[English] 日本語
Yorodumi
- PDB-7qcw: Apo-structure of serine hydroxymethyltransferase (PbzB) involved ... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more