[English] 日本語
Yorodumi
- PDB-5yvl: Crystal structure of a cyclase Hpiu5 from Fischerella sp. ATCC 43239 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yvl
TitleCrystal structure of a cyclase Hpiu5 from Fischerella sp. ATCC 43239
Componentscyclase
KeywordsTRANSFERASE / prenyltransferase
Function / homology: / HpiC1 cyclase / metal ion binding / 12-epi-hapalindole C/U synthase
Function and homology information
Biological speciesFischerella sp. ATCC 43239 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.059 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 26, 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 1.2Dec 26, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,78215
Polymers98,1004
Non-polymers68111
Water9,476526
1
A: cyclase
B: cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3317
Polymers49,0502
Non-polymers2805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-0 kcal/mol
Surface area16990 Å2
MethodPISA
2
C: cyclase
D: cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4518
Polymers49,0502
Non-polymers4016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-17 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.390, 114.311, 132.439
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 28 through 225)
21chain B
31(chain C and resid 28 through 225)
41(chain D and resid 28 through 225)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 28 - 225 / Label seq-ID: 26 - 223

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 28 through 225)AA
2chain BBB
3(chain C and resid 28 through 225)CC
4(chain D and resid 28 through 225)DD

-
Components

#1: Protein
cyclase / HpiU5


Mass: 24525.115 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella sp. ATCC 43239 (bacteria) / Gene: hpiU5 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A076NBW8
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.41 Å3/Da / Density % sol: 48.9 % / Mosaicity: 1.047 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2M sodium chloride, 20%(w/v) PEG4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 15, 2017
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.059→25 Å / Num. obs: 56433 / % possible obs: 95 % / Redundancy: 4.1 % / Biso Wilson estimate: 33.47 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.024 / Rrim(I) all: 0.053 / Χ2: 1.294 / Net I/σ(I): 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.06-2.133.60.48355080.8310.2880.5661.28194.1
2.13-2.223.70.39254510.8860.230.4571.28692.9
2.22-2.323.70.31553820.9290.1820.3661.31691.8
2.32-2.443.80.2353450.970.130.2661.39591.1
2.44-2.593.80.16854060.9810.0950.1941.45791.6
2.59-2.83.90.11855510.9890.0660.1361.35694.2
2.8-3.084.30.06756750.9970.0350.0761.26195.7
3.08-3.524.60.04958650.9980.0240.0551.74298.3
3.52-4.434.80.02860170.9990.0130.0311.242100
4.43-254.60.018623310.0090.020.72599.6

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YVK

5yvk


Resolution: 2.059→24.993 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.12
RfactorNum. reflection% reflection
Rfree0.2361 1997 3.54 %
Rwork0.1789 --
obs0.1809 56358 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.93 Å2 / Biso mean: 38.2123 Å2 / Biso min: 20.03 Å2
Refinement stepCycle: final / Resolution: 2.059→24.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6205 0 68 526 6799
Biso mean--53.3 42.57 -
Num. residues----803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146383
X-RAY DIFFRACTIONf_angle_d1.4978721
X-RAY DIFFRACTIONf_chiral_restr0.084971
X-RAY DIFFRACTIONf_plane_restr0.0121157
X-RAY DIFFRACTIONf_dihedral_angle_d11.0623713
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3696X-RAY DIFFRACTION10.4TORSIONAL
12B3696X-RAY DIFFRACTION10.4TORSIONAL
13C3696X-RAY DIFFRACTION10.4TORSIONAL
14D3696X-RAY DIFFRACTION10.4TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0591-2.13260.27481940.24265274546893
2.1326-2.2180.31991930.23465256544993
2.218-2.31880.30281910.22445188537992
2.3188-2.4410.30951890.21275153534291
2.441-2.59380.23731920.19195220541292
2.5938-2.79380.29671960.21025346554294
2.7938-3.07450.24852010.19865470567196
3.0745-3.51830.24312070.18055659586698
3.5183-4.42870.20322130.1558006013100
4.4287-24.99440.19452210.153359956216100

+
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