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- PDB-5yd2: Crystal Structure of Delta 4 mutant of EhPSAT (Phosphoserine amin... -

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Basic information

Entry
Database: PDB / ID: 5yd2
TitleCrystal Structure of Delta 4 mutant of EhPSAT (Phosphoserine aminotransferase of Entamoeba histolytica)
ComponentsPhosphoserine aminotransferase
KeywordsTRANSFERASE / Delta4_EhPSAT
Function / homology
Function and homology information


phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / L-serine biosynthetic process
Similarity search - Function
Phosphoserine aminotransferase / Aminotransferase class V domain / Aminotransferase class-V / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Phosphoserine transaminase
Similarity search - Component
Biological speciesEntamoeba histolytica HM-3:IMSS (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSingh, R.K. / Gourinath, S.
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: N-terminal residues are crucial for quaternary structure and active site conformation for the phosphoserine aminotransferase from enteric human parasite E. histolytica.
Authors: Singh, R.K. / Tomar, P. / Dharavath, S. / Kumar, S. / Gourinath, S.
History
DepositionSep 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation.year
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1426
Polymers80,5772
Non-polymers5654
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-55 kcal/mol
Surface area28070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.238, 67.904, 95.030
Angle α, β, γ (deg.)90.00, 110.93, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 7 - 351 / Label seq-ID: 7 - 351

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

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Components

#1: Protein Phosphoserine aminotransferase


Mass: 40288.645 Da / Num. of mol.: 2 / Mutation: Deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica HM-3:IMSS (eukaryote)
Gene: KM1_040390 / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / References: UniProt: M7XC02
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG2000MME 100 mM Tris pH-8.5 200 mM TMAO

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Data collection

DiffractionMean temperature: 77.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 25, 2016
RadiationMonochromator: Cu-Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 31390 / % possible obs: 95 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.023 / Rrim(I) all: 0.06 / Χ2: 1.438 / Net I/σ(I): 20.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.393.20.42111250.9280.2430.4891.15668.5
2.39-2.433.60.36612570.9530.1950.4171.2276.1
2.43-2.484.10.33313070.9660.1660.3741.16679.4
2.48-2.534.60.33614080.9760.1620.3751.10186.7
2.53-2.594.90.34415170.9740.1610.3811.14492.1
2.59-2.655.40.3416070.9740.1550.3751.18497.9
2.65-2.7160.31216640.9820.1350.3411.18699.6
2.71-2.796.50.27416130.990.1160.2981.21999.9
2.79-2.876.80.2316570.9930.0950.251.279100
2.87-2.966.80.2116480.9910.0860.2281.297100
2.96-3.076.90.16216320.9950.0660.1761.376100
3.07-3.196.80.12416400.9970.0510.1351.439100
3.19-3.336.80.09716420.9980.040.1051.474100
3.33-3.516.80.0816610.9980.0330.0861.597100
3.51-3.736.20.07316460.9970.0310.0792.65599.3
3.73-4.026.50.05316530.9990.0220.0581.82199.5
4.02-4.426.80.0416530.9990.0170.0441.55899.9
4.42-5.066.80.03516610.9990.0140.0381.40799.9
5.06-6.376.90.03716740.9990.0150.041.407100
6.37-506.60.0317250.9990.0130.0331.34699.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YB0

5yb0


Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / SU B: 27.338 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R: 0.493 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28695 1595 5.1 %RANDOM
Rwork0.22909 ---
obs0.23196 29564 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.222 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å2-2.98 Å2
2--2.27 Å20 Å2
3----1.01 Å2
Refinement stepCycle: 1 / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5539 0 34 24 5597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195672
X-RAY DIFFRACTIONr_bond_other_d0.0040.025585
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9677646
X-RAY DIFFRACTIONr_angle_other_deg1.022312875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8495693
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33325.143245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.624151082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1011520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026301
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021245
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_it3.2184.0452778
X-RAY DIFFRACTIONr_mcbond_other3.2174.0452777
X-RAY DIFFRACTIONr_mcangle_it5.0046.0573469
X-RAY DIFFRACTIONr_mcangle_other5.0046.0573470
X-RAY DIFFRACTIONr_scbond_it3.2844.3882894
X-RAY DIFFRACTIONr_scbond_other3.2844.3882895
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1196.4074178
X-RAY DIFFRACTIONr_long_range_B_refined7.64932.0916510
X-RAY DIFFRACTIONr_long_range_B_other7.64832.0916508
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 20923 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 93 -
Rwork0.322 1576 -
obs--69.51 %
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)
10.59070.19050.45580.41060.41730.7904-0.0293-0.05990.0055-0.0759-0.00980.0552-0.07910.14140.03910.2027-0.0365-0.12180.3685-0.03060.0843-24.549834.2783112.0261
21.01060.0859-0.1640.1127-0.18730.39070.1036-0.3911-0.1067-0.10740.01360.09320.1171-0.1388-0.11710.2178-0.0443-0.18630.34980.05340.1601-54.71320.1781109.0331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 516
2X-RAY DIFFRACTION2B7 - 508

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