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- PDB-2w7f: Crystal structure of Y51FbsSHMT L-Ser external aldimine -

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Basic information

Entry
Database: PDB / ID: 2w7f
TitleCrystal structure of Y51FbsSHMT L-Ser external aldimine
ComponentsSERINE HYDROXYMETHYLTRANSFERASE
KeywordsTRANSFERASE / ONE-CARBON METABOLISM / PLP-DEPENDENT ENZYMES
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / pyridoxal phosphate binding / cytoplasm
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 / PHOSPHATE ION / SERINE / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsRajaram, V. / Bhavani, B.S. / Bisht, S. / Kaul, P. / Prakash, V. / Appaji Rao, N. / Savithri, H.S. / Murthy, M.R.N.
CitationJournal: FEBS J. / Year: 2008
Title: Importance of Tyrosine Residues of Bacillus Stearothermophilus Serine Hydroxymethyltransferase in Cofactor Binding and L-Allo-Thr Cleavage.
Authors: Bhavani, B.S. / Rajaram, V. / Bisht, S. / Kaul, P. / Prakash, V. / Murthy, M.R.N. / Appaji Rao, N. / Savithri, H.S.
History
DepositionDec 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9426
Polymers44,2581
Non-polymers6845
Water7,837435
1
A: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules

A: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,88312
Polymers88,5162
Non-polymers1,36710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10190 Å2
ΔGint-101.4 kcal/mol
Surface area26800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.010, 106.510, 57.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SERINE HYDROXYMETHYLTRANSFERASE /


Mass: 44258.184 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-405 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SCHIFF LINKAGE BETWEEN LYS A226 AND PLP A501
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q7SIB6, glycine hydroxymethyltransferase

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Non-polymers , 5 types, 440 molecules

#2: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 51 TO PHE

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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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growDetails: 50% MPD, 0.1 M HEPES PH 7.5, 0.2 MM EDTA, 5 MM 2-MERCAPTOETHANOL, 10 MM L-SER

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: OSMIC MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.66→30 Å / Num. obs: 43037 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 20.1 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.8
Reflection shellResolution: 1.66→1.72 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.8 / % possible all: 83.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KL1

1kl1


Resolution: 1.67→22.45 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.882 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2158 5 %RANDOM
Rwork0.18 ---
obs0.182 40878 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.67→22.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3115 0 43 435 3593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223255
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.9684426
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4575416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03324.172151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39815530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8721521
X-RAY DIFFRACTIONr_chiral_restr0.0880.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022487
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21692
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22259
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2311
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.2100
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.261
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7031.52079
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08923263
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.99331294
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.094.51157
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.71 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.59 142
Rwork0.459 2833

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