[English] 日本語
Yorodumi
- PDB-2pgn: The crystal structure of FAD and ThDP-dependent Cyclohexane-1,2-d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pgn
TitleThe crystal structure of FAD and ThDP-dependent Cyclohexane-1,2-dione Hydrolase in Complex with Cyclohexane-1,2-dione
ComponentsCyclohexane-1,2-dione Hydrolase (Cdh)
KeywordsHYDROLASE / Three alpha/beta domains
Function / homologyThiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / CYCLOHEXANE-1,2-DIONE / FLAVIN-ADENINE DINUCLEOTIDE / THIAMINE DIPHOSPHATE
Function and homology information
Biological speciesAzoarcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / known crystal structure / Resolution: 1.2 Å
AuthorsFraas, S. / Warkentin, E. / Ermler, U.
CitationJournal: To be Published
Title: The crystal structure of FAD and ThDP-dependent Cyclohexane-1,2-dione Hydrolase in Complex with Cyclohexane-1,2-dione
Authors: Fraas, S. / Steinbach, A.K. / Warkentin, E. / Kroneck, P.M.H. / Ermler, U.
History
DepositionApr 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence The sequence is not available in UniProt database at the time of processing.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclohexane-1,2-dione Hydrolase (Cdh)
B: Cyclohexane-1,2-dione Hydrolase (Cdh)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,96119
Polymers126,7262
Non-polymers5,23617
Water22,8431268
1
A: Cyclohexane-1,2-dione Hydrolase (Cdh)
B: Cyclohexane-1,2-dione Hydrolase (Cdh)
hetero molecules

A: Cyclohexane-1,2-dione Hydrolase (Cdh)
B: Cyclohexane-1,2-dione Hydrolase (Cdh)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,92338
Polymers253,4524
Non-polymers10,47134
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area50500 Å2
ΔGint-175 kcal/mol
Surface area64100 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.600, 123.600, 144.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2037-

HOH

21B-846-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Cyclohexane-1,2-dione Hydrolase (Cdh)


Mass: 63362.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azoarcus sp. (bacteria) / Strain: 22Lin

-
Non-polymers , 6 types, 1285 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#6: Chemical ChemComp-CXO / CYCLOHEXANE-1,2-DIONE / 1,2-Cyclohexanedione


Mass: 112.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1268 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 23% PEG 400, 0.01M sodium acetate, 3mM HEPES, 0.5mM ThDP, 0.5mM NAD, 0.1M NaCl. Crystal soaked in 47% PEG 400, 0.02M sodium acetate, 5mM 1,2 cyclohexanedione, pH 7.0, VAPOR DIFFUSION, ...Details: 23% PEG 400, 0.01M sodium acetate, 3mM HEPES, 0.5mM ThDP, 0.5mM NAD, 0.1M NaCl. Crystal soaked in 47% PEG 400, 0.02M sodium acetate, 5mM 1,2 cyclohexanedione, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→40 Å / Num. all: 388867 / Num. obs: 379045 / % possible obs: 84.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 12.26 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.58
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.7 / Num. measured obs: 187829 / Num. unique all: 50802 / % possible all: 49.9

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
XDSdata reduction
RefinementMethod to determine structure: known crystal structure / Resolution: 1.2→10 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.52 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.176 16593 5 %RANDOM
Rwork0.149 ---
all0.15 333858 --
obs0.15 333858 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2--0.75 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8886 0 290 1268 10444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0229702
X-RAY DIFFRACTIONr_bond_other_d0.0010.028927
X-RAY DIFFRACTIONr_angle_refined_deg2.0521.97913163
X-RAY DIFFRACTIONr_angle_other_deg1.391320764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73651188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85923.598428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.719151557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8221573
X-RAY DIFFRACTIONr_chiral_restr0.1280.21436
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210697
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021946
X-RAY DIFFRACTIONr_nbd_refined0.2220.21772
X-RAY DIFFRACTIONr_nbd_other0.1920.28504
X-RAY DIFFRACTIONr_nbtor_refined0.1710.24438
X-RAY DIFFRACTIONr_nbtor_other0.0840.24879
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.250.2753
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3170.266
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.2257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.256
X-RAY DIFFRACTIONr_mcbond_it1.9951.57581
X-RAY DIFFRACTIONr_mcbond_other1.7661.52435
X-RAY DIFFRACTIONr_mcangle_it2.39429498
X-RAY DIFFRACTIONr_scbond_it3.23534492
X-RAY DIFFRACTIONr_scangle_it4.0054.53659
X-RAY DIFFRACTIONr_rigid_bond_restr2.139310987
X-RAY DIFFRACTIONr_sphericity_free8.3773366
X-RAY DIFFRACTIONr_sphericity_bonded5.47738582
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 1019 -
Rwork0.302 19282 -
obs-20301 81.63 %

+
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