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- PDB-3tm1: Crystal structure of mature ThnT, a pantetheine hydrolase -

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Basic information

Entry
Database: PDB / ID: 3tm1
TitleCrystal structure of mature ThnT, a pantetheine hydrolase
Componentscysteine transferase
KeywordsHYDROLASE / DOM-fold / amidohydrolase / autoproteolytic / carbapenem / DmpA/OAT superfamily / Pantetheine hydrolase / thienamcyin biosynthesis
Function / homology
Function and homology information


aminopeptidase activity / transferase activity / identical protein binding
Similarity search - Function
Peptidase S58, DmpA / Peptidase family S58 / L-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / ArgJ-like domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative cysteine transferase
Similarity search - Component
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSchildbach, J.F. / Wright, N.T. / Buller, A.R.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Autoproteolytic Activation of ThnT Results in Structural Reorganization Necessary for Substrate Binding and Catalysis.
Authors: Buller, A.R. / Labonte, J.W. / Freeman, M.F. / Wright, N.T. / Schildbach, J.F. / Townsend, C.A.
History
DepositionAug 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: cysteine transferase
B: cysteine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9284
Polymers82,7442
Non-polymers1842
Water7,728429
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: cysteine transferase
B: cysteine transferase
hetero molecules

A: cysteine transferase
B: cysteine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,8578
Polymers165,4884
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area16430 Å2
ΔGint-51 kcal/mol
Surface area44430 Å2
MethodPISA
3
A: cysteine transferase
hetero molecules

A: cysteine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9284
Polymers82,7442
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area3980 Å2
ΔGint-12 kcal/mol
Surface area26400 Å2
MethodPISA
4
B: cysteine transferase
hetero molecules

B: cysteine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9284
Polymers82,7442
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area4000 Å2
ΔGint-12 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.648, 67.765, 73.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein cysteine transferase


Mass: 41372.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cattleya (bacteria) / Strain: 29303 / Gene: ThnT / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): RosettaII(DE3) / References: UniProt: Q83XN4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% PEG3350, 0.5M NaAcetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 63864 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.853.30.415172
1.85-1.914.40.428187
1.91-1.985.80.375197.1
1.98-2.067.30.308199.2
2.06-2.158.40.261199.7
2.15-2.279.30.222199.7
2.27-2.419.80.188199.8
2.41-2.69.90.158199.9
2.6-2.869.90.122199.9
2.86-3.279.80.089199.9
3.27-4.129.60.062199.9
4.12-509.10.05199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.93 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å25.53 Å
Translation2.5 Å25.53 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→25.53 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 5.1 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1195 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19685 3163 5 %RANDOM
Rwork0.16948 ---
obs0.17085 60481 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.233 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--0.85 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5068 0 12 429 5509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215168
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9657072
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6695730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1522.151186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12715648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2781552
X-RAY DIFFRACTIONr_chiral_restr0.1050.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214036
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8271.53594
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47325648
X-RAY DIFFRACTIONr_scbond_it2.29231574
X-RAY DIFFRACTIONr_scangle_it3.7974.51424
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 157 -
Rwork0.32 3225 -
obs--69.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9302-0.13980.13230.37380.07820.2638-0.04030.2650.2101-0.01190.00980.0292-0.033-0.01650.03050.0054-0.0066-0.01410.09010.04480.1136-16.155-25.75334.394
22.032-0.13540.15290.30470.050.8155-0.0729-0.506-0.17030.04480.06690.06750.0357-0.15760.0060.01210.01790.02640.20090.05570.0828-17.682-37.88763.356
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 397
2X-RAY DIFFRACTION2B24 - 397

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