[English] 日本語
Yorodumi
- PDB-2vss: Wild-type Hydroxycinnamoyl-CoA hydratase lyase in complex with ac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vss
TitleWild-type Hydroxycinnamoyl-CoA hydratase lyase in complex with acetyl- CoA and vanillin
Components(P-HYDROXYCINNAMOYL COA ...) x 3
KeywordsLYASE / ALDOLASE / CROTONASE / HYDRATASE
Function / homology
Function and homology information


feruloyl-CoA hydratase/lyase / feruloyl-CoA hydratase/lyase activity / isoprenoid catabolic process
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2850 / : / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ClpP/crotonase-like domain superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2850 / : / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ClpP/crotonase-like domain superfamily / Helix non-globular / Special / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / 4-hydroxy-3-methoxybenzaldehyde / Hydroxycinnamoyl-CoA hydratase-lyase
Similarity search - Component
Biological speciesPSEUDOMONAS FLUORESCENS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsBennett, J.P. / Bertin, L.M. / Brzozowski, A.M. / Walton, N.J. / Grogan, G.
CitationJournal: Biochem.J. / Year: 2008
Title: A Ternary Complex of Hydroxycinnamoyl-Coa Hydratase-Lyase (Hchl) with Acetyl-Coa and Vanillin Gives Insights Into Substrate Specificity and Mechanism.
Authors: Bennett, J.P. / Bertin, L.M. / Moulton, B. / Fairlamb, I.J.S. / Brzozowski, A.M. / Walton, N.J. / Grogan, G.
History
DepositionApr 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 4, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_database_status / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
B: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
C: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
D: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
E: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
F: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,66311
Polymers186,2736
Non-polymers3,3905
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32900 Å2
ΔGint-109 kcal/mol
Surface area45240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.223, 130.595, 144.663
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
P-HYDROXYCINNAMOYL COA ... , 3 types, 6 molecules ABCDEF

#1: Protein
P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE / HYDROXYCINNAMOYL-COA HYDRATASE-LYASE


Mass: 31044.613 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: AN103 / Description: INSTITUTE OF FOOD RESEARCH, NORWICH U.K. / Plasmid: YSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69762, trans-feruloyl-CoA hydratase
#2: Protein P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE / HYDROXYCINNAMOYL-COA HYDRATASE-LYASE


Mass: 31021.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: AN103 / Description: INSTITUTE OF FOOD RESEARCH, NORWICH U.K. / Plasmid: YSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69762, trans-feruloyl-CoA hydratase
#3: Protein P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE / HYDROXYCINNAMOYL-COA HYDRATASE-LYASE


Mass: 31072.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: AN103 / Description: INSTITUTE OF FOOD RESEARCH, NORWICH U.K. / Plasmid: YSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69762, trans-feruloyl-CoA hydratase

-
Non-polymers , 3 types, 321 molecules

#4: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#5: Chemical ChemComp-V55 / 4-hydroxy-3-methoxybenzaldehyde / p-vanillin


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.3 Å3/Da / Density % sol: 46.4 % / Description: NONE
Crystal growDetails: PROTEIN CONCENTRATION OF 10 MG ML-1 IN 11% (W/V) PEG 20 000 DA WITH 8% (V/V) PEG 550 DA MONOMETHYL ETHER, 0.8 M SODIUM FORMATE AND 0.2% (V/V) BUTANE 1,4-DIOL IN 0.05 M 2-(N-MORPHOLINO) ...Details: PROTEIN CONCENTRATION OF 10 MG ML-1 IN 11% (W/V) PEG 20 000 DA WITH 8% (V/V) PEG 550 DA MONOMETHYL ETHER, 0.8 M SODIUM FORMATE AND 0.2% (V/V) BUTANE 1,4-DIOL IN 0.05 M 2-(N-MORPHOLINO)ETHANESULFONIC ACID BUFFER PH 5.6. 10MM FERULOYL-COA

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178
DetectorDate: Aug 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.22→97.13 Å / Num. obs: 73967 / % possible obs: 91.5 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9
Reflection shellResolution: 2.22→2.27 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.9 / % possible all: 50.3

-
Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J5I

2j5i


Resolution: 2.22→97.13 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.102 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3933 5 %RANDOM
Rwork0.183 ---
obs0.186 73967 91.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2---1.84 Å20 Å2
3---2.22 Å2
Refinement stepCycle: LAST / Resolution: 2.22→97.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11344 0 215 316 11875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02211847
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9661.98516074
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94951455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42524.122524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.883152033
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7141588
X-RAY DIFFRACTIONr_chiral_restr0.1240.21769
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028907
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.25825
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.27924
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2603
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3030.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0691.57516
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58211560
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.86135144
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1424.54514
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.22→2.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 152
Rwork0.217 2976
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)
10.90080.38280.35390.92620.22410.6087-0.20750.351-0.0751-0.23270.2378-0.0036-0.06450.2783-0.0303-0.0109-0.11050.02340.1156-0.0391-0.131226.5466-32.3851-53.2759
20.54470.40460.36550.7246-0.00920.9182-0.05650.00170.0819-0.05390.02510.2968-0.0037-0.04880.0313-0.0493-0.0233-0.0527-0.09630.02440.1085-3.6727-28.9575-37.5513
30.9757-0.14630.28251.0790.35920.4292-0.23830.19480.284-0.3620.11690.2217-0.21990.1380.12140.1062-0.1562-0.1918-0.06640.12480.025811.2412-2.7222-51.1565
40.55770.15790.27930.8674-0.15380.61580.0083-0.08520.05590.1076-0.03470.11590.0096-0.03890.0264-0.0465-0.00020.0211-0.0526-0.0126-0.012611.2089-24.644-10.671
50.65410.23520.2320.55120.07580.4665-0.04190.0931-0.06360.02750.0522-0.09030.01970.1089-0.0102-0.08230.0178-0.0211-0.01290.00130.009841.1271-26.9545-25.7769
60.6351-0.01430.02880.5470.120.3884-0.09910.03870.16520.05360.0163-0.0175-0.07690.04960.0828-0.0302-0.0349-0.078-0.09510.02650.056425.75833.5392-23.7749
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 249
2X-RAY DIFFRACTION2B4 - 250
3X-RAY DIFFRACTION3C5 - 249
4X-RAY DIFFRACTION4D3 - 248
5X-RAY DIFFRACTION5E4 - 249
6X-RAY DIFFRACTION6F3 - 248

+
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