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- PDB-6czx: Crystal structure of Arabidopsis thaliana phosphoserine aminotran... -

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Basic information

Entry
Database: PDB / ID: 6czx
TitleCrystal structure of Arabidopsis thaliana phosphoserine aminotransferase isoform 1 (AtPSAT1) in complex with PLP internal aldimine
ComponentsPhosphoserine aminotransferase 1, chloroplasticPhosphoserine transaminase
KeywordsTRANSFERASE / serine biosynthesis / pyridoxal 5'-phosphate / PLP / transaminase / PSAT
Function / homology
Function and homology information


phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / L-serine biosynthetic process / plastid / chloroplast stroma / chloroplast / pyridoxal phosphate binding / protein homodimerization activity
Similarity search - Function
Phosphoserine aminotransferase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Phosphoserine aminotransferase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Phosphoserine aminotransferase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsSekula, B. / Ruszkowski, M. / Dauter, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)The Intramural Research Program United States
CitationJournal: Front Plant Sci / Year: 2018
Title: Structural Analysis of Phosphoserine Aminotransferase (Isoform 1) FromArabidopsis thaliana- the Enzyme Involved in the Phosphorylated Pathway of Serine Biosynthesis.
Authors: Sekula, B. / Ruszkowski, M. / Dauter, Z.
History
DepositionApr 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoserine aminotransferase 1, chloroplastic
B: Phosphoserine aminotransferase 1, chloroplastic
C: Phosphoserine aminotransferase 1, chloroplastic
D: Phosphoserine aminotransferase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,72521
Polymers162,0174
Non-polymers1,70717
Water33,7781875
1
A: Phosphoserine aminotransferase 1, chloroplastic
B: Phosphoserine aminotransferase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,01112
Polymers81,0092
Non-polymers1,00310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-110 kcal/mol
Surface area27610 Å2
MethodPISA
2
C: Phosphoserine aminotransferase 1, chloroplastic
D: Phosphoserine aminotransferase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7139
Polymers81,0092
Non-polymers7057
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-82 kcal/mol
Surface area27540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.221, 105.929, 186.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Phosphoserine aminotransferase 1, chloroplastic / Phosphoserine transaminase / AtPSAT1 / Phosphohydroxythreonine aminotransferase


Mass: 40504.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: Leaves / Gene: PSAT1, At4g35630, F8D20.140 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96255, phosphoserine transaminase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1875 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate, 17% PEG 3350 and 0.1 M Tris at pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2018
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.57→76.78 Å / Num. obs: 230909 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.33
Reflection shellResolution: 1.57→1.66 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.965 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 36591 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSMay 1, 2016data reduction
XDSMay 1, 2016data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XK1

4xk1


Resolution: 1.57→76.78 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.971 / SU B: 3.018 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17524 1155 0.5 %RANDOM
Rwork0.15745 ---
obs0.15755 229752 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.943 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20 Å2
2---0.31 Å2-0 Å2
3----0.93 Å2
Refinement stepCycle: 1 / Resolution: 1.57→76.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11346 0 97 1875 13318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911902
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211084
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.97516111
X-RAY DIFFRACTIONr_angle_other_deg0.844325906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36651511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19325.295525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.626152126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9031543
X-RAY DIFFRACTIONr_chiral_restr0.0920.21757
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113175
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022292
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_it0.9071.5345871
X-RAY DIFFRACTIONr_mcbond_other0.9061.5345870
X-RAY DIFFRACTIONr_mcangle_it1.4562.2977352
X-RAY DIFFRACTIONr_mcangle_other1.4572.2977353
X-RAY DIFFRACTIONr_scbond_it1.4931.7656031
X-RAY DIFFRACTIONr_scbond_other1.4931.7666032
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3912.5558730
X-RAY DIFFRACTIONr_long_range_B_refined4.99220.52214280
X-RAY DIFFRACTIONr_long_range_B_other4.99220.52414281
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 83 -
Rwork0.277 16552 -
obs--97.37 %
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)
10.167-0.06760.0790.1482-0.10560.30530.0001-0.0211-0.0056-0.010.03840.01310.0457-0.0768-0.03850.0136-0.0207-0.0220.07040.0260.05221.80642.03723.168
20.0325-0.10970.00120.47160.21350.6102-0.0387-0.0377-0.02150.08690.10980.0321-0.1169-0.107-0.07110.06450.06580.03540.08260.02180.032815.13460.85139.583
30.15-0.012-0.01370.0697-0.03950.2776-0.00420.0050.0266-0.0004-0.0006-0.04280.0221-0.0210.00480.0253-0.0051-0.0030.03760.01070.067447.24444.80617.945
40.0399-0.17360.0090.87380.12120.4793-0.0006-0.00060.03230.07770.0285-0.10550.16090.0183-0.02790.07220.0081-0.02760.0050.01070.083859.27823.94826.936
50.33570.11860.11520.10050.01670.1766-0.01060.0149-0.00450.00640.0119-0.00770.03150.0359-0.00130.0220.0037-0.01490.055-0.00350.051962.24640.74872.262
60.25040.11590.0170.778-0.19270.1619-0.08580.11250.0593-0.05050.0993-0.01860.00340.0334-0.01350.0297-0.0331-0.01660.08820.03780.056969.4459.83956.513
70.24520.0474-0.02840.03310.0220.2704-0.0181-0.0290.0504-0.0107-0.00830.04250.01680.01660.02640.02830.00180.00130.0374-0.01370.066136.80343.76277.551
80.16610.2384-0.01781.06540.13230.0724-0.0097-0.02660.0015-0.0690.00070.12280.02210.02590.00890.03790.0085-0.01710.0165-0.00790.084623.85123.8667.41
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A69 - 325
2X-RAY DIFFRACTION2A326 - 430
3X-RAY DIFFRACTION3B70 - 325
4X-RAY DIFFRACTION4B326 - 430
5X-RAY DIFFRACTION5C70 - 325
6X-RAY DIFFRACTION6C326 - 430
7X-RAY DIFFRACTION7D70 - 325
8X-RAY DIFFRACTION8D326 - 430

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