[English] 日本語
Yorodumi
- PDB-6ltw: Crystal structure of Apo form of I122A/I330A variant of S-adenosy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ltw
TitleCrystal structure of Apo form of I122A/I330A variant of S-adenosylmethionine synthetase from Cryptosporidium hominis
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / Mutanat / Methionine adenosyltransferase
Function / homology
Function and homology information


methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / ATP binding / metal ion binding
Similarity search - Function
S-adenosylmethionine synthetase / S-adenosylmethionine synthetase, N-terminal / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal / S-adenosylmethionine synthetase, conserved site / S-adenosylmethionine synthetase superfamily / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal domain / S-adenosylmethionine synthase signature 1. / S-adenosylmethionine synthase signature 2.
Similarity search - Domain/homology
PHOSPHATE ION / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesCryptosporidium hominis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsSingh, R.K. / Michailidou, F. / Rentmeister, A. / Kuemmel, D.
Funding support1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KU2531/2
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Engineered SAM Synthetases for Enzymatic Generation of AdoMet Analogs with Photocaging Groups and Reversible DNA Modification in Cascade Reactions.
Authors: Michailidou, F. / Klocker, N. / Cornelissen, N.V. / Singh, R.K. / Peters, A. / Ovcharenko, A. / Kummel, D. / Rentmeister, A.
History
DepositionJan 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 29, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,21910
Polymers91,7422
Non-polymers4778
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-86 kcal/mol
Surface area27930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.877, 100.360, 66.842
Angle α, β, γ (deg.)90.000, 95.860, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein S-adenosylmethionine synthase


Mass: 45871.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium hominis (eukaryote) / Gene: CHUDEA7_2650 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0S4TKQ5, methionine adenosyltransferase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12 % MPD (v/v), 12 % PEG 1000 (w/v) , 12 % PEG 3350 (w/v), 0.1 MES/imidazole pH 6.5, 0.03 M sodium phosphate dibasic dihydrate, 0.03 M ammonium sulfate and 0.03 M sodium nitrate.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9802 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9802 Å / Relative weight: 1
ReflectionResolution: 1.65→48.08 Å / Num. obs: 97449 / % possible obs: 99 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.5 / Num. measured all: 650367 / Scaling rejects: 65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.65-1.685.70.9722380241450.7651.685.3
9.06-48.086.60.0341546250.99944.898.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata reduction
Aimless0.6.3data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ODJ

4odj


Resolution: 1.65→48.08 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.187 / WRfactor Rwork: 0.1523 / FOM work R set: 0.8554 / SU B: 3.835 / SU ML: 0.064 / SU R Cruickshank DPI: 0.0827 / SU Rfree: 0.0857 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.191 4768 4.9 %RANDOM
Rwork0.1562 ---
obs0.158 92649 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.51 Å2 / Biso mean: 29.104 Å2 / Biso min: 13.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å2-0.13 Å2
2---1.33 Å20 Å2
3---0.81 Å2
Refinement stepCycle: final / Resolution: 1.65→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5886 0 24 580 6490
Biso mean--27.01 38.81 -
Num. residues----759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0196068
X-RAY DIFFRACTIONr_bond_other_d0.0010.025720
X-RAY DIFFRACTIONr_angle_refined_deg2.2921.9688194
X-RAY DIFFRACTIONr_angle_other_deg1.009313298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5125771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59424.368261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.253151104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2211536
X-RAY DIFFRACTIONr_chiral_restr0.1460.2921
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021203
LS refinement shellResolution: 1.654→1.697 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 357 -
Rwork0.312 6269 -
all-6626 -
obs--91.41 %
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)
10.0186-0.0308-0.05860.5879-0.07010.2397-0.01380.0098-0.0102-0.0188-0.0367-0.06020.0522-0.0310.05050.04860.0016-0.01270.0170.00290.0463-29.097217.0358-20.8558
20.0021-0.0096-0.01960.8038-0.04840.23660.00890.0054-0.00030.0883-0.0422-0.0872-0.1568-0.0430.03320.1180.0183-0.03790.01550.00360.0293-29.997239.5095-12.3131
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 406
2X-RAY DIFFRACTION2B21 - 406

+
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