[English] 日本語
Yorodumi
- PDB-2c2w: The fluorinase from Streptomyces cattleya is also a chlorinase. S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2c2w
TitleThe fluorinase from Streptomyces cattleya is also a chlorinase. Structure of 5'-chloro-5'-deoxyadenosine crystallised in the fluorinase.
Components5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE
KeywordsTRANSFERASE / FLUORINASE / 5'-CHLORO-5'-DEOXYADENOSINE / FLA / BACTERIAL FLUORINATING ENZYME / BACTERIAL CHLORINATING ENZYME / STREPTOMYCES CATTLEYA / CHLORINASE
Function / homology
Function and homology information


adenosyl-fluoride synthase / adenosyl-fluoride synthase activity
Similarity search - Function
Adenosyl-fluoride synthase / Bacterial fluorinating enzyme like / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain / SAM hydroxide adenosyltransferase C-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain superfamily / SAM hydroxide adenosyltransferase N-terminal domain ...Adenosyl-fluoride synthase / Bacterial fluorinating enzyme like / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain / SAM hydroxide adenosyltransferase C-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain superfamily / SAM hydroxide adenosyltransferase N-terminal domain / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5'-CHLORO-5'-DEOXYADENOSINE / Fluorinase
Similarity search - Component
Biological speciesSTREPTOMYCES CATTLEYA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMcEwan, A.R. / Naismith, J.H. / O'Hagan, D.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2006
Title: The fluorinase from Streptomyces cattleya is also a chlorinase.
Authors: Deng, H. / Cobb, S.L. / McEwan, A.R. / McGlinchey, R.P. / Naismith, J.H. / O'Hagan, D. / Robinson, D.A. / Spencer, J.B.
History
DepositionSep 30, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 28, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE
B: 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE
C: 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,31013
Polymers97,2043
Non-polymers1,10510
Water10,070559
1
A: 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE
B: 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE
C: 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE
hetero molecules

A: 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE
B: 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE
C: 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,61926
Polymers194,4096
Non-polymers2,21020
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
MethodPQS
Unit cell
Length a, b, c (Å)75.510, 129.206, 183.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE


Mass: 32401.490 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CATTLEYA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q70GK9, adenosyl-fluoride synthase
#2: Chemical ChemComp-5CD / 5'-CHLORO-5'-DEOXYADENOSINE


Mass: 285.687 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H12ClN5O3
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 559 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNCBI CQ871083.1

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 0.87 %
Description: LIGANDS AND WATER WERE REMOVED FROM 1RQR BEFORE MOLREP
Crystal growpH: 4
Details: 32% PEG 1000, 0.1M PHOSPHATE-CITRATE PH4.2, 0.2 M LI2SO4, pH 4.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 21, 2005 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND 111-GE-20 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→44.5 Å / Num. obs: 59706 / % possible obs: 98.8 % / Observed criterion σ(I): 2.4 / Redundancy: 4.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RQR

1rqr


Resolution: 2→45 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.909 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3032 5.1 %RANDOM
Rwork0.196 ---
obs0.198 56675 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 2→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6660 0 64 559 7283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226921
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9789459
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6365870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94523.131297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.117151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4811551
X-RAY DIFFRACTIONr_chiral_restr0.0750.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025376
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2620.33744
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.330.54723
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.5934
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3830.3129
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.520.536
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.561.54432
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92126996
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.37432845
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1744.52463
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→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.325 221
Rwork0.248 4216
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)
11.6821-0.6180.52830.7965-0.31871.0839-0.03680.15440.3370.0081-0.1321-0.2065-0.20160.15780.1689-0.0264-0.0374-0.0325-0.16430.0358-0.183415.6150.131-22.824
20.99140.3584-0.72830.6778-0.70361.406-0.090.0058-0.2492-0.1213-0.0886-0.1730.38680.1230.17870.05820.02980.0071-0.1825-0.0023-0.173110.40719.255-21.851
30.31130.0687-0.0181.32340.25631.3174-0.0082-0.00860.02470.0158-0.03230.31350.0775-0.27820.0405-0.0295-0.0220.0101-0.1429-0.0117-0.186-13.29239.384-18.001
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 290
2X-RAY DIFFRACTION2B10 - 290
3X-RAY DIFFRACTION3C10 - 290

+
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