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- PDB-4i45: Crystal Structure of Orf6 protein from Photobacterium profundum, ... -

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Basic information

Entry
Database: PDB / ID: 4i45
TitleCrystal Structure of Orf6 protein from Photobacterium profundum, Mg2+-bound form
ComponentsORF6 thioesterase
KeywordsHYDROLASE / thioesterase / polyketide synthase / polyunsaturated fatty acid / hot dog
Function / homology
Function and homology information


thiolester hydrolase activity / metal ion binding
Similarity search - Function
4-hydroxybenzoyl-CoA thioesterase, active site / 4-hydroxybenzoyl-CoA thioesterase family active site. / Acyl-CoA thioester hydrolase YbgC/YbaW family / Thioesterase-like superfamily / : / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesPhotobacterium profundum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsRodriguez-Guilbe, M.M. / Baerga-Ortiz, A. / Schreiter, E.R.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure, Activity, and Substrate Selectivity of the Orf6 Thioesterase from Photobacterium profundum.
Authors: Rodriguez-Guilbe, M. / Oyola-Robles, D. / Schreiter, E.R. / Baerga-Ortiz, A.
History
DepositionNov 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF6 thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5872
Polymers15,5631
Non-polymers241
Water3,081171
1
A: ORF6 thioesterase
hetero molecules

A: ORF6 thioesterase
hetero molecules

A: ORF6 thioesterase
hetero molecules

A: ORF6 thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3488
Polymers62,2514
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area7690 Å2
ΔGint-67 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.292, 54.362, 88.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

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Components

#1: Protein ORF6 thioesterase


Mass: 15562.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium profundum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q93CG9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 1.98 Å3/Da / Density % sol: 37.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 30% v/v Polyethylene glycol monomethyl ether 550, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2009
RadiationMonochromator: double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→46.3 Å / Num. all: 24736 / Num. obs: 23821 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.4→1.45 Å / % possible all: 76.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0111refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R87

3r87


Resolution: 1.4→46.3 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.934 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19606 1215 5.1 %RANDOM
Rwork0.1482 ---
obs0.15052 22606 96.3 %-
all-22606 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.875 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20 Å2
2---0.87 Å2-0 Å2
3---2.36 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1055 0 1 171 1227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221127
X-RAY DIFFRACTIONr_bond_other_d0.0020.02770
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9371538
X-RAY DIFFRACTIONr_angle_other_deg0.90331878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4995143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22723.57156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26315197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.692157
X-RAY DIFFRACTIONr_chiral_restr0.0960.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021264
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02247
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr2.95131897
X-RAY DIFFRACTIONr_sphericity_free38.03548
X-RAY DIFFRACTIONr_sphericity_bonded19.17151984
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 65 -
Rwork0.196 1232 -
obs--74.07 %

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