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- PDB-7qcw: Apo-structure of serine hydroxymethyltransferase (PbzB) involved ... -

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Basic information

Entry
Database: PDB / ID: 7qcw
TitleApo-structure of serine hydroxymethyltransferase (PbzB) involved in benzobactin biosynthesis in P. chlororaphis subsp. piscium DSM 21509
ComponentsSerine hydroxymethyltransferase
KeywordsBIOSYNTHETIC PROTEIN / natural product biosynthesis / benzobactin / serine hydroxymethyltransferase / benzoxazolinate
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation / cytoplasm
Similarity search - Function
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
Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesPseudomonas chlororaphis subsp. piscium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsCzech, L. / Bange, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Genome Mining Enabled by Biosynthetic Characterization Uncovers a Class of Benzoxazolinate-Containing Natural Products in Diverse Bacteria.
Authors: Shi, Y.M. / Crames, J.J. / Czech, L. / Bozhuyuk, K.A.J. / Shi, Y.N. / Hirschmann, M. / Lamberth, S. / Claus, P. / Paczia, N. / Ruckert, C. / Kalinowski, J. / Bange, G. / Bode, H.B.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Genome Mining Enabled by Biosynthetic Characterization Uncovers a Class of Benzoxazolinate-Containing Natural Products in Diverse Bacteria.
Authors: Shi, Y.M. / Crames, J.J. / Czech, L. / Bozhuyuk, K.A.J. / Shi, Y.N. / Hirschmann, M. / Lamberth, S. / Claus, P. / Paczia, N. / Ruckert, C. / Kalinowski, J. / Bange, G. / Bode, H.B.
#2: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Genome mining enabled by biosynthetic characterization of benzoxazolinate unravels a widespread class of benzoxazolinate-containing natural products
Authors: Czech, L. / Bange, G.
History
DepositionNov 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 21, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase


Theoretical massNumber of molelcules
Total (without water)98,9142
Polymers98,9142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-35 kcal/mol
Surface area31490 Å2
Unit cell
Length a, b, c (Å)132.400, 59.640, 112.120
Angle α, β, γ (deg.)90.00, 109.41, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 49457.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas chlororaphis subsp. piscium (bacteria)
Gene: glyA, C4K37_3196 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A3G7DQ80, glycine hydroxymethyltransferase

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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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M potassium chloride; 0.1 M HEPES pH7.5; 15% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 2.81→49.21 Å / Num. obs: 20309 / % possible obs: 99.61 % / Redundancy: 4.9 % / Biso Wilson estimate: 68.66 Å2 / CC1/2: 0.994 / Net I/σ(I): 8.67
Reflection shellResolution: 2.81→2.91 Å / Redundancy: 5 % / Num. unique obs: 1992 / CC1/2: 0.764 / % possible all: 98.47

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VMB

5vmb


Resolution: 2.81→49.21 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2947 1016 5 %
Rwork0.2358 --
obs0.2388 20300 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.81→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6027 0 0 0 6027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066090
X-RAY DIFFRACTIONf_angle_d1.1448240
X-RAY DIFFRACTIONf_dihedral_angle_d20.894874
X-RAY DIFFRACTIONf_chiral_restr0.061978
X-RAY DIFFRACTIONf_plane_restr0.0071082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.960.48861430.37752702X-RAY DIFFRACTION99
2.96-3.140.39131450.30392764X-RAY DIFFRACTION100
3.14-3.390.31991430.27772705X-RAY DIFFRACTION100
3.39-3.730.33511450.2472757X-RAY DIFFRACTION100
3.73-4.270.32051450.23422768X-RAY DIFFRACTION100
4.27-5.370.27581450.21052748X-RAY DIFFRACTION100
5.38-49.210.23021500.20122840X-RAY DIFFRACTION99

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