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- PDB-3g8m: Serine Hydroxymethyltransferase Y55F Mutant -

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Basic information

Entry
Database: PDB / ID: 3g8m
TitleSerine Hydroxymethyltransferase Y55F Mutant
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / SHMT / E. coli / Y55F / One-carbon metabolism / Pyridoxal phosphate
Function / homology
Function and homology information


glycine catabolic process / L-allo-threonine aldolase activity / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion ...glycine catabolic process / L-allo-threonine aldolase activity / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding / protein homodimerization activity / zinc ion binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / 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 ...Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / 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 / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsAngelucci, F. / Ilari, A.
CitationJournal: Biochemistry / Year: 2009
Title: Role of a conserved active site cation-pi interaction in Escherichia coli serine hydroxymethyltransferase.
Authors: Vivoli, M. / Angelucci, F. / Ilari, A. / Morea, V. / Angelaccio, S. / di Salvo, M.L. / Contestabile, R.
History
DepositionFeb 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6042
Polymers45,3561
Non-polymers2471
Water00
1
A: Serine hydroxymethyltransferase
hetero molecules

A: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2074
Polymers90,7132
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area9840 Å2
ΔGint-57 kcal/mol
Surface area29910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.590, 112.590, 68.929
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Serine hydroxymethyltransferase / Serine methylase / SHMT


Mass: 45356.477 Da / Num. of mol.: 1 / Mutation: Y55F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: b2551, Escherichia coli glyA, glyA, JW2535 / Plasmid: pBS::glyA / Production host: Escherichia coli (E. coli) / Strain (production host): GS1993 recA-
References: UniProt: P0A825, glycine hydroxymethyltransferase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P

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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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes (N-(2-hydroxylethyl)piperazine-N -2 ethansulfonic acid) pH 7.5, 1.4M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97623 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 6600 / % possible obs: 94 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.7
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.5 / Num. unique all: 734 / % possible all: 97.3

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dfo

1dfo


Resolution: 3.3→50 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.897 / SU B: 80.811 / SU ML: 0.579 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.669 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27535 319 4.8 %RANDOM
Rwork0.25528 ---
obs0.25625 6356 94.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.946 Å2
Baniso -1Baniso -2Baniso -3
1-3.17 Å20 Å20 Å2
2--3.17 Å20 Å2
3----6.34 Å2
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 15 0 3200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223283
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7761.9684451
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4045416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63724.755143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00915540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.5041514
X-RAY DIFFRACTIONr_chiral_restr0.050.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.022504
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1340.21278
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2840.22265
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0660.249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0950.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0310.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0221.52129
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.0423296
X-RAY DIFFRACTIONr_scbond_it0.05131325
X-RAY DIFFRACTIONr_scangle_it0.0894.51155
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 21 -
Rwork0.344 464 -
obs--96.61 %
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)
13.87911.95663.22160.99611.4346.63710.19480.8845-0.24241.41850.0235-1.0547-0.09651.3472-0.21831.25790.2292-0.47820.1826-0.09380.6273-22.40976.165816.7165
23.89890.12993.39455.5680.68565.8931-0.5531-0.18320.32970.01630.4977-0.1381-0.59331.00090.0554-0.0197-0.15070.0350.4921-0.07550.0539-19.650132.970312.4208
37.67711.6866-2.17363.328-3.61673.9475-1.0311.14530.2462-1.11510.55991.1532-0.51310.15810.47111.0823-0.2707-0.45090.50580.08960.5964-40.446137.231-3.4941
47.4761-0.8817-1.49872.13972.10059.7614-0.71020.68510.4166-0.82690.01140.3089-1.39291.20190.69880.3954-0.4208-0.25050.42720.06280.1947-26.862234.2863-2.4213
51.80141.85461.96453.63362.92453.7176-0.16920.3231-0.0218-0.28930.30480.112-0.15860.4899-0.13560.1345-0.03860.01330.3851-0.04110.1509-30.373915.7579-3.4097
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 35
2X-RAY DIFFRACTION2A36 - 118
3X-RAY DIFFRACTION3A119 - 192
4X-RAY DIFFRACTION4A193 - 229
5X-RAY DIFFRACTION5A230 - 417

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