[English] 日本語
Yorodumi
- PDB-2fcv: SyrB2 with Fe(II), bromide, and alpha-ketoglutarate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fcv
TitleSyrB2 with Fe(II), bromide, and alpha-ketoglutarate
Componentssyringomycin biosynthesis enzyme 2
KeywordsBIOSYNTHETIC PROTEIN / mononuclear iron / cupin / halogenase
Function / homology
Function and homology information


L-threonyl-[L-threonyl-carrier protein] 4-chlorinase / oxidoreductase activity / metal ion binding
Similarity search - Function
Chlorinating enzyme / q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / BROMIDE ION / Chem-DSU / : / : / L-threonyl-[L-threonyl-carrier protein] 4-chlorinase
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY / Resolution: 1.8 Å
AuthorsBlasiak, L.C. / Drennan, C.L.
CitationJournal: Nature / Year: 2006
Title: Crystal structure of the non-haem iron halogenase SyrB2 in syringomycin biosynthesis.
Authors: Blasiak, L.C. / Vaillancourt, F.H. / Walsh, C.T. / Drennan, C.L.
History
DepositionDec 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: syringomycin biosynthesis enzyme 2
B: syringomycin biosynthesis enzyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,58511
Polymers71,3652
Non-polymers1,2209
Water8,377465
1
A: syringomycin biosynthesis enzyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5416
Polymers35,6831
Non-polymers8585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: syringomycin biosynthesis enzyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0445
Polymers35,6831
Non-polymers3624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.12, 89.35, 125.06
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein syringomycin biosynthesis enzyme 2


Mass: 35682.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: SyrB2 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 5748808, UniProt: Q9RBY6*PLUS

-
Non-polymers , 5 types, 474 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-DSU / ((2R,3S,4S,5S)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)-5-((2R,3S,4S,5S,6R)-3,4,5-TRIHYDROXY-6-METHOXY-TETRAHYDRO-2H-PYRAN-2-YLOXY)-TETRAHYDROFURAN-2-YL)METHYL NONANOATE


Mass: 496.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H40O12
#5: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 3350, 250 mM Na formate, spermine tetra-HCl, n-decanoyl sucrose , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9195 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 4, 2005 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 1.8→42.18 Å / Num. all: 57215 / Num. obs: 57215 / % possible obs: 95.3 % / Redundancy: 7.6 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.072 / Net I/σ(I): 18.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 7474 / Rsym value: 0.337 / % possible all: 86.4

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: RIGID BODY
Starting model: SyrB2 with Fe(II), chloride, and alpha-ketoglutarate

Resolution: 1.8→42.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.307 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3341 5.9 %Same as starting model
Rwork0.171 ---
all0.173 56498 --
obs0.173 56498 93.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.096 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.35 Å2
Refine analyzeLuzzati coordinate error obs: 0.183 Å
Refinement stepCycle: LAST / Resolution: 1.8→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 60 465 5339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225020
X-RAY DIFFRACTIONr_bond_other_d0.0020.024267
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9346811
X-RAY DIFFRACTIONr_angle_other_deg1.34539943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8365599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64423.91266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48615768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9231534
X-RAY DIFFRACTIONr_chiral_restr0.0970.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025687
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021097
X-RAY DIFFRACTIONr_nbd_refined0.2080.2926
X-RAY DIFFRACTIONr_nbd_other0.2030.24267
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22384
X-RAY DIFFRACTIONr_nbtor_other0.0890.22572
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2361
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.212
X-RAY DIFFRACTIONr_mcbond_it1.3871.53819
X-RAY DIFFRACTIONr_mcbond_other0.2521.51220
X-RAY DIFFRACTIONr_mcangle_it1.53524823
X-RAY DIFFRACTIONr_scbond_it2.47432422
X-RAY DIFFRACTIONr_scangle_it3.4374.51988
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 296 -
Rwork0.201 3309 -
obs-3605 82.01 %

+
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