[English] 日本語
Yorodumi
- PDB-5yvp: Crystal structure of an apo form cyclase Filc1 from Fischerella s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yvp
TitleCrystal structure of an apo form cyclase Filc1 from Fischerella sp. TAU
Componentscyclase A
KeywordsTRANSFERASE / prenyltransferase
Function / homology12-epi-hapalindole U synthase
Function and homology information
Biological speciesFischerella sp. TAU (Cyanobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.051 Å
AuthorsHu, X.Y. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: The Crystal Structure of a Class of Cyclases that Catalyze the Cope Rearrangement
Authors: Chen, C.C. / Hu, X. / Tang, X. / Yang, Y. / Ko, T.P. / Gao, J. / Zheng, Y. / Huang, J.W. / Yu, Z. / Li, L. / Han, S. / Cai, N. / Zhang, Y. / Liu, W. / Guo, R.T.
History
DepositionNov 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 2, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cyclase A
B: cyclase A
C: cyclase A
D: cyclase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,39714
Polymers97,6884
Non-polymers70910
Water6,648369
1
A: cyclase A
C: cyclase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1997
Polymers48,8442
Non-polymers3555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-3 kcal/mol
Surface area17180 Å2
MethodPISA
2
B: cyclase A
D: cyclase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1997
Polymers48,8442
Non-polymers3555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-5 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.758, 255.893, 34.912
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-479-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 28 through 225)
21(chain B and resid 28 through 225)
31chain C
41chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 28 through 225)A28 - 225
211(chain B and resid 28 through 225)B28 - 225
311chain CC28 - 225
411chain DD28 - 225

-
Components

#1: Protein
cyclase A / FilC1


Mass: 24422.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella sp. TAU (Cyanobacteria) / Gene: filC1 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1P8VSI6
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 1.98 Å3/Da / Density % sol: 37.99 % / Mosaicity: 0.714 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.0M sodium citrate, 0.1M Imidazole pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 4, 2017
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. obs: 49655 / % possible obs: 99.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 33.44 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.038 / Rrim(I) all: 0.082 / Χ2: 1.935 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.124.90.448560.9560.2010.4491.66299.9
2.12-2.214.90.31549180.9690.1570.3531.694100
2.21-2.314.90.2449410.9840.120.2691.796100
2.31-2.434.90.17949180.9890.0890.2011.887100
2.43-2.584.90.13249340.9920.0670.1482.00199.9
2.58-2.784.80.10749890.9940.0540.122.03899.7
2.78-3.064.80.07749570.9940.040.0882.16899.6
3.06-3.550.05750370.9960.0290.0642.09399.1
3.5-4.414.90.05549450.9950.0290.0632.01597.1
4.41-254.90.05251600.9940.0280.0591.98596.3

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(1.11.1_2575: ???)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YVK
Resolution: 2.051→24.242 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.03
RfactorNum. reflection% reflection
Rfree0.255 1993 4.03 %
Rwork0.2123 --
obs0.214 49490 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.66 Å2 / Biso mean: 42.5092 Å2 / Biso min: 21.41 Å2
Refinement stepCycle: final / Resolution: 2.051→24.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6120 0 34 369 6523
Biso mean--64.55 45.13 -
Num. residues----794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076292
X-RAY DIFFRACTIONf_angle_d1.1098586
X-RAY DIFFRACTIONf_chiral_restr0.066966
X-RAY DIFFRACTIONf_plane_restr0.0061130
X-RAY DIFFRACTIONf_dihedral_angle_d9.9063654
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3681X-RAY DIFFRACTION13.062TORSIONAL
12B3681X-RAY DIFFRACTION13.062TORSIONAL
13C3681X-RAY DIFFRACTION13.062TORSIONAL
14D3681X-RAY DIFFRACTION13.062TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0508-2.1020.33921340.25853199333397
2.102-2.15880.32621450.251134123557100
2.1588-2.22230.31141400.245533513491100
2.2223-2.2940.30071420.241233543496100
2.294-2.37590.32341420.248533673509100
2.3759-2.47090.32581430.240834343577100
2.4709-2.58330.31991410.238533493490100
2.5833-2.71930.31251420.24534223564100
2.7193-2.88940.29391440.24063401354599
2.8894-3.11210.28271410.23563414355599
3.1121-3.42450.23671430.21763409355299
3.4245-3.91820.21621430.19533417356098
3.9182-4.92970.1981430.16493375351896
4.9297-24.24380.23361500.19663593374397
Refinement TLS params.Method: refined / Origin x: -21.8275 Å / Origin y: -14.6614 Å / Origin z: -8.4694 Å
111213212223313233
T0.2586 Å20.0116 Å20.0408 Å2-0.294 Å20.0159 Å2--0.275 Å2
L-0.0236 °20.026 °20.0447 °2-1.6087 °20.101 °2--0.0663 °2
S-0.0456 Å °-0.0031 Å °-0.0174 Å °-0.0387 Å °0.036 Å °-0.1131 Å °0.0284 Å °-0.0208 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA27 - 225
2X-RAY DIFFRACTION1allB27 - 225
3X-RAY DIFFRACTION1allC28 - 225
4X-RAY DIFFRACTION1allD28 - 225
5X-RAY DIFFRACTION1allE1 - 8
6X-RAY DIFFRACTION1allF1 - 2
7X-RAY DIFFRACTION1allS1 - 369

+
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