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- PDB-2h2w: Crystal structure of Homoserine O-succinyltransferase (EC 2.3.1.4... -

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Basic information

Entry
Database: PDB / ID: 2h2w
TitleCrystal structure of Homoserine O-succinyltransferase (EC 2.3.1.46) (Homoserine O-transsuccinylase) (HTS) (tm0881) from THERMOTOGA MARITIMA at 2.52 A resolution
ComponentsHomoserine O-succinyltransferase
KeywordsTRANSFERASE / tm0881 / Homoserine O-succinyltransferase / (EC 2.3.1.46) / Homoserine O-transsuccinylase / HTS / (tm0881) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


homoserine O-succinyltransferase activity / L-methionine biosynthetic process from homoserine via O-succinyl-L-homoserine and cystathionine / homoserine O-acetyltransferase / homoserine O-acetyltransferase 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-acetyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.52 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Homoserine O-succinyltransferase (EC 2.3.1.46) (Homoserine O-transsuccinylase) (HTS) (tm0881) from THERMOTOGA MARITIMA at 2.52 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE RESIDUES ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE RESIDUES 1-300 OF THE TARGET SEQUENCE. THE CONSTRUCT WITH RESIDUES 301-304 ELIMINATED PRODUCED THE BEST DIFFRACTING CRYSTAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homoserine O-succinyltransferase


Theoretical massNumber of molelcules
Total (without water)36,7721
Polymers36,7721
Non-polymers00
Water28816
1
A: Homoserine O-succinyltransferase

A: Homoserine O-succinyltransferase


Theoretical massNumber of molelcules
Total (without water)73,5442
Polymers73,5442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Unit cell
Length a, b, c (Å)72.609, 72.609, 126.913
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.

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Components

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


Mass: 36772.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: metA / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZY3, homoserine O-succinyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.88 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8
Details: 10.0% iso-Propanol, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 21, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.52→42.3 Å / Num. obs: 13643 / % possible obs: 99.9 % / Redundancy: 10.98 % / Biso Wilson estimate: 70.22 Å2 / Rmerge(I) obs: 0.046 / Χ2: 1.481 / Net I/σ(I): 18.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsΧ2% possible all
2.52-2.6199.70.3876.113271.0199.7
2.61-2.7199.80.32513311.3
2.71-2.841000.20713381.011
2.84-2.991000.13113480.921
2.99-3.171000.08613470.992
3.17-3.4299.90.06613461.279
3.42-3.7699.60.05813542.108
3.76-4.311000.04913811.921
4.31-5.431000.04413881.799
5.43-5099.50.03414831.68

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
MolProbity3beta29model building
REFMAC5.2.0005refinement
SCALEPACKdata scaling
PDB_EXTRACT1.701data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GHR

2ghr


Resolution: 2.52→42.3 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.915 / SU B: 21.895 / SU ML: 0.221 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.502 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. DUE TO STRONG SALT AND SOLVENT RINGS, 1024 REFLECTIONS BETWEEN 2.90-3.02 ANGSTROMS WERE OMITTED FROM THE REFINEMENT. 3. THE LARGE GAP ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. DUE TO STRONG SALT AND SOLVENT RINGS, 1024 REFLECTIONS BETWEEN 2.90-3.02 ANGSTROMS WERE OMITTED FROM THE REFINEMENT. 3. THE LARGE GAP BETWEEN THE RWORK AND RFREE IS LIKELY DUE TO ARTIFACTS IN THE DIFFRACTION IMAGES. 4. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 613 4.9 %RANDOM
Rwork0.19 ---
all0.194 ---
obs-12573 92.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.358 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20.99 Å20 Å2
2--1.98 Å20 Å2
3----2.97 Å2
Refinement stepCycle: LAST / Resolution: 2.52→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 0 16 2389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222455
X-RAY DIFFRACTIONr_bond_other_d0.0010.022191
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.953352
X-RAY DIFFRACTIONr_angle_other_deg0.6235086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0545289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.47723.675117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0315392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0471512
X-RAY DIFFRACTIONr_chiral_restr0.070.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022694
X-RAY DIFFRACTIONr_gen_planes_other00.02519
X-RAY DIFFRACTIONr_nbd_refined0.2280.3488
X-RAY DIFFRACTIONr_nbd_other0.2170.32101
X-RAY DIFFRACTIONr_nbtor_refined0.2020.51179
X-RAY DIFFRACTIONr_nbtor_other0.0930.51257
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.595
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.337
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.57
X-RAY DIFFRACTIONr_mcbond_it1.85921540
X-RAY DIFFRACTIONr_mcbond_other0.442573
X-RAY DIFFRACTIONr_mcangle_it2.74932375
X-RAY DIFFRACTIONr_scbond_it3.01331132
X-RAY DIFFRACTIONr_scangle_it4.2375976
LS refinement shellResolution: 2.52→2.584 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 46 -
Rwork0.272 936 -
obs-982 99.9 %
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)
16.1871.778-1.01291.3310.40194.98850.25070.0239-0.244-0.90630.04240.92890.1753-0.7883-0.29310.36160.0191-0.08850.36310.06730.137111.908-15.3592.891
21.28840.5323-0.71932.2519-0.38752.3827-0.0489-0.0373-0.037-0.1262-0.0405-0.2342-0.07310.14860.08940.3027-0.00510.00440.33690.0353-0.059129.751-18.09113.254
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
112 - 2614 - 38
2233 - 29645 - 308

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