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- PDB-6mtg: A Single Reactive Noncanonical Amino Acid is Able to Dramatically... -

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Basic information

Entry
Database: PDB / ID: 6mtg
TitleA Single Reactive Noncanonical Amino Acid is Able to Dramatically Stabilize Protein Structure
ComponentsHomoserine O-succinyltransferase
KeywordsTRANSFERASE / noncanonical amino acid / isothiocyanate / crosslink / thiourea / stabilization
Function / homology
Function and homology information


homoserine O-succinyltransferase / homoserine O-succinyltransferase activity / L-methionine biosynthetic process from homoserine via O-succinyl-L-homoserine and cystathionine / homoserine O-acetyltransferase activity / cytoplasm
Similarity search - Function
Homoserine O-succinyltransferase MetA / MetA family / Homoserine O-succinyltransferase / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
FORMIC ACID / DI(HYDROXYETHYL)ETHER / Homoserine O-succinyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsLi, J.C. / Nasertorabi, F. / Xuan, W. / Han, G.W. / Stevens, R.C. / Schultz, P.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM062159 United States
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: A Single Reactive Noncanonical Amino Acid Is Able to Dramatically Stabilize Protein Structure.
Authors: Li, J.C. / Nastertorabi, F. / Xuan, W. / Han, G.W. / Stevens, R.C. / Schultz, P.G.
History
DepositionOct 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homoserine O-succinyltransferase
B: Homoserine O-succinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,70310
Polymers70,1692
Non-polymers5348
Water9,800544
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, As expected, gel filtration, Elutes as native dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-18 kcal/mol
Surface area25160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.948, 100.036, 125.218
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 2 - 296 / Label seq-ID: 2 - 296

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Homoserine O-succinyltransferase / / HST / Homoserine transsuccinylase / HTS


Mass: 35084.328 Da / Num. of mol.: 2 / Mutation: P257I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: metAS, metA, b4013, JW3973 / Plasmid: Modified PET22b / Details (production host): Inserted a T5 promotor / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P07623, homoserine O-succinyltransferase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.35 Å3/Da / Density % sol: 47.57 % / Description: Thin Hexagonal
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 100mM Potassium Formate and 26% PEG 3350 / PH range: 7.2-7.8

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2018
Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→78.157 Å / Num. obs: 56066 / % possible obs: 99.3 % / Redundancy: 13.4 % / CC1/2: 0.998 / Rpim(I) all: 0.044 / Rrim(I) all: 0.162 / Rsym value: 0.156 / Net I/av σ(I): 4.1 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.85-1.9513.91.5231.880440.7210.4191.5811.52399.3
1.95-2.0713.50.94976510.2650.9860.94999.5
2.07-2.2112.90.63471440.1810.6610.63498.6
2.21-2.3913.90.43167630.1190.4470.43199.5
2.39-2.6213.60.27962530.0770.2890.27999.9
2.62-2.93130.18155820.0520.1890.18198.8
2.93-3.3813.80.10650410.0290.110.10699.9
3.38-4.1412.70.07842590.0230.0810.07899.1
4.14-5.8513.10.06233970.0180.0640.06299.8
5.85-29.87611.90.05819320.0170.0610.05897.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0232refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H2W

2h2w


Resolution: 1.85→29.89 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.819 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.131
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 2829 5.1 %RANDOM
Rwork0.1693 ---
obs0.1718 53171 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.86 Å2 / Biso mean: 28.1 Å2 / Biso min: 16.82 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å20 Å2
2---0.23 Å20 Å2
3----1.64 Å2
Refinement stepCycle: final / Resolution: 1.85→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4721 0 35 545 5301
Biso mean--44.54 38.73 -
Num. residues----583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0134976
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174426
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.6446788
X-RAY DIFFRACTIONr_angle_other_deg1.5041.56810259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3525600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08622.737285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67415760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.611529
X-RAY DIFFRACTIONr_chiral_restr0.1680.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025611
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021088
Refine LS restraints NCS

Ens-ID: 1 / Number: 9086 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 196 -
Rwork0.26 3848 -
all-4044 -
obs--99.39 %
Refinement TLS params.

L12: -0.0241 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.03170.08940.2483-0.02530.26730.00830.00430.0049-0.0006-0.01670.00290.0212-0.00370.00840.0021-0.00280.00120.0330.00980.0125-7.1383-13.478932.4079
20.0189-0.07250.09560.13590.557-0.0066-0.00830.01880.02260.0334-0.01640.02980.0425-0.02680.00650.0038-0.00430.0295-0.01290.02840.8245-2.89260.8786
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 297
2X-RAY DIFFRACTION2B2 - 296

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