[English] 日本語
Yorodumi
- PDB-3gl0: Crystal structure of dicamba monooxygenase bound to 3,6 dichloros... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gl0
TitleCrystal structure of dicamba monooxygenase bound to 3,6 dichlorosalicylic acid (DCSA)
ComponentsDdmC
KeywordsOXIDOREDUCTASE / Rieske protein / non-heme mononuclear iron / oxygenase
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen into the other donor / : / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
Vanillate O-demethylase oxygenase-like, C-terminal catalytic domain / Vanillate O-demethylase oxygenase C-terminal domain / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. ...Vanillate O-demethylase oxygenase-like, C-terminal catalytic domain / Vanillate O-demethylase oxygenase C-terminal domain / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / 3,6-dichloro-2-hydroxybenzoic acid / OXYGEN MOLECULE / Dicamba O-demethylase, oxygenase component
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsWilson, M.A. / Dumitru, R. / Jiang, W.Z. / Weeks, D.P.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of dicamba monooxygenase: a Rieske nonheme oxygenase that catalyzes oxidative demethylation.
Authors: Dumitru, R. / Jiang, W.Z. / Weeks, D.P. / Wilson, M.A.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: 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 / struct_conn / struct_ncs_dom_lim / 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 / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DdmC
B: DdmC
C: DdmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,66322
Polymers115,9253
Non-polymers1,73819
Water16,646924
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint-89 kcal/mol
Surface area40630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.205, 81.205, 158.557
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 2 - 155 / Label seq-ID: 2 - 155

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein DdmC / dicamba monooxygenase


Mass: 38641.695 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Strain: DI-6 / Gene: ddmC / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5S3I3

-
Non-polymers , 6 types, 943 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-HXX / 3,6-dichloro-2-hydroxybenzoic acid / 3,6 dichlorosalicylic acid


Mass: 207.011 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H4Cl2O3
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 924 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 5% PEG 4000, 100 mM sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2007 / Details: Bent Rh coated conical Si mirror
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→70 Å / Num. all: 118165 / Num. obs: 117603 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 27.8
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.6 / Num. unique all: 11814 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.75→42.25 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.679 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.1 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20619 5898 5 %RANDOM
Rwork0.1678 ---
obs0.16972 117603 99.5 %-
all-118165 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7672 0 82 924 8678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227925
X-RAY DIFFRACTIONr_bond_other_d00.025377
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9610763
X-RAY DIFFRACTIONr_angle_other_deg0.735313029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1895987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92623.59376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.693151221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8811567
X-RAY DIFFRACTIONr_chiral_restr0.090.21161
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028937
X-RAY DIFFRACTIONr_gen_planes_other00.021608
X-RAY DIFFRACTIONr_nbd_refined0.2270.21608
X-RAY DIFFRACTIONr_nbd_other0.2420.25890
X-RAY DIFFRACTIONr_nbtor_refined0.1870.23782
X-RAY DIFFRACTIONr_nbtor_other0.090.24156
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2643
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3280.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4370.233
X-RAY DIFFRACTIONr_mcbond_it3.2391.56347
X-RAY DIFFRACTIONr_mcbond_other1.1191.51991
X-RAY DIFFRACTIONr_mcangle_it3.49327926
X-RAY DIFFRACTIONr_scbond_it5.33533446
X-RAY DIFFRACTIONr_scangle_it6.6954.52830
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A886medium positional0.260.5
2B886medium positional0.270.5
3C886medium positional0.250.5
1A1087loose positional0.375
2B1087loose positional0.385
3C1087loose positional0.45
1A886medium thermal1.832
2B886medium thermal1.832
3C886medium thermal1.52
1A1087loose thermal2.4910
2B1087loose thermal2.5110
3C1087loose thermal210
LS refinement shellResolution: 1.75→1.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 449 -
Rwork0.257 8298 -
obs--99.61 %

+
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