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

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Basic information

Entry
Database: PDB / ID: 6czy
TitleCrystal structure of Arabidopsis thaliana phosphoserine aminotransferase isoform 1 (AtPSAT1) in complex with Pyridoxamine-5'-phosphate (PMP)
ComponentsPhosphoserine aminotransferase 1, chloroplasticPhosphoserine transaminase
KeywordsTRANSFERASE / serine biosynthesis / pyridoxal 5'-phosphate / PLP / transaminase / PSAT / pyridoxamine / PMP
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 / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Phosphoserine aminotransferase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 ...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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)163,12319
Polymers161,1054
Non-polymers2,01915
Water36,5882031
1
A: Phosphoserine aminotransferase 1, chloroplastic
B: Phosphoserine aminotransferase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,65811
Polymers80,5522
Non-polymers1,1069
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-101 kcal/mol
Surface area27620 Å2
MethodPISA
2
C: Phosphoserine aminotransferase 1, chloroplastic
D: Phosphoserine aminotransferase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4658
Polymers80,5522
Non-polymers9136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-68 kcal/mol
Surface area27490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.601, 106.485, 187.832
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 40276.176 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

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Non-polymers , 6 types, 2046 molecules

#2: Chemical
ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2031 / 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: 2.63 Å3/Da / Density % sol: 53.16 %
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: 1.75→77.14 Å / Num. obs: 170626 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 14.3
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.915 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 26555 / % possible all: 96.6

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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: 1.75→77.14 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.179 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.093 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18727 1024 0.6 %RANDOM
Rwork0.15327 ---
obs0.15348 169601 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.936 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å2-0 Å2
2---0.11 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: 1 / Resolution: 1.75→77.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11286 0 122 2031 13439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01911831
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211048
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.9716004
X-RAY DIFFRACTIONr_angle_other_deg0.849325803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35651501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85525.23522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.081152130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6341544
X-RAY DIFFRACTIONr_chiral_restr0.0980.21745
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113103
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022285
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_it0.9831.5725855
X-RAY DIFFRACTIONr_mcbond_other0.9831.5715854
X-RAY DIFFRACTIONr_mcangle_it1.6022.3497327
X-RAY DIFFRACTIONr_mcangle_other1.6022.3497328
X-RAY DIFFRACTIONr_scbond_it1.5691.8135976
X-RAY DIFFRACTIONr_scbond_other1.5691.8135976
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5522.6228651
X-RAY DIFFRACTIONr_long_range_B_refined5.78121.38714444
X-RAY DIFFRACTIONr_long_range_B_other5.78121.38914445
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 70 -
Rwork0.294 11595 -
obs--92.76 %
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)
10.1867-0.04820.08730.1585-0.08720.2529-0.0002-0.0061-0.0116-0.00360.03270.00370.0311-0.0639-0.03250.0675-0.019-0.01540.08030.01860.00822.10942.40823.161
20.107-0.013-0.08570.74640.14140.3599-0.02390.0113-0.00360.11880.07970.0349-0.074-0.046-0.05580.0850.02160.03190.06480.01380.016815.53861.45239.47
30.2024-0.0365-0.02660.0895-0.04980.3002-0.010.02180.03280.0085-0.0027-0.0550.0204-0.03910.01260.0788-0.0066-0.00380.0390.00880.03647.66945.2218.114
40.0381-0.2039-0.00841.185-0.00510.3915-0.00920.00250.0250.0714-0.0007-0.09570.1074-0.00290.00980.09150.0029-0.02250.00140.00550.052659.43924.0727.38
50.30990.09190.1170.13980.01470.1968-0.01440.0118-0.01220.00650.0118-0.01050.03260.03870.00260.07420.0088-0.01530.0603-0.00430.006262.27740.92572.851
60.31310.152-0.02691.1769-0.3390.1335-0.0870.10950.0691-0.06440.1014-0.00360.01030.0106-0.01440.0457-0.0233-0.00340.10.02550.037969.45260.31757.1
70.240.0428-0.03820.06750.03590.3048-0.0245-0.02420.0447-0.0047-0.00730.04410.01790.0220.03180.08220.0053-0.00040.0412-0.00640.03136.70344.09677.904
80.17780.17580.01311.29330.0770.1046-0.0053-0.0143-0.0009-0.04810.00360.08880.02650.01240.00170.07150.0031-0.01720.0146-0.00340.049923.93423.95867.508
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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