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- PDB-5f8v: Crystal structure of PLP bound phosphoserine aminotransferase (PS... -

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Basic information

Entry
Database: PDB / ID: 5f8v
TitleCrystal structure of PLP bound phosphoserine aminotransferase (PSAT) from Trichomonas vaginalis
ComponentsAminotransferase, class V family protein
KeywordsTRANSFERASE / Alpha-family / Aminotransferase / Alpha-beta domains
Function / homology
Function and homology information


phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / L-serine biosynthetic process / pyridoxal phosphate binding / 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
phosphoserine transaminase
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsSingh, R.K. / Gourinath, S.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific and Industrial Research (CSIR) India
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Structural investigation and inhibitory response of halide on phosphoserine aminotransferase from Trichomonas vaginalis.
Authors: Singh, R.K. / Mazumder, M. / Sharma, B. / Gourinath, S.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Derived calculations
Category: citation / pdbx_related_exp_data_set / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 8, 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

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Assembly

Deposited unit
A: Aminotransferase, class V family protein
E: Aminotransferase, class V family protein
B: Aminotransferase, class V family protein
C: Aminotransferase, class V family protein
D: Aminotransferase, class V family protein
F: Aminotransferase, class V family protein
G: Aminotransferase, class V family protein
H: Aminotransferase, class V family protein


Theoretical massNumber of molelcules
Total (without water)346,2358
Polymers346,2358
Non-polymers00
Water13,493749
1
A: Aminotransferase, class V family protein
E: Aminotransferase, class V family protein


Theoretical massNumber of molelcules
Total (without water)86,5592
Polymers86,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminotransferase, class V family protein
C: Aminotransferase, class V family protein


Theoretical massNumber of molelcules
Total (without water)86,5592
Polymers86,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Aminotransferase, class V family protein
F: Aminotransferase, class V family protein


Theoretical massNumber of molelcules
Total (without water)86,5592
Polymers86,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Aminotransferase, class V family protein
H: Aminotransferase, class V family protein


Theoretical massNumber of molelcules
Total (without water)86,5592
Polymers86,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.967, 235.434, 134.520
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.486006, -0.453573, -0.747041), (-0.422542, -0.626286, 0.655151), (-0.765021, 0.634064, 0.112725)115.179588, -70.073143, 118.885071
3given(1), (1), (1)
4given(0.999988, -0.004688, 0.001272), (0.004686, 0.999988, 0.00156), (-0.001279, -0.001555, 0.999998)-0.35183, -2.44235, 67.02491
5given(1), (1), (1)
6given(-0.484525, -0.458652, -0.744898), (-0.420989, -0.624178, 0.658157), (-0.766814, 0.632487, 0.109342)65.914192, -24.68774, 125.127441
7given(1), (1), (1)
8given(0.99998, 0.006253, -0.001202), (0.006265, -0.999934, 0.009667), (-0.001142, -0.009674, -0.999953)26.402399, -115.984108, 120.017372
9given(1), (1), (1)
10given(-0.483496, 0.457295, 0.7464), (-0.43554, 0.613971, -0.658289), (-0.7593, -0.643367, -0.097682)64.793327, 69.953537, 37.68116
11given(1), (1), (1)
12given(0.999996, 0.002785, -0.000587), (0.002789, -0.999974, 0.006696), (-0.000568, -0.006697, -0.999977)26.123791, -113.055923, 53.17424
13given(1), (1), (1)
14given(-0.482667, 0.446209, 0.753611), (-0.442018, 0.618736, -0.64945), (-0.756077, -0.646578, -0.101411)112.963493, 25.057341, 32.154339
15given(1), (1), (1)
16given(-0.486869, -0.419256, -0.766279), (-0.457201, -0.625181, 0.632547), (-0.744262, 0.658311, 0.112697)67.231773, -22.84347, 124.768593
17given(1), (1), (1)
18given(0.999994, 0.003377, 4.2E-5), (-0.003376, 0.999979, -0.005482), (-6.1E-5, 0.005481, 0.999985)-0.00235, -2.08513, 67.234863
19given(1), (1), (1)
20given(-0.487982, 0.427424, 0.76104), (-0.457418, 0.617361, -0.640027), (-0.7434, -0.660435, -0.105749)61.74715, 69.753899, 36.422081
21given(1), (1), (1)
22given(0.999911, 0.008818, -0.010037), (0.008941, -0.999884, 0.012305), (-0.009927, -0.012393, -0.999874)27.27453, -116.300888, 120.167648
23given(1), (1), (1)
24given(-0.486934, 0.426757, 0.762085), (-0.455054, 0.620792, -0.638391), (-0.745534, -0.657645, -0.108087)111.743118, 25.62986, 30.98505
25given(1), (1), (1)
26given(0.999776, 0.015561, -0.014354), (0.015576, -0.999878, 0.000924), (-0.014338, -0.001147, -0.999897)27.152309, -113.537086, 54.175091
27given(1), (1), (1)
28given(-0.485315, -0.461861, -0.742398), (-0.418531, -0.622779, 0.661043), (-0.76766, 0.63153, 0.108941)66.080238, -22.582741, 58.135719
29given(1), (1), (1)
30given(0.999998, 0.002051, -2.0E-6), (0.002051, -0.999941, 0.010696), (2.0E-5, -0.010696, -0.999943)26.19635, -113.730339, 52.890961
31given(1), (1), (1)
32given(-0.484414, 0.4587, 0.744941), (-0.434752, 0.612707, -0.659985), (-0.759166, -0.643571, -0.097383)65.20298, 72.126251, -29.394711
33given(1), (1), (1)
34given(0.999999, -0.001344, 0.000664), (-0.001349, -0.99997, 0.007688), (0.000654, -0.007688, -0.99997)26.01436, -110.736427, -13.94782
35given(1), (1), (1)
36given(-0.483464, 0.449121, 0.751367), (-0.439703, 0.617606, -0.652092), (-0.756917, -0.645642, -0.10111)113.406281, 27.06571, -34.751492
37given(1), (1), (1)
38given(-0.486302, 0.425965, 0.762932), (-0.46264, 0.615185, -0.638366), (-0.741265, -0.663402, -0.102097)61.560429, 71.885597, -31.17436
39given(1), (1), (1)
40given(0.999874, 0.012286, -0.010077), (0.01236, -0.999897, 0.007248), (-0.009987, -0.007372, -0.999923)27.674629, -113.859001, 53.521381
41given(1), (1), (1)
42given(-0.485524, 0.424754, 0.764101), (-0.460614, 0.618583, -0.636545), (-0.743035, -0.661014, -0.10469)111.658089, 27.886021, -36.39967
43given(1), (1), (1)
44given(0.99972, 0.018877, -0.014302), (0.018813, -0.999813, -0.004555), (-0.014386, 0.004285, -0.999887)27.525009, -111.425797, -12.45206
45given(1), (1), (1)
46given(-0.485475, 0.459714, 0.743625), (0.441906, -0.604887, 0.662443), (0.754343, 0.650212, 0.090507)39.361851, -184.88736, 84.281593
47given(1), (1), (1)
48given(0.999994, -0.003389, 0.000665), (0.003387, 0.99999, 0.003), (-0.000675, -0.002998, 0.999995)-0.1772, -2.27989, 66.869553
49given(1), (1), (1)
50given(-0.484383, 0.45019, 0.750135), (0.446814, -0.609872, 0.654532), (0.75215, 0.652215, 0.09426)87.481857, -139.686813, 89.148407
51given(1), (1), (1)
52given(-0.483934, 0.439435, 0.756772), (0.459161, -0.608675, 0.64706), (0.744969, 0.660615, 0.092787)86.650322, -140.032028, 90.058723
53given(1), (1), (1)
54given(0.999987, 0.003979, -0.00306), (-0.003947, 0.99994, 0.010212), (0.003101, -0.0102, 0.999943)0.29573, -2.05629, 66.198021
55given(1), (1), (1)
56given(-0.483452, 0.448001, 0.752044), (0.445857, -0.613305, 0.651972), (0.753316, 0.650501, 0.096759)87.209969, -137.749313, 21.901899

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Components

#1: Protein
Aminotransferase, class V family protein


Mass: 43279.371 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_224040 / Plasmid: pET21c / Details (production host): Contain His Tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A2DW27
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 25-30% PEG 3350 (w/v),100mM sodium acetate pH 4.5-5.0, 200mM sodium malonate, 10% glycerol (v/v)
PH range: 4.5-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 19, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.759
11-h,-k,l20.241
ReflectionResolution: 2.14→50 Å / Num. obs: 177429 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 32.43 Å2 / Rsym value: 0.15 / Net I/σ(I): 7.9
Reflection shellResolution: 2.14→2.23 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BJN

1bjn


Resolution: 2.14→37.42 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.321 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23905 9041 5.1 %RANDOM
Rwork0.20869 ---
obs0.21022 168230 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.791 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å26.77 Å2
2---4.37 Å2-0 Å2
3---4.25 Å2
Refinement stepCycle: LAST / Resolution: 2.14→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22852 0 0 749 23601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01923475
X-RAY DIFFRACTIONr_bond_other_d0.0010.0221822
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.94931860
X-RAY DIFFRACTIONr_angle_other_deg0.912350163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7635.0032895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31823.9381064
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.726153726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.75815135
X-RAY DIFFRACTIONr_chiral_restr0.0720.23360
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02126797
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025604
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_it0.8132.48811606
X-RAY DIFFRACTIONr_mcbond_other0.8132.48711605
X-RAY DIFFRACTIONr_mcangle_it1.3813.72714490
X-RAY DIFFRACTIONr_mcangle_other1.3813.72814491
X-RAY DIFFRACTIONr_scbond_it0.7692.53911869
X-RAY DIFFRACTIONr_scbond_other0.7692.5411870
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3183.77717371
X-RAY DIFFRACTIONr_long_range_B_refined2.56219.52726874
X-RAY DIFFRACTIONr_long_range_B_other2.55519.52526863
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.135→2.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 565 -
Rwork0.236 11807 -
obs--93.33 %

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