin y: 0.589454493421 Å / Origin z: 36.5490639077 Å
111213212223313233
T0.275331585386 Å20.0050094785678 Å2-0.00353100349931 Å2-0.171099680096 Å2-0.00752427643471 Å2--0.194919434737 Å2
L0.479720614169 °2-0.101711407323 °20.426616363127 °2-0.660110615008 °2-0.245299565804 °2--1.31110980506 °2
S-0.0168356086926 Å °0.0886836053884 Å °0.02092427346 Å °-0.227707780259 Å °-0.0253565168953 Å °0.0444833562795 Å °-0.054384665379 Å °0.0332153963942 Å °0.0218902652315 Å °
Refinement TLS groupSelection details: all

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