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- PDB-3e77: Human phosphoserine aminotransferase in complex with PLP -

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Basic information

Entry
Database: PDB / ID: 3.0E+77
TitleHuman phosphoserine aminotransferase in complex with PLP
ComponentsPhosphoserine aminotransferasePhosphoserine transaminase
KeywordsTRANSFERASE / Phosphoserine aminotransferase / SERC / PLP / Structural Genomics / Structural Genomics Consortium / SGC / Amino-acid biosynthesis / Aminotransferase / Disease mutation / Pyridoxal phosphate / Serine biosynthesis
Function / homology
Function and homology information


phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / Serine biosynthesis / pyridoxine biosynthetic process / L-serine biosynthetic process / pyridoxal phosphate binding / extracellular exosome / identical protein binding / cytosol / cytoplasm
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
PYRIDOXAL-5'-PHOSPHATE / Phosphoserine aminotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLehtio, L. / Karlberg, T. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. ...Lehtio, L. / Karlberg, T. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Thorsell, S.G. / Tresaugues, L. / Van Den Berg, S. / Welin, M. / Wikstrom, M. / Wisniewska, M. / Weigelt, J. / Schueler, H. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Human phosphoserine aminotransferase in complex with PLP
Authors: Lehtio, L. / Karlberg, T. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / ...Authors: Lehtio, L. / Karlberg, T. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Thorsell, S.G. / Tresaugues, L. / Van Den Berg, S. / Welin, M. / Wikstrom, M. / Wisniewska, M. / Weigelt, J. / Schueler, H. / Structural Genomics Consortium (SGC)
History
DepositionAug 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Aug 30, 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 / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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
B: Phosphoserine aminotransferase
C: Phosphoserine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,0526
Polymers124,4663
Non-polymers5863
Water2,990166
1
A: Phosphoserine aminotransferase
B: Phosphoserine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5645
Polymers82,9772
Non-polymers5863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-26 kcal/mol
Surface area26920 Å2
MethodPISA
2
C: Phosphoserine aminotransferase

C: Phosphoserine aminotransferase


Theoretical massNumber of molelcules
Total (without water)82,9772
Polymers82,9772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area4070 Å2
ΔGint-19 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.000, 171.000, 103.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 4 / Auth seq-ID: 9 - 369 / Label seq-ID: 16 - 376

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein Phosphoserine aminotransferase / Phosphoserine transaminase / Phosphohydroxythreonine aminotransferase / PSAT


Mass: 41488.590 Da / Num. of mol.: 3 / Fragment: UNP residues 17 to 370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSAT1, PSA / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)gold Prare2 / References: UniProt: Q9Y617, phosphoserine transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.51 Å3/Da / Density % sol: 64.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.1 M Malic acid, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97623 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2008 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 60117 / Num. obs: 60117 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 10.47
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2.08 / Num. unique all: 4406 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0044refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BJO

1bjo


Resolution: 2.5→19.59 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.908 / SU B: 20.656 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24409 3005 5 %RANDOM
Rwork0.19637 ---
all0.19875 57102 --
obs0.19875 57102 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.465 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å20 Å2
2--0.15 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8334 0 36 166 8536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228542
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.96911571
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2151084
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29925.127353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.625151449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5541526
X-RAY DIFFRACTIONr_chiral_restr0.0920.21304
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216383
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.41.55393
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7728670
X-RAY DIFFRACTIONr_scbond_it1.39133149
X-RAY DIFFRACTIONr_scangle_it2.2954.52901
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2754 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.310.5
Bmedium positional0.330.5
Cmedium positional0.360.5
Amedium thermal0.812
Bmedium thermal0.582
Cmedium thermal0.832
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 216 -
Rwork0.319 4113 -
obs--100 %
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)
11.0063-0.1905-0.01570.73010.08051.2114-0.0627-0.1179-0.00640.0420.05170.0675-0.0006-0.23260.01090.00560.00830.00060.06790.01890.060266.093-48.36430.767
20.748-0.2175-0.12660.990.0311.5582-0.03820.0825-0.0546-0.09980.03370.07260.2797-0.14170.00450.0766-0.05540.00130.0596-0.0070.102469.824-75.01610.472
31.4389-0.2503-0.26480.5779-0.2921.3226-0.0144-0.27910.20890.02770.0440.0459-0.3093-0.2084-0.02950.11710.0736-0.00160.1462-0.08990.159232.396-24.31722.498
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 370
2X-RAY DIFFRACTION2B9 - 370
3X-RAY DIFFRACTION3C8 - 369

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