[English] 日本語
Yorodumi
- PDB-3nx1: Crystal structure of Enterobacter sp. Px6-4 Ferulic Acid Decarboxylase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nx1
TitleCrystal structure of Enterobacter sp. Px6-4 Ferulic Acid Decarboxylase
ComponentsFerulic acid decarboxylase
KeywordsLYASE / Ferulic acid / decarboxylase / 4-vinylguaiacol / catalytic mechanism / phenolic acid decarboxylase superfamily
Function / homologyPhenolic acid decarboxylase / Phenolic acid decarboxylase (PAD) / carboxy-lyase activity / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta / Ferulic acid decarboxylase
Function and homology information
Biological speciesEnterobacter sp. Px6-4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGu, W. / Yang, J.K. / Lou, Z.Y. / Meng, Z.H. / Zhang, K.-Q.
CitationJournal: Plos One / Year: 2011
Title: Structural Basis of Enzymatic Activity for the Ferulic Acid Decarboxylase (FADase) from Enterobacter sp. Px6-4
Authors: Gu, W. / Yang, J.K. / Lou, Z.Y. / Liang, L.M. / Sun, Y. / Huang, J.W. / Li, X.M. / Cao, Y. / Meng, Z.H. / Zhang, K.-Q.
History
DepositionJul 12, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferulic acid decarboxylase
B: Ferulic acid decarboxylase


Theoretical massNumber of molelcules
Total (without water)38,3352
Polymers38,3352
Non-polymers00
Water1,72996
1
A: Ferulic acid decarboxylase


Theoretical massNumber of molelcules
Total (without water)19,1671
Polymers19,1671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferulic acid decarboxylase


Theoretical massNumber of molelcules
Total (without water)19,1671
Polymers19,1671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-15 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.477, 88.715, 49.264
Angle α, β, γ (deg.)90.00, 102.25, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ferulic acid decarboxylase


Mass: 19167.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter sp. Px6-4 (bacteria) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C6F3U5, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE SEVERAL DISCREPANCIES BETWEEN THE DEPOSITED SEQUENCE AND UNIPROT DATABASE. THE DEPOSITOR ...THERE ARE SEVERAL DISCREPANCIES BETWEEN THE DEPOSITED SEQUENCE AND UNIPROT DATABASE. THE DEPOSITOR STATES THAT THE DEPOSITED SEQUENCE IS CORRECT AND A WRONG SEQUENCE HAS BEEN DEPOSITED ON UNIPROT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 20%(w/v) PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 21, 2008
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 12722 / Num. obs: 12090 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GC9

2gc9


Resolution: 2.4→36.87 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.901 / SU B: 18.595 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.624 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26163 625 4.9 %RANDOM
Rwork0.16198 ---
obs0.16668 12090 93.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.106 Å2
Baniso -1Baniso -2Baniso -3
1-4.17 Å20 Å21.27 Å2
2---2.75 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.4→36.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 0 96 2724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0360.0222714
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9541.9263706
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.045325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.9524.539141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.19715407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4291512
X-RAY DIFFRACTIONr_chiral_restr0.2530.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022147
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2580.21190
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.330.21759
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2136
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3361.51688
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.24422664
X-RAY DIFFRACTIONr_scbond_it3.61531215
X-RAY DIFFRACTIONr_scangle_it5.1624.51042
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.403→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 28 -
Rwork0.227 636 -
obs--64.91 %
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)
10.53640.50910.0570.48560.09560.71060.00520.02510.0082-0.07060.0355-0.0017-0.05960.0519-0.0407-0.00820.02750.0133-0.0477-0.0042-0.00541.981519.160910.0633
20.57350.4253-0.03841.3910.34410.980.0199-0.0638-0.0448-0.0381-0.03250.05620.0633-0.15940.0125-0.03620.0240.0129-0.0654-0.0087-0.0243-14.82440.853912.1717
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 166
2X-RAY DIFFRACTION2B4 - 166

+
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://pdbjlvh1.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