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- PDB-7cbe: Crystal structure of Homoserine O-succinyltransferase from Escher... -

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Basic information

Entry
Database: PDB / ID: 7cbe
TitleCrystal structure of Homoserine O-succinyltransferase from Escherichia coli K-12
ComponentsHomoserine O-succinyltransferase
KeywordsTRANSFERASE / Homoserine O-succinyltransferase
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 / protein homodimerization activity / cytoplasm
Similarity search - Function
Homoserine O-succinyltransferase MetA / MetA family / Homoserine O-succinyltransferase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Homoserine O-succinyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSagong, H.-Y. / Kim, K.-J.
CitationJournal: To Be Published
Title: Crystal structure of Homoserine O-succinyltransferase from Escherichia coli K-12
Authors: Sagong, H.-Y. / Kim, K.-J.
History
DepositionJun 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)71,8756
Polymers71,5282
Non-polymers3464
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-43 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.348, 81.027, 98.093
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 35764.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: metAS, metA, b4013, JW3973
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P07623, homoserine O-succinyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% Polyethylene glycol 3350, 0.1M Bis-tris pH 5.5, 0.2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 65291 / % possible obs: 97 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.031 / Rrim(I) all: 0.081 / Χ2: 2.626 / Net I/σ(I): 12.7 / Num. measured all: 342170
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.733.70.28231760.9130.1540.3241.20995.8
1.73-1.763.70.26132070.9380.1410.2981.35696
1.76-1.793.80.25831590.9420.1380.2951.4195.4
1.79-1.833.90.22431880.9580.1160.2541.50196.3
1.83-1.874.10.21132090.9650.1070.2381.6896.3
1.87-1.914.20.19532070.9720.0970.2191.7896.3
1.91-1.964.40.17832350.9760.0850.1981.95696.8
1.96-2.024.70.16432000.9820.0770.1822.14196.3
2.02-2.074.90.14732510.9870.0660.1622.40397.2
2.07-2.145.10.13432230.9910.0590.1472.61196.6
2.14-2.225.40.1232380.9920.0520.1322.74496.9
2.22-2.315.40.11332660.9940.0480.1232.91297.2
2.31-2.415.50.10432200.9910.0440.1142.91196.5
2.41-2.545.70.09532790.9950.040.1032.93396.9
2.54-2.75.90.08932840.9950.0370.0972.99897.4
2.7-2.916.20.0832960.9960.0320.0863.07498.2
2.91-3.26.60.07133470.9970.0280.0763.13898.5
3.2-3.667.20.06433960.9980.0250.0693.34899.4
3.66-4.617.20.05934160.9970.0230.0633.51398.8
4.61-506.70.05634940.9960.0230.0612.95196.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H2W

2h2w


Resolution: 1.7→26.75 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.582 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 3117 4.8 %RANDOM
Rwork0.2246 ---
obs0.226 62145 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.18 Å2 / Biso mean: 25.325 Å2 / Biso min: 12.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å2-0 Å2
3----0.24 Å2
Refinement stepCycle: final / Resolution: 1.7→26.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4710 0 20 220 4950
Biso mean--41.9 27.71 -
Num. residues----575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134858
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174345
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.6446624
X-RAY DIFFRACTIONr_angle_other_deg1.3611.56810077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.175570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52622.847288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03515762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9031529
X-RAY DIFFRACTIONr_chiral_restr0.0790.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021054
LS refinement shellResolution: 1.702→1.746 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.489 224 -
Rwork0.46 4400 -
all-4624 -
obs--93.93 %

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