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- PDB-5z0y: Crystallization and structure determination of cytoplasm serine h... -

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Basic information

Entry
Database: PDB / ID: 5z0y
TitleCrystallization and structure determination of cytoplasm serine hydroxymethyltransferase (SHMT) from Pichia pastoris
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / SHMT / pichia pastoris / cytoplasm serine hydroxymethyltransferase
Function / homology
Function and homology information


serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / methyltransferase activity / pyridoxal phosphate binding ...serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / methyltransferase activity / pyridoxal phosphate binding / methylation / zinc ion 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 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, 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 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesKomagataella phaffii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChen, Z. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Key Research and Development Program of China2016YFC1200400 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structure and function of cytoplasmic serine hydroxymethyltransferase from Pichia pastoris
Authors: Zhang, M. / Wu, W. / Chen, Z.
History
DepositionDec 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2432
Polymers52,1511
Non-polymers921
Water1,08160
1
A: Serine hydroxymethyltransferase
hetero molecules

A: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4874
Polymers104,3022
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1690 Å2
ΔGint-17 kcal/mol
Surface area34890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.315, 114.743, 84.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Serine hydroxymethyltransferase


Mass: 52151.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1) (fungus)
Strain: ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1
Gene: SHM2, PP7435_Chr4-0570 / Production host: Komagataella pastoris (fungus)
References: UniProt: F2QZA4, glycine hydroxymethyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 18% PEG8000, 0.1M MES pH 6.0, 0.2M Ca(OAc)2

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 17959 / % possible obs: 99.4 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 2.46
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.924 / Num. unique obs: 874

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LS3

1ls3


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.529 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.415 / ESU R Free: 0.272 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25995 883 4.9 %RANDOM
Rwork0.22662 ---
obs0.22827 16985 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.933 Å2
Baniso -1Baniso -2Baniso -3
1-9.99 Å20 Å2-0 Å2
2---3.46 Å20 Å2
3----6.53 Å2
Refinement stepCycle: 1 / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 6 60 2860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192843
X-RAY DIFFRACTIONr_bond_other_d0.0010.022700
X-RAY DIFFRACTIONr_angle_refined_deg1.1091.9663844
X-RAY DIFFRACTIONr_angle_other_deg0.87836191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4685366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87524.425113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32715471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3681515
X-RAY DIFFRACTIONr_chiral_restr0.0590.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213201
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02605
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_it2.337.0571482
X-RAY DIFFRACTIONr_mcbond_other2.3297.0551481
X-RAY DIFFRACTIONr_mcangle_it3.95210.5561842
X-RAY DIFFRACTIONr_mcangle_other3.95110.5591843
X-RAY DIFFRACTIONr_scbond_it2.2327.2941361
X-RAY DIFFRACTIONr_scbond_other2.2327.2941361
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.86410.8712003
X-RAY DIFFRACTIONr_long_range_B_refined6.26254.9873053
X-RAY DIFFRACTIONr_long_range_B_other6.26154.9753048
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 76 -
Rwork0.409 1185 -
obs--97 %

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