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- PDB-6vby: Cinnamate 4-hydroxylase (C4H1) from Sorghum bicolor -

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Basic information

Entry
Database: PDB / ID: 6vby
TitleCinnamate 4-hydroxylase (C4H1) from Sorghum bicolor
ComponentsCinnamic acid 4-hydroxylase
KeywordsOXIDOREDUCTASE / CYP / Biofuel / monooxgenase / lignin / monolignol / ELECTRON TRANSPORT
Function / homology
Function and homology information


trans-cinnamate 4-monooxygenase / lignin metabolic process / trans-cinnamate 4-monooxygenase 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 / Trans-cinnamate 4-monooxygenase
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhang, B. / Kang, C. / Lewis, K.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 1804699 United States
Department of Energy (DOE, United States)DE-PI0000031 United States
United States Department of Agriculture (USDA)2011-1006-30358 United States
CitationJournal: Plant Physiol. / Year: 2020
Title: Structure and Function of the Cytochrome P450 Monooxygenase Cinnamate 4-hydroxylase fromSorghum bicolor.
Authors: Zhang, B. / Lewis, K.M. / Abril, A. / Davydov, D.R. / Vermerris, W. / Sattler, S.E. / Kang, C.
History
DepositionDec 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cinnamic acid 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0655
Polymers58,0261
Non-polymers1,0394
Water13,259736
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.278, 132.278, 79.431
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-603-

GOL

21A-705-

HOH

31A-1177-

HOH

41A-1226-

HOH

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Components

#1: Protein Cinnamic acid 4-hydroxylase


Mass: 58026.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: C4H, SORBI_3002G126600 / Production host: Escherichia coli (E. coli) / References: UniProt: Q94IP1, EC: 1.14.13.11
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 736 / 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: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 12% (v/v) isopropanol and 14% (w/v) PEG 2,000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→65.275 Å / Num. obs: 87984 / % possible obs: 99.92 % / Redundancy: 18.6 % / CC1/2: 0.995 / Net I/σ(I): 4.75
Reflection shellResolution: 1.7→1.761 Å / Mean I/σ(I) obs: 1.12 / Num. unique obs: 8712 / CC1/2: 0.462

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R1Z

4r1z


Resolution: 1.7→65.275 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.06
RfactorNum. reflection% reflection
Rfree0.2148 2000 2.27 %
Rwork0.1985 --
obs0.1988 87922 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.09 Å2 / Biso mean: 26.353 Å2 / Biso min: 9.78 Å2
Refinement stepCycle: final / Resolution: 1.7→65.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3794 0 132 736 4662
Biso mean--27.33 35.53 -
Num. residues----470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.7001-1.74260.32331400.32016086
1.7426-1.78970.30051450.29976077
1.7897-1.84240.29491410.27326098
1.8424-1.90180.26581400.2566095
1.9018-1.96980.28751430.24986101
1.9698-2.04870.22511450.22616113
2.0487-2.14190.23761410.20516110
2.1419-2.25490.22451400.20146088
2.2549-2.39620.2261430.19536144
2.3962-2.58120.2441440.19126147
2.5812-2.84090.2311430.19446114
2.8409-3.2520.19551410.17966172
3.252-4.09710.17831440.15946209
4.0971-65.2750.16221500.17176368
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.54010.2025-0.24180.6977-0.32320.7509-0.02630.0209-0.02490.03030.0391-0.00330.07170.0321-0.01780.18350.0011-0.00740.0788-0.01080.1074-61.870312.766231.7318
21.83040.1306-0.32451.945-1.44313.9050.0540.25690.2015-0.3250.02170.1587-0.0657-0.1384-0.07360.25460.05990.00140.10540.0240.1757-75.769925.264231.0761
30.65210.1974-0.14550.659-0.07750.7675-0.02130.0162-0.07910.03690.0092-0.08960.06360.09230.01380.1935-0.0013-0.01440.0769-0.00490.1172-50.700313.423226.2686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 231 )A32 - 231
2X-RAY DIFFRACTION2chain 'A' and (resid 232 through 272 )A232 - 272
3X-RAY DIFFRACTION3chain 'A' and (resid 273 through 501 )A273 - 501

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