[English] 日本語
Yorodumi
- PDB-2wm2: CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUIN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wm2
TitleCRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) FROM ARTHROBACTER NITROGUAJACOLICUS RU61A IN COMPLEX WITH CHLORIDE
Components1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE
Function / homology
Function and homology information


3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase / 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / :
Similarity search - Function
Uteroglobin - #20 / Uteroglobin / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / S,R MESO-TARTARIC ACID / 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase / 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
Similarity search - Component
Biological speciesARTHROBACTER NITROGUAJACOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.7 Å
AuthorsSteiner, R.A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural Basis for Cofactor-Independent Dioxygenation of N-Heteroaromatic Compounds at the {Alpha}/{Beta}-Hydrolase Fold.
Authors: Steiner, R.A. / Janssen, H.J. / Roversi, P. / Oakley, A.J. / Fetzner, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization and Preliminary X-Ray Analysis of 1H-3-Hydroxy-4-Oxoquinaldine 2,4-Dioxygenase from Arthrobacter Nitroguajacolicus Ru61A: A Cofactor-Devoid Dioxygenase of the Alpha/Beta-Hydrolase-Fold Superfamily.
Authors: Steiner, R.A. / Frerichs-Deeken, U. / Fetzner, S.
History
DepositionJun 29, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
B: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
C: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
D: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,16843
Polymers128,6654
Non-polymers2,50339
Water2,918162
1
A: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,15513
Polymers32,1661
Non-polymers98812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,79410
Polymers32,1661
Non-polymers6289
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,66710
Polymers32,1661
Non-polymers5019
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: 1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,55210
Polymers32,1661
Non-polymers3869
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.770, 167.000, 166.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A5 - 274
2113B5 - 274
3113C5 - 274
4113D5 - 274

NCS oper:
IDCodeMatrixVector
1given(0.99978, 0.01469, 0.01514), (-0.0144, 0.99972, -0.01885), (-0.01542, 0.01863, 0.99971)-1.72376, 70.07345, -68.28546
2given(0.99982, -0.01899, 0.00139), (-0.00102, 0.01943, 0.99981), (-0.01901, -0.99963, 0.01941)-9.89228, 24.85552, 124.5489
3given(0.99998, -0.00369, 0.00426), (-0.00423, 0.00662, 0.99997), (-0.00372, -0.99997, 0.00661)-11.77406, -41.83904, 56.37671

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE


Mass: 32166.139 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARTHROBACTER NITROGUAJACOLICUS (bacteria)
Strain: RU61A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15/PREP4
References: UniProt: A4V8M9, UniProt: O31266*PLUS, 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase

-
Non-polymers , 6 types, 201 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 69 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 69 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 69 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 69 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 69 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 69 TO SER

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.32 % / Description: NONE
Crystal growpH: 7
Details: HIS6-HOD AT 150 MG/ML IN STORAGE BUFFER IN THE PRESENCE OF A RESERVOIR COMPOSED OF 1.65 M SODIUM/POTASSIUM TARTRATE, 0.1 M HEPES PH 7.0 SOAKING WITH 1M NACL FOR 60 SECONDS

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 2.0664
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2009 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.0664 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.527
11-H, L, K20.473
ReflectionResolution: 2.7→55.64 Å / Num. obs: 35477 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 70.1 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.8
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.3 / % possible all: 96.1

-
Processing

Software
NameVersionClassification
REFMAC5.5.0093refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.7→46.38 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.89 / SU B: 13.071 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 0 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. EXTRA RESIDUES BELONGING TO THE N-TERMINAL PURIFICATION TAG ARE VISIBLE IN SOME OF THE CHAINS
RfactorNum. reflection% reflectionSelection details
Rfree0.24569 1786 5 %RANDOM
Rwork0.21094 ---
obs0.21272 33360 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.303 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20 Å2-0 Å2
2--2.43 Å20 Å2
3----4.1 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8992 0 142 162 9296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0219408
X-RAY DIFFRACTIONr_bond_other_d0.0010.026454
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.94812791
X-RAY DIFFRACTIONr_angle_other_deg0.8083.00115574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74251105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56423.374489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.389151480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8871573
X-RAY DIFFRACTIONr_chiral_restr0.0610.21304
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110499
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021994
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.361.55512
X-RAY DIFFRACTIONr_mcbond_other0.0651.52213
X-RAY DIFFRACTIONr_mcangle_it0.70228902
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.94433896
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6334.53886
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
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1575tight positional0.020.05
2B1575tight positional0.020.05
3C1575tight positional0.020.05
4D1575tight positional0.020.05
1A2162loose positional0.025
2B2162loose positional0.025
3C2162loose positional0.025
4D2162loose positional0.025
1A1575tight thermal0.040.5
2B1575tight thermal0.040.5
3C1575tight thermal0.040.5
4D1575tight thermal0.040.5
1A2162loose thermal0.0410
2B2162loose thermal0.0410
3C2162loose thermal0.0510
4D2162loose thermal0.0410
LS refinement shellResolution: 2.698→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.513 98 -
Rwork0.407 2349 -
obs--95.51 %

+
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://pdbjlvh1.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