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- PDB-6ymd: Crystal structure of serine hydroxymethyltransferase from Aphanot... -

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Basic information

Entry
Database: PDB / ID: 6ymd
TitleCrystal structure of serine hydroxymethyltransferase from Aphanothece halophytica in the covalent complex with malonate
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / SERINE BIOSYNTHESIS / GLYCINE / PLP / ONE-CARBON METABOLISM / TETRAHYDROFOLATE
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 / cytosol
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
MALONATE ION / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesAphanothece halophytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsRuszkowski, M. / Sekula, B. / Nogues, I. / Tramonti, A. / Angelaccio, S. / Contestabile, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structural and kinetic properties of serine hydroxymethyltransferase from the halophytic cyanobacterium Aphanothece halophytica provide a rationale for salt tolerance.
Authors: Nogues, I. / Tramonti, A. / Angelaccio, S. / Ruszkowski, M. / Sekula, B. / Contestabile, R.
History
DepositionApr 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 17, 2020Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)98,36913
Polymers97,3122
Non-polymers1,05711
Water16,232901
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10450 Å2
ΔGint-48 kcal/mol
Surface area27340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.050, 94.202, 142.972
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Serine hydroxymethyltransferase / Serine methylase


Mass: 48656.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aphanothece halophytica (bacteria) / Gene: glyrA, glyA / Plasmid: pET28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I7H6W6, glycine hydroxymethyltransferase

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Non-polymers , 5 types, 912 molecules

#2: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 901 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M sodium malonate at pH 5.0 and 20% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 10, 2018
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→71.49 Å / Num. obs: 226857 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 13 Å2 / CC1/2: 1 / Rrim(I) all: 0.053 / Net I/σ(I): 21.4
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 32794 / CC1/2: 0.73 / Rrim(I) all: 0.057 / % possible all: 87.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHASERphasing
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kkj

1kkj


Resolution: 1.25→71.49 Å / SU ML: 0.1357 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.3629
RfactorNum. reflection% reflection
Rfree0.1501 1135 0.5 %
Rwork0.1288 --
obs0.1289 226826 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.54 Å2
Refinement stepCycle: LAST / Resolution: 1.25→71.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6431 0 66 901 7398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01126700
X-RAY DIFFRACTIONf_angle_d1.20339087
X-RAY DIFFRACTIONf_chiral_restr0.09261004
X-RAY DIFFRACTIONf_plane_restr0.00861215
X-RAY DIFFRACTIONf_dihedral_angle_d15.75932477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.30.31911220.270624300X-RAY DIFFRACTION84.55
1.3-1.370.21511420.187428120X-RAY DIFFRACTION97.61
1.37-1.460.18931420.149328304X-RAY DIFFRACTION98.12
1.46-1.570.15961430.126828434X-RAY DIFFRACTION98.48
1.57-1.730.15041440.105128655X-RAY DIFFRACTION99.01
1.73-1.980.13361450.108428869X-RAY DIFFRACTION99.36
1.98-2.490.13341460.118229131X-RAY DIFFRACTION99.76
2.49-71.490.13971510.127229878X-RAY DIFFRACTION99.94

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