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- PDB-3r87: Crystal Structure of Orf6 protein from Photobacterium profundum -

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Basic information

Entry
Database: PDB / ID: 3r87
TitleCrystal Structure of Orf6 protein from Photobacterium profundum
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


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: 1.05 Å
AuthorsRodriguez-Guilbe, M.M. / Schreiter, E.R. / Baerga Ortiz, A.
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
DepositionMar 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Mar 6, 2013Group: Database references
Revision 1.3May 1, 2013Group: Database references
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)15,5631
Polymers15,5631
Non-polymers00
Water2,000111
1
A: Putative uncharacterized protein

A: Putative uncharacterized protein

A: Putative uncharacterized protein

A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)62,2514
Polymers62,2514
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area8940 Å2
ΔGint-41 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.370, 103.370, 64.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Putative uncharacterized protein


Mass: 15562.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium profundum (bacteria) / Plasmid: pGEX 4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL / References: UniProt: Q93CG9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES monohydrate, 1.6M Magnesium sulfate heptahydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332, 0.9329
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 25, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.93291
ReflectionResolution: 1.05→52.44 Å / Num. all: 88811 / Num. obs: 88811 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.05→1.077 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→52.44 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.563 / SU ML: 0.013 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16481 1893 2.1 %RANDOM
Rwork0.14888 ---
all0.14921 88811 --
obs0.14921 88811 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.555 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.31 Å20 Å2
2--0.63 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.05→52.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 0 0 111 1187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0221195
X-RAY DIFFRACTIONr_angle_refined_deg2.1621.9461641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5435161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2723.57156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57915218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.43157
X-RAY DIFFRACTIONr_chiral_restr0.1360.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021919
X-RAY DIFFRACTIONr_mcbond_it2.5571.5708
X-RAY DIFFRACTIONr_mcangle_it3.86121164
X-RAY DIFFRACTIONr_scbond_it5.3013487
X-RAY DIFFRACTIONr_scangle_it7.3334.5462
X-RAY DIFFRACTIONr_rigid_bond_restr2.75631195
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 103 -
Rwork0.244 4841 -
obs--100 %

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