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- PDB-2pgn: The crystal structure of FAD and ThDP-dependent Cyclohexane-1,2-d... -

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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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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


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


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


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


Mass: 18.015 Da / Num. of mol.: 1268 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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 %

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