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- PDB-3tm2: Crystal structure of mature ThnT with a covalently bound product mimic -

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Basic information

Entry
Database: PDB / ID: 3tm2
TitleCrystal structure of mature ThnT with a covalently bound product mimic
Componentscysteine transferase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / DOM-fold / amidohydrolase / autoproteolytic / carbapenem / pantetheine / inhibitor / DmpA/OAT superfamily / Pantetheine hydrolase / thienamycin biosynthesis / O-(2-oxo-4-pantoamindobutyl)threonine / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
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
Chem-TXI / Putative cysteine transferase
Similarity search - Component
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cysteine transferase
B: cysteine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2484
Polymers82,7442
Non-polymers5032
Water6,612367
1


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

A: cysteine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2484
Polymers82,7442
Non-polymers5032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3070 Å2
ΔGint-10 kcal/mol
Surface area26230 Å2
MethodPISA
3
A: cysteine transferase
hetero molecules

B: cysteine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2484
Polymers82,7442
Non-polymers5032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area1460 Å2
ΔGint-11 kcal/mol
Surface area27890 Å2
MethodPISA
4
B: cysteine transferase
hetero molecules

B: cysteine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2484
Polymers82,7442
Non-polymers5032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3050 Å2
ΔGint-11 kcal/mol
Surface area26330 Å2
MethodPISA
5
A: cysteine transferase
B: cysteine transferase
hetero molecules

A: cysteine transferase
B: cysteine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,4958
Polymers165,4884
Non-polymers1,0074
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area14600 Å2
ΔGint-47 kcal/mol
Surface area44080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.543, 67.324, 73.792
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-TXI / (2R)-N-(4-chloro-3-oxobutyl)-2,4-dihydroxy-3,3-dimethylbutanamide


Mass: 251.707 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18ClNO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 42.11 %
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: SSRL / Beamline: BL12-2 / Wavelength: 0.80011 Å
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: May 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.80011 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 47965 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.121 / Χ2: 1.054 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.055.50.65335611.059198.1
2.05-2.115.90.58436231.113198.9
2.11-2.186.20.51636131.078199.4
2.18-2.266.40.44336421.176199.9
2.26-2.356.60.36636541.1021100
2.35-2.466.80.33736781.111100
2.46-2.5970.29136691.0661100
2.59-2.757.20.23536811.0391100
2.75-2.967.20.16936881.011100
2.96-3.267.20.11237020.9931100
3.26-3.737.10.06637390.9991100
3.73-4.77.10.04337681.0231100
4.7-506.70.03339470.974199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.98 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.4 Å
Translation2.5 Å30.4 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
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
Starting model: PDB Entry 3S3U

3s3u


Resolution: 2→30.4 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1698 / WRfactor Rwork: 0.1384 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8768 / SU B: 8.17 / SU ML: 0.101 / SU R Cruickshank DPI: 0.1625 / SU Rfree: 0.1435 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 2358 4.9 %RANDOM
Rwork0.1646 ---
obs0.1665 47719 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.75 Å2 / Biso mean: 27.2127 Å2 / Biso min: 8.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å20 Å2
2--1.47 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5068 0 30 367 5465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0215194
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9727108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0465730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90722.151186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68215648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7261552
X-RAY DIFFRACTIONr_chiral_restr0.1020.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214032
X-RAY DIFFRACTIONr_mcbond_it0.8361.53597
X-RAY DIFFRACTIONr_mcangle_it1.37125648
X-RAY DIFFRACTIONr_scbond_it2.21731597
X-RAY DIFFRACTIONr_scangle_it3.4394.51459
LS refinement shellResolution: 2.004→2.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 176 -
Rwork0.253 3140 -
all-3316 -
obs--94.82 %
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)
11.3728-0.1209-0.1030.3657-0.03930.2771-0.02870.1405-0.1377-0.00270.0084-0.02710.01710.04580.02020.0018-0.00280.00630.1021-0.02780.0416.15625.634.484
21.3576-0.083-0.16610.1951-0.08431.0027-0.0731-0.33250.1530.03440.0677-0.0579-0.03770.16390.00540.01040.0133-0.01610.1911-0.04780.029717.62737.75163.518
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 397
2X-RAY DIFFRACTION2B24 - 397

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