[English] 日本語
Yorodumi
- PDB-7qpe: Crystal structure of serine hydroxymethyltransferase, isoform 6 f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qpe
TitleCrystal structure of serine hydroxymethyltransferase, isoform 6 from Arabidopsis thaliana (SHM6)
ComponentsSerine hydroxymethyltransferase 6
KeywordsTRANSFERASE / one-carbon metabolism / tetrahydrofolate
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / 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 / 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
NITRATE ION / Serine hydroxymethyltransferase 6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsRuszkowski, M. / Grzechowiak, M. / Sekula, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plant Physiol Biochem. / Year: 2022
Title: Arabidopsis thaliana serine hydroxymethyltransferases: functions, structures, and perspectives.
Authors: Nogues, I. / Sekula, B. / Angelaccio, S. / Grzechowiak, M. / Tramonti, A. / Contestabile, R. / Ruszkowski, M.
History
DepositionJan 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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 6
B: Serine hydroxymethyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4353
Polymers106,3732
Non-polymers621
Water2,288127
1
A: Serine hydroxymethyltransferase 6
B: Serine hydroxymethyltransferase 6
hetero molecules

A: Serine hydroxymethyltransferase 6
B: Serine hydroxymethyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,8716
Polymers212,7474
Non-polymers1242
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area21910 Å2
ΔGint-95 kcal/mol
Surface area61150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.683, 129.683, 302.305
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11B-667-

HOH

21B-669-

HOH

-
Components

#1: Protein Serine hydroxymethyltransferase 6 / AtSHMT6 / Glycine hydroxymethyltransferase 6 / Serine methylase 6


Mass: 53186.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SHM6, SHMT6, At1g22020, F2E2.7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9LM59, glycine hydroxymethyltransferase
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 0.18 M Ammonium nitrate, 0.09 M Sodium cacodylate 5.3, 20% v/v PEG Smear Low, 10% Ethylene glycol (based on the D1 condition of the BCS screen, Molecular Dimensions). Cryoprotection was ...Details: 0.18 M Ammonium nitrate, 0.09 M Sodium cacodylate 5.3, 20% v/v PEG Smear Low, 10% Ethylene glycol (based on the D1 condition of the BCS screen, Molecular Dimensions). Cryoprotection was obtained by increasing the ethylene glycol concentration to 20 % in the drop with crystals.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.18→105.28 Å / Num. obs: 49107 / % possible obs: 62 % / Redundancy: 38.5 % / Biso Wilson estimate: 56.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 29.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2% possible all
7.23-105.2833.10.03195.524540.99999.9
2.18-2.4334.42.182.224560.82511.4

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PZZ

7pzz


Resolution: 2.18→63.4 Å / SU ML: 0.2068 / Cross valid method: FREE R-VALUE / Phase error: 38.803
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.23 981 2 %
Rwork0.2076 48062 -
obs0.2081 49043 61.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.76 Å2
Refinement stepCycle: LAST / Resolution: 2.18→63.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6720 0 4 127 6851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00796873
X-RAY DIFFRACTIONf_angle_d0.94779273
X-RAY DIFFRACTIONf_chiral_restr0.0508992
X-RAY DIFFRACTIONf_plane_restr0.0071209
X-RAY DIFFRACTIONf_dihedral_angle_d14.94682552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.290.5104120.4218599X-RAY DIFFRACTION5.52
2.29-2.440.3792400.36021968X-RAY DIFFRACTION18.07
2.44-2.620.3312810.29313933X-RAY DIFFRACTION36.02
2.62-2.890.32171580.27927752X-RAY DIFFRACTION70.54
2.89-3.310.25192240.260711018X-RAY DIFFRACTION99.76
3.31-4.170.22662280.193211150X-RAY DIFFRACTION99.86
4.17-63.40.20442380.181411642X-RAY DIFFRACTION99.57
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.61779213750.5719094863590.4179390511192.60444300383-0.829871650131.67150349762-0.0375213735346-0.472930604867-0.2053697058810.2382718807090.198063481049-0.06356285450380.182226409037-0.139937790958-0.1540808791240.348217006980.06515696088540.05723960763170.809176902855-0.0302133656340.32911282586163.235697511-1.73920717492110.456868795
22.765375200720.257792682697-0.9224620773233.28548679290.1329613318554.077590887-0.0961108518314-0.1845414915380.272880742008-0.3648135952420.225401028550.181775103422-0.472223106079-0.0420223565724-0.1054646787380.362659158804-0.123545899448-0.07780666491370.4164720309710.02496379655160.27436930839358.020786137116.791602749385.8364574777
32.277340052530.8449202234950.2709083430943.10526684964-0.00613784577811.26200295491-0.117163719265-0.1773640744560.1513496399040.09503515563290.195486753967-0.00387024523431-0.134294218431-0.00363327247998-0.06171642775010.448400127717-0.0583351437149-0.005945563326170.651414754364-0.1258489674710.31786806302568.609137073821.0548542461101.088695728
41.916489343330.06668227250560.2191759382042.038158729580.2934763737651.38584171387-0.175227093850.383382072578-0.168273781637-0.3832745135510.0623698014005-0.005213154079190.1044801215130.03985958157150.09866927524370.38153309055-0.2745404591550.04408991455220.4459010867170.03612877120770.21327011630366.44358214-1.7587395946628.6397398493
51.373469250660.7365117716350.07490930981673.19165802123-0.4457491930843.00759423372-0.03078158725080.009796915018270.1762863450980.478602134546-0.05898397978580.191350763937-0.375994475550.01211396917990.08401517251070.535774805618-0.25953305575-0.07787279274730.3608137416460.007986143840220.37353765635971.544126847916.797184407153.2800396746
61.55652427064-0.006124903530850.0491630230292.898579003680.1080298314042.43361428492-0.1705920318020.1050767412140.2174694917760.005755035404560.01396908040380.0282993556227-0.353864469245-0.0119852755620.1263022843470.393467931366-0.243808500841-0.07286253098030.2966230038510.04967034280280.24610127995666.273837108117.935385022341.2545322458
72.68370523343-0.438046815844-0.8321129121532.426127735210.7982929544163.43718016437-0.008177598085220.3568383263390.706613998049-0.561020294106-0.1011061885810.423588838913-0.792137233172-0.561513780410.2362365947730.631092899461-0.154036057274-0.2610109125250.5020758094130.1116672051540.49930034997652.20672684926.401555913432.4650033284
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 124 through 220 )AA124 - 2201 - 97
22chain 'A' and (resid 221 through 381 )AA221 - 38198 - 243
33chain 'A' and (resid 382 through 598 )AA382 - 598244 - 429
44chain 'B' and (resid 124 through 220 )BB124 - 2201 - 97
55chain 'B' and (resid 221 through 381 )BB221 - 38198 - 243
66chain 'B' and (resid 382 through 509 )BB382 - 509244 - 358
77chain 'B' and (resid 510 through 598 )BB510 - 598359 - 429

+
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