[English] 日本語
Yorodumi
- PDB-8jt3: Crystal structure of aminotransferase CrmG from Actinoalloteichus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jt3
TitleCrystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in complex with amino donor L-Arg
ComponentsCrmG
KeywordsTRANSFERASE / Transaminase / complex / amino donor
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding / identical protein binding
Similarity search - Function
: / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
ACETATE ION / Chem-EQJ / CrmG
Similarity search - Component
Biological speciesActinoalloteichus sp. 2216-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSu, K. / Zhang, Y. / Xu, J. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31500638 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Co-crystal structure provides insights on transaminase CrmG recognition amino donor L-Arg.
Authors: Chen, R. / Su, K. / Zhang, Y. / Zhu, Y. / Liu, J. / Xu, J.
History
DepositionJun 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CrmG
C: CrmG
B: CrmG
D: CrmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,10315
Polymers228,8784
Non-polymers2,22511
Water8,719484
1
A: CrmG
B: CrmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,7069
Polymers114,4392
Non-polymers1,2677
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11330 Å2
ΔGint-51 kcal/mol
Surface area36030 Å2
MethodPISA
2
C: CrmG
D: CrmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,3976
Polymers114,4392
Non-polymers9584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint-48 kcal/mol
Surface area36520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.849, 113.280, 157.681
Angle α, β, γ (deg.)90.00, 91.74, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
CrmG


Mass: 57219.520 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoalloteichus sp. 2216-6 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: H8Y6N2
#2: Chemical
ChemComp-EQJ / (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-arginine


Mass: 403.328 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H22N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium acetate, 0.1 M TRIS pH 8.5, 32%PEG 3350, 2% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.35→40.19 Å / Num. obs: 84776 / % possible obs: 93.7 % / Redundancy: 3.8 % / CC1/2: 0.989 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.075 / Rrim(I) all: 0.15 / Net I/σ(I): 7.6 / Num. measured all: 322678
Reflection shellResolution: 2.35→2.39 Å / % possible obs: 92.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.593 / Num. measured all: 17008 / Num. unique obs: 4290 / CC1/2: 0.777 / Rpim(I) all: 0.335 / Rrim(I) all: 0.685 / Net I/σ(I) obs: 2.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→40.19 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.592 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.507 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23741 4173 4.9 %RANDOM
Rwork0.19688 ---
obs0.19891 80589 93.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.151 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.18 Å2
2--0.56 Å20 Å2
3----0.56 Å2
Refinement stepCycle: 1 / Resolution: 2.35→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15815 0 148 484 16447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01316223
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715528
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.64921966
X-RAY DIFFRACTIONr_angle_other_deg1.3081.58435556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99452037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.93620.402946
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.165152694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.54815180
X-RAY DIFFRACTIONr_chiral_restr0.0760.22106
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218471
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023833
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7032.8498188
X-RAY DIFFRACTIONr_mcbond_other2.7012.8488186
X-RAY DIFFRACTIONr_mcangle_it4.1014.26310211
X-RAY DIFFRACTIONr_mcangle_other4.1024.26310212
X-RAY DIFFRACTIONr_scbond_it3.1443.1638035
X-RAY DIFFRACTIONr_scbond_other3.1443.1638036
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.94.62811756
X-RAY DIFFRACTIONr_long_range_B_refined6.60133.31817586
X-RAY DIFFRACTIONr_long_range_B_other6.60133.3217587
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A160280.06
12C160280.06
21A161480.06
22B161480.06
31A161970.05
32D161970.05
41C160740.05
42B160740.05
51C160230.06
52D160230.06
61B161630.06
62D161630.06
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 281 -
Rwork0.267 5893 -
obs--92.62 %

+
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