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- PDB-3kh8: Crystal structure of MaoC-like dehydratase from Phytophthora Capsici -

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Basic information

Entry
Database: PDB / ID: 3kh8
TitleCrystal structure of MaoC-like dehydratase from Phytophthora Capsici
ComponentsMaoC-like dehydratase
KeywordsLYASE / Hot dog domain
Function / homology
Function and homology information


17-beta-hydroxysteroid dehydrogenase (NAD+) activity / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / peroxisome
Similarity search - Function
: / MFE-2 hydratase 2 N-terminal domain / MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
MaoC-like dehydratase
Similarity search - Component
Biological speciesPhytophthora Capsici (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, H. / Zhang, K. / Guo, J. / Zhou, Q. / Zheng, X. / Sun, F. / Pang, H. / Zhang, X.
CitationJournal: To be Published
Title: Crystal structure of MaoC-like dehydratase from Phytophthora Capsici
Authors: Wang, H. / Zhang, K. / Guo, J. / Zhou, Q. / Zheng, X. / Sun, F. / Pang, H. / Zhang, X.
History
DepositionOct 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MaoC-like dehydratase
B: MaoC-like dehydratase


Theoretical massNumber of molelcules
Total (without water)72,7502
Polymers72,7502
Non-polymers00
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-7 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.458, 82.614, 124.228
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MaoC-like dehydratase


Mass: 36375.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora Capsici (eukaryote) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: E3T2G3*PLUS, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHOR HAS ALREADY SUBMITTED THE SEQUENCE TO GENBANK, AND THE ID IS GU190361. IT WILL BE ...THE AUTHOR HAS ALREADY SUBMITTED THE SEQUENCE TO GENBANK, AND THE ID IS GU190361. IT WILL BE APPEARED IN UNP DATABASE SOON.

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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: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes, 6% PEG6000, 5% (+/-)-2-methy-2,4-pentanediol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 9, 2009
RadiationMonochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.93→31.49 Å / Num. all: 63785 / Num. obs: 62446 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 19.6
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2.56 / Num. unique all: 3007 / % possible all: 95.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S9C

1s9c


Resolution: 2→31.49 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.206 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.158 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22977 2877 5.1 %RANDOM
Rwork0.19845 ---
all0.20006 57310 --
obs0.20006 53390 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.668 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20 Å2
2---1.12 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2→31.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4495 0 0 545 5040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224604
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.031.9696223
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.265575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.724.058207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.96515766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4571527
X-RAY DIFFRACTIONr_chiral_restr0.0730.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213544
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4921.52875
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92724640
X-RAY DIFFRACTIONr_scbond_it1.05231729
X-RAY DIFFRACTIONr_scangle_it1.8424.51583
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 218 -
Rwork0.241 3778 -
obs-3778 96.38 %

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