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- PDB-4ihe: Crystal Structure of Uncleaved ThnT T282A -

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Basic information

Entry
Database: PDB / ID: 4ihe
TitleCrystal Structure of Uncleaved ThnT T282A
ComponentsThnT protein
KeywordsHYDROLASE / DOM-fold / Clan PE / Family P1 / Autoproteolysis / Pantetheine Hydrolase / Thienamycin Biosynthesis / Ethylmercury derivatization of C282
Function / homology
Function and homology information


aminopeptidase activity / transferase activity / identical protein binding / plasma membrane
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 / Resolution: 1.5 Å
AuthorsBuller, A.R. / Schildbach, J.F. / Townsend, C.A.
CitationJournal: Biochemistry / Year: 2014
Title: Exploring the Role of Conformational Heterogeneity in cis-Autoproteolytic Activation of ThnT.
Authors: Buller, A.R. / Freeman, M.F. / Schildbach, J.F. / Townsend, C.A.
History
DepositionDec 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: ThnT protein
B: ThnT protein


Theoretical massNumber of molelcules
Total (without water)82,6842
Polymers82,6842
Non-polymers00
Water11,494638
1
A: ThnT protein

A: ThnT protein


Theoretical massNumber of molelcules
Total (without water)82,6842
Polymers82,6842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3450 Å2
ΔGint-17 kcal/mol
Surface area24470 Å2
MethodPISA
2
B: ThnT protein

B: ThnT protein


Theoretical massNumber of molelcules
Total (without water)82,6842
Polymers82,6842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3490 Å2
ΔGint-13 kcal/mol
Surface area24760 Å2
MethodPISA
3
A: ThnT protein
B: ThnT protein

A: ThnT protein
B: ThnT protein


Theoretical massNumber of molelcules
Total (without water)165,3684
Polymers165,3684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area14270 Å2
ΔGint-30 kcal/mol
Surface area41890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.754, 67.959, 73.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-447-

HOH

21B-538-

HOH

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Components

#1: Protein ThnT protein


Mass: 41342.055 Da / Num. of mol.: 2 / Mutation: T282A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cattleya (bacteria) / Gene: ThnT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta II / References: UniProt: Q83XN4, pantetheine hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / 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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 26% PEG 3350, 0.3M sodium acetate, 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: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 25, 2011
RadiationMonochromator: Si(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→33.59 Å / Num. all: 833025 / Num. obs: 798871 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 34.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.2 / % possible all: 74.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→33.59 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.187 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17967 5428 5 %RANDOM
Rwork0.16547 ---
obs0.16617 103037 95.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.239 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å20 Å2
2--0.61 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4947 0 0 638 5585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195263
X-RAY DIFFRACTIONr_bond_other_d0.0050.025101
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.9647231
X-RAY DIFFRACTIONr_angle_other_deg0.66311646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6765768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.25822.124193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46215678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.851556
X-RAY DIFFRACTIONr_chiral_restr0.0650.2853
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216321
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021163
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 319 -
Rwork0.301 5672 -
obs--72.62 %
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)
10.44240.01490.16440.11990.04930.4904-0.01920.0864-0.03590.00240.0436-0.01680.00710.0992-0.02440.0268-0.01560.00480.0779-0.02350.007717.367-1.33182.808
20.56260.0164-0.09860.2924-0.07650.20930.0137-0.03760.0397-0.01420.00210.0007-0.02350.0452-0.01580.0055-0.00060.00260.0626-0.01670.023415.388.337113.72
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 397
2X-RAY DIFFRACTION2B25 - 397

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