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

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Basic information

Entry
Database: PDB / ID: 2pgo
TitleThe crystal structure of FAD and ThDP dependent Cyclohexane-1,2-dione Hydrolase (Cdh) from Azoarcus sp. strain 22Lin
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 / FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / THIAMINE DIPHOSPHATE
Function and homology information
Biological speciesAzoarcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MIRAS / Resolution: 1.26 Å
AuthorsSteinbach, A.K. / Warkentin, E. / Kroneck, P.M.H. / Ermler, U.
CitationJournal: To be Published
Title: The crystal structure of FAD and ThDP dependent Cyclohexane-1,2-dione Hydrolase (Cdh) from Azoarcus sp. strain 22Lin
Authors: Steinbach, A.K. / Harder, J. / 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 1.2Feb 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

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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)129,59813
Polymers126,7262
Non-polymers2,87311
Water21,8341212
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)259,19726
Polymers253,4524
Non-polymers5,74522
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area44770 Å2
ΔGint-380 kcal/mol
Surface area63190 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-1200-

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 , 7 types, 1223 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1212 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Description: the structure was solved by combined SAD and MIR. Anomalous data were collected at 1.005 A for a crystal soaked with mercuric acetate (up to 2.5A res.) and at 1.072 A for a K2PtCl6 ...Description: the structure was solved by combined SAD and MIR. Anomalous data were collected at 1.005 A for a crystal soaked with mercuric acetate (up to 2.5A res.) and at 1.072 A for a K2PtCl6 soaked crystal (up to 2.8A res.) both at ESRF ID14-4. Further data were colleted in-house (Cu-Ka) for a 'Pip' and a 'Terpy' heavy atom derivative, respectively, both up to 2.7 A resolution. The deposited coordinates are from high resolution data collected a 0.939A.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 60% MPD, 0.02M sodium acetate, 0.2M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
1,2,3,41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.939
SYNCHROTRONESRF ID14-421.0052, 1.0093, 1.023
SYNCHROTRONESRF ID14-431.005
SYNCHROTRONESRF ID14-441.072
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 9, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111)SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
3SINGLE WAVELENGTHMx-ray3
4SINGLE WAVELENGTHMx-ray4
Radiation wavelength
IDWavelength (Å)Relative weight
10.9391
21.00521
31.00931
41.0231
51.0051
61.0721
ReflectionResolution: 1.2→40 Å / Num. obs: 259345 / % possible obs: 77 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.48 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 12
Reflection shellResolution: 1.2→1.3 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 5.1 / Num. unique all: 20256 / % possible all: 14

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD, MIRAS / Resolution: 1.26→5 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.736 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.031 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.11963 13524 5 %RANDOM
Rwork0.09669 ---
all0.09782 259345 --
obs0.09782 259345 93.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.189 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.26→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8886 0 183 1212 10281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.1339657
X-RAY DIFFRACTIONr_bond_other_d0.020.0838864
X-RAY DIFFRACTIONr_angle_refined_deg2.0142.13513164
X-RAY DIFFRACTIONr_angle_other_deg1.4193.07920601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73351204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98723.628430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.543151572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2261573
X-RAY DIFFRACTIONr_chiral_restr0.1250.21454
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210746
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021951
X-RAY DIFFRACTIONr_nbd_refined0.2330.21885
X-RAY DIFFRACTIONr_nbd_other0.1980.28632
X-RAY DIFFRACTIONr_nbtor_refined0.1790.24618
X-RAY DIFFRACTIONr_nbtor_other0.090.24682
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2734
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4020.251
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3590.2198
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.267
X-RAY DIFFRACTIONr_mcbond_it1.9771.57619
X-RAY DIFFRACTIONr_mcbond_other1.2281.52451
X-RAY DIFFRACTIONr_mcangle_it2.35629564
X-RAY DIFFRACTIONr_scbond_it3.08634386
X-RAY DIFFRACTIONr_scangle_it3.9074.53588
X-RAY DIFFRACTIONr_rigid_bond_restr1.849310940
X-RAY DIFFRACTIONr_sphericity_free5.0333255
X-RAY DIFFRACTIONr_sphericity_bonded4.49438586
LS refinement shellResolution: 1.26→1.291 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.141 518 -
Rwork0.1 9571 -
obs-9571 49.32 %

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