[English] 日本語
Yorodumi
- PDB-4r1t: Crystal structure of Petunia hydrida cinnamoyl-CoA reductase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r1t
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
molecular iodine / Cinnamoyl-CoA reductase 1
Similarity search - Component
Biological speciesPetunia x hybrida (garden petunia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cinnamoyl CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5232
Polymers37,2701
Non-polymers2541
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.844, 127.844, 80.016
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-546-

HOH

21A-717-

HOH

-
Components

#1: Protein cinnamoyl CoA reductase


Mass: 37269.555 Da / Num. of mol.: 1
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-I2I / molecular iodine / Iodine


Mass: 253.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.87 %
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, 0.2 M sodium iodide, and 2 mM DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
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: Aug 2, 2012 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→41.847 Å / Num. all: 42777 / Num. obs: 42777 / % possible obs: 100 % / Redundancy: 18.7 % / Rsym value: 0.061 / Net I/σ(I): 29.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.799.60.471.65900961320.47100
1.79-1.99.70.2632.95658758250.263100
1.9-2.0313.30.1754.17310054860.175100
2.03-2.1920.10.1315.510260751030.131100
2.19-2.425.40.0997.112064747440.099100
2.4-2.69260.0729.411195442990.072100
2.69-3.125.60.0649.79827038320.064100
3.1-3.824.60.0629.48045832670.062100
3.8-5.3823.50.0512.26083025880.05100
5.38-41.84723.30.03816.23496815010.03898.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation41.85 Å2.5 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.21data scaling
MOLREPphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→41.847 Å / FOM work R set: 0.8765 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2145 5.02 %random
Rwork0.1764 ---
obs0.1773 42736 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.41 Å2 / Biso mean: 34.39 Å2 / Biso min: 11.67 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2441 0 2 250 2693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012502
X-RAY DIFFRACTIONf_angle_d1.1753406
X-RAY DIFFRACTIONf_chiral_restr0.071396
X-RAY DIFFRACTIONf_plane_restr0.006436
X-RAY DIFFRACTIONf_dihedral_angle_d13.164918
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.73950.24881340.204826552789100
1.7395-1.78310.24061410.208626542795100
1.7831-1.83130.22811410.193826512792100
1.8313-1.88510.23481410.192226862827100
1.8851-1.9460.21051300.18226812811100
1.946-2.01550.20541320.173526842816100
2.0155-2.09620.16791490.163526692818100
2.0962-2.19160.18251730.158926372810100
2.1916-2.30720.19211400.162827022842100
2.3072-2.45170.22871420.166826932835100
2.4517-2.6410.19471400.176227082848100
2.641-2.90670.20051320.176727492881100
2.9067-3.32720.21231430.184927292872100
3.3272-4.19130.17091680.161527742942100
4.1913-41.85940.19041390.18862919305899
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)
13.0910.3434-0.18312.32810.35663.6368-0.01440.4085-0.3578-0.23410.0666-0.17610.170.20750.00350.14450.03070.01560.2185-0.06780.216916.265230.7694-9.6123
23.63420.0872-0.03942.58890.03352.8606-0.06230.26840.2914-0.12410.10240.4064-0.4078-0.525-0.03260.17350.0531-0.00640.27220.04560.2085-1.588742.4699-2.4304
32.48841.4817-0.20382.2074-0.3381.86360.1499-0.19220.15870.3139-0.1325-0.0482-0.48120.1425-0.00830.2717-0.0331-0.02590.1416-0.01450.146616.74449.25485.6677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 88 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 175 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 321 )A0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more