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- PDB-4ihd: Crystal Structure of Uncleaved ThnT T282C, derivatized at the act... -

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Basic information

Entry
Database: PDB / ID: 4ihd
TitleCrystal Structure of Uncleaved ThnT T282C, derivatized at the active site with EtHg
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
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
ETHYL MERCURY ION / Putative cysteine transferase
Similarity search - Component
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 1.1Sep 20, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: ThnT protein
B: ThnT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2084
Polymers82,7482
Non-polymers4592
Water11,746652
1
A: ThnT protein
hetero molecules

A: ThnT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2084
Polymers82,7482
Non-polymers4592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4010 Å2
ΔGint-18 kcal/mol
Surface area25040 Å2
MethodPISA
2
B: ThnT protein
hetero molecules

B: ThnT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2084
Polymers82,7482
Non-polymers4592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4020 Å2
ΔGint-18 kcal/mol
Surface area24590 Å2
MethodPISA
3
A: ThnT protein
B: ThnT protein
hetero molecules

A: ThnT protein
B: ThnT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,4158
Polymers165,4964
Non-polymers9194
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area15070 Å2
ΔGint-46 kcal/mol
Surface area42580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.611, 68.950, 73.827
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
11B-655-

HOH

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Components

#1: Protein ThnT protein


Mass: 41374.117 Da / Num. of mol.: 2 / Mutation: T282C
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: Chemical ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12%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: 1.0036 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: 1.0036 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 81725 / Num. obs: 76644 / % possible obs: 94.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 34.2
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2138 / % possible all: 54.8

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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
Starting model: PDB ENTRY 3S3U

3s3u


Resolution: 1.65→35.7 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.298 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18453 4135 5.1 %RANDOM
Rwork0.15925 ---
obs0.16054 77527 93.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.617 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å20 Å2
2--0.18 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.65→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4960 0 6 652 5618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195262
X-RAY DIFFRACTIONr_bond_other_d0.0010.025101
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.9647230
X-RAY DIFFRACTIONr_angle_other_deg0.735311648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.635765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.31222.165194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70415683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4251556
X-RAY DIFFRACTIONr_chiral_restr0.0640.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216308
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021164
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 178 -
Rwork0.287 3057 -
obs--51.24 %
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)
10.9311-0.08130.14840.3957-0.0740.45370.0010.0072-0.0680.0010.0086-0.0160.04650.0378-0.00970.0220.00240.00060.0078-0.01250.038115.708826.1762-3.5714
21.0299-0.0665-0.29180.25940.020.7171-0.0357-0.18360.04880.01390.0373-0.0539-0.02960.1002-0.00150.02060.0227-0.01480.0591-0.02390.018817.647435.884327.3376
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 397
2X-RAY DIFFRACTION2B26 - 397

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