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- PDB-3lbe: The Crystal Structure of smu.793 from Streptococcus mutans UA159 ... -

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Basic information

Entry
Database: PDB / ID: 3lbe
TitleThe Crystal Structure of smu.793 from Streptococcus mutans UA159 bound to acetyl CoA
ComponentsPutative uncharacterized protein smu.793
KeywordsUNKNOWN FUNCTION / hypothetical protein
Function / homology
Function and homology information


fatty acyl-CoA hydrolase activity
Similarity search - Function
Acyl-coenzyme A thioesterase 13 / Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Thioesterase domain-containing protein
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSu, X.-D. / Hou, Q.M. / Fan, X.X. / Nan, J. / Liu, X.
CitationJournal: TO BE PUBLISHED
Title: The Crystal Structure of smu.793 from Streptococcus mutans UA159 bound to acetyl CoA
Authors: Su, X.-D. / Hou, Q.M. / Fan, X.X. / Nan, J. / Liu, X.
History
DepositionJan 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: Putative uncharacterized protein smu.793
B: Putative uncharacterized protein smu.793
C: Putative uncharacterized protein smu.793
D: Putative uncharacterized protein smu.793
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,80512
Polymers71,5934
Non-polymers3,2128
Water6,612367
1
A: Putative uncharacterized protein smu.793
B: Putative uncharacterized protein smu.793
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4387
Polymers35,7962
Non-polymers1,6415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-8 kcal/mol
Surface area11470 Å2
MethodPISA
2
C: Putative uncharacterized protein smu.793
D: Putative uncharacterized protein smu.793
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3675
Polymers35,7962
Non-polymers1,5713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-8 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.536, 68.536, 118.817
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
Putative uncharacterized protein smu.793


Mass: 17898.201 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: smu.793 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DUV0
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 1.95 Å3/Da / Density % sol: 36.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 1000, 0.2M NaCl, 0.1M Na/K phosphate pH6.5, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 62297 / Num. obs: 61674 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 25.54 Å2
Reflection shellResolution: 1.7→1.76 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.refine)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PSU

1psu


Resolution: 1.7→34.292 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.907 / SU ML: 0.2 / σ(F): 0.09 / Phase error: 15.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1875 3053 5.08 %
Rwork0.1294 57042 -
obs0.1323 60095 96.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.532 Å2 / ksol: 0.392 e/Å3
Displacement parametersBiso max: 83.91 Å2 / Biso mean: 32.803 Å2 / Biso min: 13.02 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20 Å2
2--1.132 Å2-0 Å2
3---0.008 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3829 0 196 367 4392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074208
X-RAY DIFFRACTIONf_angle_d1.1285719
X-RAY DIFFRACTIONf_dihedral_angle_d18.9781507
X-RAY DIFFRACTIONf_chiral_restr0.075660
X-RAY DIFFRACTIONf_plane_restr0.003692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72660.1761280.09532330X-RAY DIFFRACTION87
1.7266-1.75490.19771390.09312412X-RAY DIFFRACTION92
1.7549-1.78510.20331430.09412483X-RAY DIFFRACTION94
1.7851-1.81760.19991200.10312494X-RAY DIFFRACTION94
1.8176-1.85250.20371250.09492555X-RAY DIFFRACTION94
1.8525-1.89030.17561260.09552489X-RAY DIFFRACTION95
1.8903-1.93140.19261590.09532557X-RAY DIFFRACTION97
1.9314-1.97640.1711550.09762595X-RAY DIFFRACTION98
1.9764-2.02580.1671270.09422650X-RAY DIFFRACTION99
2.0258-2.08060.21841180.09822648X-RAY DIFFRACTION99
2.0806-2.14180.18261560.10562658X-RAY DIFFRACTION99
2.1418-2.21090.15271550.09852648X-RAY DIFFRACTION99
2.2109-2.28990.18231350.09722632X-RAY DIFFRACTION99
2.2899-2.38160.1871240.1012651X-RAY DIFFRACTION99
2.3816-2.48990.18871420.1162639X-RAY DIFFRACTION99
2.4899-2.62110.19431530.1262681X-RAY DIFFRACTION99
2.6211-2.78530.21551310.13132659X-RAY DIFFRACTION99
2.7853-3.00020.19911180.13422724X-RAY DIFFRACTION99
3.0002-3.30190.16271630.13942705X-RAY DIFFRACTION100
3.3019-3.77920.16311600.12852709X-RAY DIFFRACTION100
3.7792-4.75940.16351440.12192662X-RAY DIFFRACTION96
4.7594-34.29860.22141320.17692461X-RAY DIFFRACTION85

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