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- PDB-6uld: Crystal structure of serine hydroxymethyltransferase from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 6uld
TitleCrystal structure of serine hydroxymethyltransferase from Mycobacterium tuberculosis with bound PLP forming a Schiff base with substrate Serine in one monomer and PLP forming a Schiff base with product Glycine in the other monomer
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / SSGCID / Serine hydroxymethyltransferase / Mycobacterium tuberculosis / Pyridoxal phosphate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / methyltransferase activity / 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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
GLYCINE / PYRIDOXAL-5'-PHOSPHATE / SERINE / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of serine hydroxymethyltransferase from Mycobacterium tuberculosis with bound PLP forming a Schiff base with substrate Serine in one monomer and PLP forming a Schiff base ...Title: Crystal structure of serine hydroxymethyltransferase from Mycobacterium tuberculosis with bound PLP forming a Schiff base with substrate Serine in one monomer and PLP forming a Schiff base with product Glycine in the other monomer
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionOct 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6568
Polymers94,7462
Non-polymers9116
Water10,701594
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-82 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.650, 60.010, 101.660
Angle α, β, γ (deg.)90.000, 92.993, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Serine hydroxymethyltransferase / Serine methylase / MytuD.00783.a


Mass: 47372.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: glyA1, glyA, ERS124361_03156 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0T9NP28, glycine hydroxymethyltransferase

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Non-polymers , 5 types, 600 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 39.89 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MytuD.00783.a.A1.PS00175 at 20.2 mg/ml, incubated with 5 mM pyrazinoic acid, mixed 1:1 with 12.5% (w/v) PEG-1000, 12.5% (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M MES/imidazole, pH=6.5, 0.02 M ...Details: MytuD.00783.a.A1.PS00175 at 20.2 mg/ml, incubated with 5 mM pyrazinoic acid, mixed 1:1 with 12.5% (w/v) PEG-1000, 12.5% (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M MES/imidazole, pH=6.5, 0.02 M of sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine. Tray: 311079g8, puck: ved0-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 11, 2019 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 121439 / % possible obs: 99.1 % / Redundancy: 4.088 % / Biso Wilson estimate: 25.784 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.046 / Χ2: 1.054 / Net I/σ(I): 18.62
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.543.3550.5172.2384650.7850.61493.7
1.54-1.583.9630.4662.9886870.8640.53998.8
1.58-1.634.1820.3773.8784760.9150.43299.1
1.63-1.684.1990.2924.9682520.9450.33599.2
1.68-1.734.1880.2296.2379660.9680.26299.4
1.73-1.794.2010.1817.8677500.9780.20899.4
1.79-1.864.2010.13710.2675350.9860.15799.6
1.86-1.944.1940.10512.9672120.9920.1299.8
1.94-2.024.1880.07716.9869100.9950.08999.8
2.02-2.124.1840.06320.867020.9960.07399.7
2.12-2.244.1760.04925.4562830.9980.05699.8
2.24-2.374.1650.04328.6859580.9980.04999.6
2.37-2.544.1460.03831.6356300.9980.04499.7
2.54-2.744.1290.03434.7552510.9990.03999.8
2.74-34.0980.0338.7848300.9990.03499.6
3-3.354.0690.02642.8243850.9990.0399.7
3.35-3.874.0590.02346.8838410.9990.02799.7
3.87-4.744.0620.02149.0632970.9990.02499.8
4.74-6.714.0520.0248.8925750.9990.02499.8
6.71-503.8750.0249.514340.9990.02398.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.17rc1-3602refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H7F

3h7f


Resolution: 1.5→38.76 Å / SU ML: 0.1182 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.8296
RfactorNum. reflection% reflection
Rfree0.1631 2036 1.68 %
Rwork0.1256 --
obs0.1263 121428 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.75 Å2
Refinement stepCycle: LAST / Resolution: 1.5→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6311 0 58 594 6963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00526710
X-RAY DIFFRACTIONf_angle_d0.82729181
X-RAY DIFFRACTIONf_chiral_restr0.04921056
X-RAY DIFFRACTIONf_plane_restr0.00551235
X-RAY DIFFRACTIONf_dihedral_angle_d15.7034096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.22641420.19057449X-RAY DIFFRACTION93.26
1.53-1.570.22531440.16567817X-RAY DIFFRACTION98.54
1.57-1.620.18181330.14297977X-RAY DIFFRACTION99.13
1.62-1.660.18791380.1277896X-RAY DIFFRACTION99.2
1.66-1.720.16591280.11687994X-RAY DIFFRACTION99.28
1.72-1.780.15661400.11257918X-RAY DIFFRACTION99.4
1.78-1.850.17181220.10757962X-RAY DIFFRACTION99.57
1.85-1.930.17521590.10647992X-RAY DIFFRACTION99.72
1.93-2.040.12661420.09758002X-RAY DIFFRACTION99.78
2.04-2.160.1617950.10148015X-RAY DIFFRACTION99.77
2.16-2.330.13131340.10767990X-RAY DIFFRACTION99.69
2.33-2.560.1471370.12138059X-RAY DIFFRACTION99.7
2.56-2.940.16831250.12698047X-RAY DIFFRACTION99.76
2.94-3.70.15831710.12728048X-RAY DIFFRACTION99.68
3.7-38.760.17471260.14458226X-RAY DIFFRACTION99.58

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