[English] 日本語
Yorodumi
- PDB-6jcb: Crystal structure of aminotransferase CrmG from Actinoalloteichus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jcb
TitleCrystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in C2 space group
ComponentsCrmG
KeywordsTRANSFERASE / aminotransferase / CrmG
Function / homologyAminotransferase class-III / Aminotransferase class-III / transaminase activity / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / pyridoxal phosphate binding / identical protein binding / CrmG
Function and homology information
Biological speciesActinoalloteichus sp. WH1-2216-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsXu, J. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31500638 China
CitationJournal: Commun Biol / Year: 2020
Title: Structural studies reveal flexible roof of active site responsible for omega-transaminase CrmG overcoming by-product inhibition.
Authors: Xu, J. / Tang, X. / Zhu, Y. / Yu, Z. / Su, K. / Zhang, Y. / Dong, Y. / Zhu, W. / Zhang, C. / Wu, R. / Liu, J.
History
DepositionJan 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)228,8784
Polymers228,8784
Non-polymers00
Water2,144119
1
A: CrmG
B: CrmG


Theoretical massNumber of molelcules
Total (without water)114,4392
Polymers114,4392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-26 kcal/mol
Surface area38510 Å2
MethodPISA
2
C: CrmG
D: CrmG


Theoretical massNumber of molelcules
Total (without water)114,4392
Polymers114,4392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-29 kcal/mol
Surface area38450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.130, 114.830, 156.170
Angle α, β, γ (deg.)90.000, 92.160, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22B
13A
23D
14C
24B
15C
25D
16B
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 6 - 523 / Label seq-ID: 6 - 523

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CB
12AA
22BC
13AA
23DD
14CB
24BC
15CB
25DD
16BC
26DD

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. WH1-2216-6 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H8Y6N2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.55 % / Mosaicity: 0.98 °
Crystal growTemperature: 293 K / Method: vapor diffusion / 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: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.85→38.87 Å / Num. obs: 47035 / % possible obs: 93.5 % / Redundancy: 2.5 % / CC1/2: 0.981 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.086 / Rrim(I) all: 0.146 / Net I/σ(I): 6.1 / Num. measured all: 117939 / Scaling rejects: 180
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.85-2.942.60.4531137244320.8360.3290.5632.195.9
11.4-38.872.50.04817997260.9930.0370.0611488.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DDS

5dds


Resolution: 2.85→18 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.2476 / WRfactor Rwork: 0.1939 / FOM work R set: 0.7271 / SU B: 18.531 / SU ML: 0.345 / SU Rfree: 0.4538 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.454 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 2330 5 %RANDOM
Rwork0.2101 ---
obs0.2126 44504 92.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.77 Å2 / Biso mean: 36.894 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20.92 Å2
2---0.47 Å2-0 Å2
3---0.4 Å2
Refinement stepCycle: final / Resolution: 2.85→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15021 0 0 119 15140
Biso mean---17.99 -
Num. residues----1945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01315257
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714457
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.6420639
X-RAY DIFFRACTIONr_angle_other_deg1.2221.57633237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58451929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.48320.329911
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.202152561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.30315176
X-RAY DIFFRACTIONr_chiral_restr0.0620.21988
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217429
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023427
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A15028
12C15028
21A14983
22B14983
31A15006
32D15006
41C14971
42B14971
51C15045
52D15045
61B14960
62D14960
LS refinement shellResolution: 2.85→2.922 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 166 -
Rwork0.306 3300 -
all-3466 -
obs--95.59 %

+
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://pdbjlvh1.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