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- PDB-4r9z: Mycobacterium avium subs paratuberculosis tesB protein MAP1729c -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4r9z
TitleMycobacterium avium subs paratuberculosis tesB protein MAP1729c
ComponentsUncharacterized protein
KeywordsHYDROLASE / Thioesterase / double hot-dog
Function / homology
Function and homology information


acyl-CoA metabolic process / fatty acyl-CoA hydrolase activity / fatty acid catabolic process
Similarity search - Function
Acyl-CoA thioesterase / Acyl-CoA thioesterase II domain / Acyl-CoA thioesterase / Acyl-CoA thioesterase, double hotdog domain / Acyl-CoA thioesterase, double hotdog domain / : / Acyl-CoA thioesterase N-terminal domain / Porin / HotDog domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Acyl-CoA thioesterase II
Similarity search - Component
Biological speciesMycobacterium avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSwarbrick, C.M.D. / Forwood, J.K.
CitationJournal: TO BE PUBLISHED
Title: Mycobacterium avium subs paratuberculosis tesB protein MAP1729c
Authors: Swarbrick, C.M.D. / Forwood, J.K.
History
DepositionSep 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)60,9552
Polymers60,9552
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-24 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.230, 70.110, 137.930
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 Uncharacterized protein


Mass: 30477.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Strain: K-10 / Gene: MAP_1729c / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21DE3 PLYSS / References: UniProt: Q73Z74
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 70 mM sodium cacodylate, 1.2 sodium acetate trihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2013
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→32.06 Å / Num. all: 17717 / Num. obs: 17735 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.11
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 15 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 5.9 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3RD7

3rd7


Resolution: 2.6→35.055 Å / SU ML: 0.35 / σ(F): 1.91 / Phase error: 24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 900 5.09 %RANDOM
Rwork0.2019 ---
obs0.2047 17668 99.89 %-
all-17668 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→35.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3839 0 0 45 3884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053942
X-RAY DIFFRACTIONf_angle_d1.085368
X-RAY DIFFRACTIONf_dihedral_angle_d13.7871431
X-RAY DIFFRACTIONf_chiral_restr0.041585
X-RAY DIFFRACTIONf_plane_restr0.005703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.76290.33391530.25452722X-RAY DIFFRACTION100
2.7629-2.97610.31281410.22822748X-RAY DIFFRACTION100
2.9761-3.27540.30491660.23032743X-RAY DIFFRACTION100
3.2754-3.74890.26451430.19792791X-RAY DIFFRACTION100
3.7489-4.72140.22741500.17222813X-RAY DIFFRACTION100
4.7214-35.05820.22231470.20092951X-RAY DIFFRACTION100

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