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- PDB-4r1s: Crystal structure of Petunia hydrida cinnamoyl-CoA reductase -

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Basic information

Entry
Database: PDB / ID: 4r1s
TitleCrystal structure of Petunia hydrida cinnamoyl-CoA reductase
Componentscinnamoyl CoA reductase
KeywordsOXIDOREDUCTASE / cinnamoyl-CoA reductase / short-chain dehydrogenase/reductase
Function / homology
Function and homology information


cinnamoyl-CoA reductase activity / cinnamoyl-CoA reductase / green leaf volatile biosynthetic process / phenylpropanoid biosynthetic process / lignin biosynthetic process / circadian rhythm / nucleotide binding / cytoplasm
Similarity search - Function
NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Cinnamoyl-CoA reductase 1
Similarity search - Component
Biological speciesPetunia x hybrida (garden petunia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsNoel, J.P. / Louie, G.V. / Bowman, M.E. / Bomati, E.K.
CitationJournal: Plant Cell / Year: 2014
Title: Structural Studies of Cinnamoyl-CoA Reductase and Cinnamyl-Alcohol Dehydrogenase, Key Enzymes of Monolignol Biosynthesis.
Authors: Pan, H. / Zhou, R. / Louie, G.V. / Muhlemann, J.K. / Bomati, E.K. / Bowman, M.E. / Dudareva, N. / Dixon, R.A. / Noel, J.P. / Wang, X.
History
DepositionAug 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: cinnamoyl CoA reductase
B: cinnamoyl CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0264
Polymers74,5392
Non-polymers1,4872
Water12,755708
1
A: cinnamoyl CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0132
Polymers37,2701
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cinnamoyl CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0132
Polymers37,2701
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.177, 61.232, 222.239
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cinnamoyl CoA reductase


Mass: 37269.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petunia x hybrida (garden petunia) / Gene: PhCCR1 / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A059TC02*PLUS
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 21% (w/v) polyethylene glycol 3350, 0.3 M calcium acetate, 100 mM sodium succinate, 5 mM NADP+, 0.2 M sodium iodide, and 2 mM DTT, pH 5.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2010 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→44.448 Å / Num. all: 98640 / Num. obs: 98640 / % possible obs: 90.2 % / Redundancy: 3.8 % / Rsym value: 0.067 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.691.50.2782.71398691960.27858.2
1.69-1.792.80.2762.636548130360.27687.6
1.79-1.9130.1724.337702126660.17290.5
1.91-2.073.40.1265.641964122500.12693.9
2.07-2.2640.1056.748629121420.105100
2.26-2.535.10.0927.355798110000.092100
2.53-2.925.30.07385121497540.073100
2.92-3.585.10.0628.94279683220.062100
3.58-5.064.90.05310.73169965190.05399.9
5.06-44.4485.10.03516.21915837550.03599.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.377 / Cor.coef. Fo:Fc: 0.651
Highest resolutionLowest resolution
Rotation3 Å42.14 Å
Translation3 Å42.14 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.21data scaling
MOLREP5phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→42.141 Å / FOM work R set: 0.8654 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 4909 4.98 %random
Rwork0.1691 ---
obs0.1702 98499 90.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.93 Å2 / Biso mean: 28.51 Å2 / Biso min: 9.42 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4941 0 96 708 5745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015157
X-RAY DIFFRACTIONf_angle_d1.3817042
X-RAY DIFFRACTIONf_chiral_restr0.095812
X-RAY DIFFRACTIONf_plane_restr0.007890
X-RAY DIFFRACTIONf_dihedral_angle_d14.591910
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61820.2746940.23961871196555
1.6182-1.63720.2642950.22991933202857
1.6372-1.65720.2831050.232006211158
1.6572-1.67820.2041160.22632099221562
1.6782-1.70030.24261180.2222181229964
1.7003-1.72360.29261840.23313130331492
1.7236-1.74820.25281740.22633088326290
1.7482-1.77430.27561400.22033151329191
1.7743-1.8020.25971680.2123055322390
1.802-1.83150.23151690.19573122329191
1.8315-1.86310.24431640.1913057322190
1.8631-1.8970.19741900.18473055324590
1.897-1.93350.20691400.18763092323289
1.9335-1.9730.19661660.17493032319889
1.973-2.01590.21921830.17773206338994
2.0159-2.06270.19881960.172634143610100
2.0627-2.11430.18621940.166934353629100
2.1143-2.17150.17711470.157334703617100
2.1715-2.23540.1892070.155934373644100
2.2354-2.30750.20821800.158834523632100
2.3075-2.390.18411780.156334623640100
2.39-2.48570.17951730.156534643637100
2.4857-2.59880.1761830.160134863669100
2.5988-2.73580.19631630.157835073670100
2.7358-2.90720.18591740.161734823656100
2.9072-3.13160.2331790.165934983677100
3.1316-3.44660.18051860.164935243710100
3.4466-3.9450.15281800.156335323712100
3.945-4.9690.14731920.14435793771100
4.969-42.15550.19491710.177837703941100
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)
11.3187-0.40590.42620.6151-0.1751.7425-0.05380.30630.1648-0.0515-0.0753-0.1275-0.02490.38470.07340.08790.00780.00980.23370.03730.152618.168414.64589.5575
21.1382-1.38120.65171.9712-0.10491.2374-0.08190.164-0.3390.08110.0620.40030.4096-0.4090.0190.2085-0.07330.0430.177-0.03440.22961.96761.480813.554
31.0898-0.0474-0.0568-0.037-0.22662.0518-0.0822-0.0791-0.1470.0111-0.023-0.00720.46070.2310.05110.21310.04880.04510.0830.01420.159613.22052.212828.9882
43.02810.38120.01792.9827-0.06352.9318-0.079-0.19960.16990.12290.21260.1159-0.09110.6466-0.0560.174-0.00620.02410.2361-0.00880.18820.870813.90435.5446
51.1294-0.2577-0.05691.02150.04571.20180.03830.00890.2357-0.0786-0.0025-0.0942-0.5488-0.0267-0.02130.33380.04960.03370.12310.00090.1874-2.263334.088445.9074
61.9291-0.62230.35110.854-0.23191.00080.06830.0027-0.28280.0426-0.10240.23370.1136-0.53030.06320.1441-0.02140.02380.2763-0.03760.2003-13.99316.626942.5048
70.3016-0.0526-0.28610.77461.06261.77020.09810.1810.1128-0.1876-0.16680.1128-0.6409-0.68420.02230.28170.1673-0.00510.33170.00450.1921-13.172928.923225.9451
80.05710.0154-0.05990.008-0.04410.1796-0.11480.12850.06270.1618-0.008-0.08-0.0235-0.0741-0.00340.10880.011-0.01630.12060.01530.138510.036412.977317.3787
90.0211-0.0107-0.02250.2307-0.20070.24590.02620.01320.0033-0.0939-0.0706-0.0589-0.2475-0.0935-0.02080.20250.0766-0.00330.186-0.0040.1406-3.328725.690938.3352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 91 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 175 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 300 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 301 through 322 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 91 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 92 through 175 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 176 through 321 )B0
8X-RAY DIFFRACTION8chain 'A' and (resid 401 through 401 )A401
9X-RAY DIFFRACTION9chain 'B' and (resid 401 through 401 )B401

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