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- PDB-4ncp: Crystal Structure of 4-HBT like thioesterase SAV1878 from Staphyl... -

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Basic information

Entry
Database: PDB / ID: 4ncp
TitleCrystal Structure of 4-HBT like thioesterase SAV1878 from Staphylococcus aureus subsp. aureus Mu50
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Thioesterase / Hotdog Fold / hydrolysis of thioester bond
Function / homology
Function and homology information


long-chain fatty acyl-CoA binding / thiolester hydrolase activity / acyl-CoA metabolic process / fatty acyl-CoA hydrolase activity / fatty acid metabolic process / cytosol
Similarity search - Function
Hotdog acyl-CoA thioesterase (ACOT)-type domain / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / Cytosolic acyl coenzyme A thioester hydrolase / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
HotDog ACOT-type domain-containing protein / HotDog ACOT-type domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKhandokar, Y.B. / Forwood, J.K.
CitationJournal: To be Published
Title: Expression, purification, crystallization, and X-ray diffraction analysis of hypothetical protein SAV1878 from Staphylococcus aureus subsp. aureus Mu50
Authors: Khandokar, Y.B. / Forwood, J.K.
History
DepositionOct 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)121,5896
Polymers121,5896
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18780 Å2
ΔGint-120 kcal/mol
Surface area37110 Å2
MethodPISA
2
A: Uncharacterized protein
C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)40,5302
Polymers40,5302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-23 kcal/mol
Surface area15150 Å2
MethodPISA
3
B: Uncharacterized protein
E: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)40,5302
Polymers40,5302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-24 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.930, 128.500, 83.540
Angle α, β, γ (deg.)90.00, 102.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein


Mass: 20264.883 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: SAV1878 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q931N3, UniProt: A0A0H3K033*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 296 K / pH: 5.5
Details: 200mM Sodium Malonate pH5.5, 18% PEG3350, 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
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 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: 2.5→35.33 Å / Num. obs: 35295 / % possible obs: 99.1 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.56 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
Blu-Ice(McPhillipsdata collection
CCP4model building
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VPM

1vpm


Resolution: 2.5→35.33 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / SU B: 19.563 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 1.175 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1725 5 %RANDOM
Rwork0.207 ---
obs0.209 32726 97 %-
all-33745 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å2-0.03 Å2
2---0.29 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7704 0 0 164 7868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197762
X-RAY DIFFRACTIONr_bond_other_d0.0050.027380
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.95110488
X-RAY DIFFRACTIONr_angle_other_deg0.765317008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0385964
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01124.602352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.862151372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8961542
X-RAY DIFFRACTIONr_chiral_restr0.0750.21174
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028734
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021712
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 114 -
Rwork0.225 2405 -
obs--97.26 %

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