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- PDB-2vi9: Crystal structure of S172AbsSHMT Glycine external aldimine -

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Basic information

Entry
Database: PDB / ID: 2vi9
TitleCrystal structure of S172AbsSHMT Glycine external aldimine
ComponentsSERINE HYDROXYMETHYLTRANSFERASE
KeywordsTRANSFERASE / SHMT / E53Q / FTHF / ENZYME MEMORY / PYRIDOXAL PHOSPHATE / 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 / 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) ...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
GLYCINE / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsRajaram, V. / Bhavani, B.S. / Prakash, V. / Appaji Rao, N. / Savithri, H.S. / Murthy, M.R.N.
CitationJournal: To be Published
Title: Crystal Structure of S172Absshmt and its Complexes
Authors: Rajaram, V. / Bhavani, B.S. / Prakash, V. / Appaji Rao, N. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionNov 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2007Provider: 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9126
Polymers44,2581
Non-polymers6545
Water3,639202
1
A: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules

A: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,82312
Polymers88,5162
Non-polymers1,30710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8700 Å2
ΔGint-52.7 kcal/mol
Surface area32820 Å2
MethodPQS
Unit cell
Length a, b, c (Å)61.075, 105.953, 56.890
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
Source: (gene. exp.) BACILLUS 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, 207 molecules

#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 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


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


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


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 172 TO ALA

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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 growpH: 7.5
Details: 50% MPD, 0.1 M HEPES PH7.5, 0.2 MM EDTA, 5 MM 2-MERCAPTOETHANOL, 10 MM GLY

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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 MIRROR
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 25285 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.8 / % possible all: 98.8

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Processing

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

1kl1


Resolution: 2→24.01 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.492 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1290 5.1 %RANDOM
Rwork0.195 ---
obs0.197 23992 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.07 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→24.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3115 0 41 202 3358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223221
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9861.9664371
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9455406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45224.094149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76515522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4361521
X-RAY DIFFRACTIONr_chiral_restr0.0660.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022458
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1770.21634
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22237
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2220
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2881.52090
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.4623228
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.72431278
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1864.51142
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: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.33 79
Rwork0.254 1669

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