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- PDB-4r1u: Crystal structure of Medicago truncatula cinnamoyl-CoA reductase -

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Basic information

Entry
Database: PDB / ID: 4r1u
TitleCrystal structure of Medicago truncatula 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 / phenylpropanoid biosynthetic process / lignin biosynthetic process / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / 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
ACETATE ION / Cinnamoyl-CoA reductase 2
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.18 Å
AuthorsNoel, J.P. / Bomati, E.K. / Louie, G.V. / Bowman, M.E.
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 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)77,3845
Polymers77,2072
Non-polymers1773
Water5,441302
1
A: Cinnamoyl CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6632
Polymers38,6041
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cinnamoyl CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7223
Polymers38,6041
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.795, 96.821, 106.913
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cinnamoyl CoA reductase


Mass: 38603.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MtCCR2, MTR_4g006940 / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G7JEE5
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 21% (w/v) polyethylene glycol 8000, 0.2 M potassium acetate, 100 mM HEPES, and 2 mM DTT, pH 7.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9792, 0.9184, 0.9794
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.91841
30.97941
ReflectionHighest resolution: 2.18 Å / Num. all: 38353 / Num. obs: 38353

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHARPphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.18→19.98 Å / FOM work R set: 0.781 / SU ML: 0.28 / σ(F): 0.49 / Phase error: 28.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 3835 10 %
Rwork0.1975 --
obs0.2022 38336 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.69 Å2 / Biso mean: 37.13 Å2 / Biso min: 14.58 Å2
Refinement stepCycle: LAST / Resolution: 2.18→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4825 0 12 302 5139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084938
X-RAY DIFFRACTIONf_angle_d1.0996719
X-RAY DIFFRACTIONf_chiral_restr0.074780
X-RAY DIFFRACTIONf_plane_restr0.005856
X-RAY DIFFRACTIONf_dihedral_angle_d151798
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.18-2.20760.34661500.31611239138997
2.2076-2.23660.36421410.30041220136196
2.2366-2.26720.34231500.28881247139797
2.2672-2.29950.29681470.26461228137597
2.2995-2.33380.30481210.24451245136697
2.3338-2.37020.29041450.23861251139697
2.3702-2.4090.27751330.24091237137097
2.409-2.45050.30131350.23181262139796
2.4505-2.4950.29271500.22131217136797
2.495-2.54290.26661330.21261267140098
2.5429-2.59470.27351470.2131256140398
2.5947-2.6510.26681470.20181243139098
2.651-2.71250.27741450.21041283142899
2.7125-2.78010.26041300.20991292142299
2.7801-2.85510.28931450.206612931438100
2.8551-2.93890.27941390.21481287142699
2.9389-3.03340.271350.202612941429100
3.0334-3.14140.24361340.193812991433100
3.1414-3.26670.2661210.205213201441100
3.2667-3.41470.21131310.19841313144499
3.4147-3.59370.25811560.19412731429100
3.5937-3.81740.21141560.17481302145899
3.8174-4.10980.22051590.162612861445100
4.1098-4.51910.16191480.15741302145099
4.5191-5.16310.21541580.15711321147999
5.1631-6.46810.24861440.19911341148599
6.4681-19.98130.1951350.18861383151897

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