[English] 日本語
Yorodumi
- PDB-2hmm: Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Anthracene -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hmm
TitleCrystal Structure of Naphthalene 1,2-Dioxygenase Bound to Anthracene
Components(Naphthalene 1,2-dioxygenase ...) x 2
KeywordsOXIDOREDUCTASE / Protein / Rieske Oxygenase
Function / homology
Function and homology information


naphthalene 1,2-dioxygenase / naphthalene 1,2-dioxygenase activity / 3-phenylpropionate catabolic process / dioxygenase activity / catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 ...Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / 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 / Nuclear Transport Factor 2; Chain: A, - #50 / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ANTHRACENE / : / FE2/S2 (INORGANIC) CLUSTER / Naphthalene 1,2-dioxygenase system, large oxygenase component / Naphthalene 1,2-dioxygenase system, small oxygenase component
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 1.6 Å
AuthorsFerraro, D.J. / Okerlund, A.L. / Mowers, J.C. / Ramaswamy, S.
CitationJournal: J.Bacteriol. / Year: 2006
Title: Structural basis for regioselectivity and stereoselectivity of product formation by naphthalene 1,2-dioxygenase.
Authors: Ferraro, D.J. / Okerlund, A.L. / Mowers, J.C. / Ramaswamy, S.
History
DepositionJul 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 2, 2020Group: Derived calculations / Structure summary / Category: struct_keywords / struct_site
Item: _struct_keywords.text / _struct_site.pdbx_auth_asym_id ..._struct_keywords.text / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Naphthalene 1,2-dioxygenase alpha subunit
B: Naphthalene 1,2-dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,85532
Polymers72,6332
Non-polymers2,22230
Water13,169731
1
A: Naphthalene 1,2-dioxygenase alpha subunit
B: Naphthalene 1,2-dioxygenase beta subunit
hetero molecules

A: Naphthalene 1,2-dioxygenase alpha subunit
B: Naphthalene 1,2-dioxygenase beta subunit
hetero molecules

A: Naphthalene 1,2-dioxygenase alpha subunit
B: Naphthalene 1,2-dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,56596
Polymers217,9006
Non-polymers6,66590
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)139.725, 139.725, 208.113
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-845-

HOH

DetailsThe biological assembly is and alpha3 beta3 hexamer. One alpha-beta dimer is in the assymetric unit. The others can be generated by the three-fold axis: y, -x-y, z -x-y, x, z

-
Components

-
Naphthalene 1,2-dioxygenase ... , 2 types, 2 molecules AB

#1: Protein Naphthalene 1,2-dioxygenase alpha subunit / Naphthalene 1 / 2-dioxygenase ISP alpha


Mass: 49664.355 Da / Num. of mol.: 1 / Mutation: F352V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: doxB / Plasmid: pDTG121 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: P0A111, naphthalene 1,2-dioxygenase
#2: Protein Naphthalene 1,2-dioxygenase beta subunit / Naphthalene 1 / 2-dioxygenase ISP beta


Mass: 22969.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: doxD / Plasmid: pDTG121 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: P0A113, naphthalene 1,2-dioxygenase

-
Non-polymers , 6 types, 761 molecules

#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#6: Chemical ChemComp-AN3 / ANTHRACENE


Mass: 178.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10
#7: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / 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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 279.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.9-2.2 M Ammonium Sulfate, 4-6% Dioxane, 0.1 M MES, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.04021 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Nov 3, 2004
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04021 Å / Relative weight: 1
ReflectionResolution: 1.6→15.97 Å / Num. all: 100884 / Num. obs: 100884 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.16 % / Rmerge(I) obs: 0.069 / Χ2: 0.95 / Net I/σ(I): 10 / Scaling rejects: 6502
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.94 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.3 / Num. measured all: 29139 / Num. unique all: 9731 / Χ2: 1.16 / % possible all: 95.5

-
Processing

Software
NameVersionClassificationNB
d*TREK9.4Ldata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
d*TREKdata reduction
RefinementMethod to determine structure: RIGID BODY REFINEMENT
Starting model: 1O7H

1o7h


Resolution: 1.6→15.97 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.523 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.198 5049 5 %RANDOM
Rwork0.164 ---
all0.165 100819 --
obs0.165 100819 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.738 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 0 131 731 5950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215316
X-RAY DIFFRACTIONr_bond_other_d0.0020.023652
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9457149
X-RAY DIFFRACTIONr_angle_other_deg0.89838814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4895638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22224.03268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42615869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3331535
X-RAY DIFFRACTIONr_chiral_restr0.0830.2741
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025917
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021124
X-RAY DIFFRACTIONr_nbd_refined0.2110.21110
X-RAY DIFFRACTIONr_nbd_other0.2120.24107
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22527
X-RAY DIFFRACTIONr_nbtor_other0.0880.22671
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2518
X-RAY DIFFRACTIONr_metal_ion_refined0.0210.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.2111
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.246
X-RAY DIFFRACTIONr_mcbond_it1.2621.54075
X-RAY DIFFRACTIONr_mcbond_other0.3331.51307
X-RAY DIFFRACTIONr_mcangle_it1.47525063
X-RAY DIFFRACTIONr_scbond_it2.58832550
X-RAY DIFFRACTIONr_scangle_it3.1944.52083
X-RAY DIFFRACTIONr_rigid_bond_restr2.22236540
X-RAY DIFFRACTIONr_sphericity_free9.6431
X-RAY DIFFRACTIONr_sphericity_bonded2.14335106
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 363 -
Rwork0.282 6836 -
obs-7199 95.26 %

+
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