[English] 日本語
Yorodumi
- PDB-5ddu: Crystal structure of aminotransferase CrmG from Actinoalloteichus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ddu
TitleCrystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in complex with PMP
ComponentsCrmG
KeywordsTRANSFERASE / Aminotransferase / PLP / Caerulomycin Biosynthesis
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
TRIETHYLENE GLYCOL / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / CrmG
Similarity search - Component
Biological speciesActinoalloteichus sp. WH1-2216-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsXu, J. / Feng, Z. / Liu, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation of China31500638 China
Natural Science Foundation of Guangdong Province2014A030310356 China
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Biochemical and Structural Insights into the Aminotransferase CrmG in Caerulomycin Biosynthesis
Authors: Zhu, Y. / Xu, J. / Mei, X. / Feng, Z. / Zhang, L. / Zhang, Q. / Zhang, G. / Zhu, W. / Liu, J. / Zhang, C.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: CrmG
C: CrmG
D: CrmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,85018
Polymers228,8784
Non-polymers1,97214
Water5,008278
1
A: CrmG
B: CrmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,54610
Polymers114,4392
Non-polymers1,1078
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11910 Å2
ΔGint-50 kcal/mol
Surface area36700 Å2
MethodPISA
2
C: CrmG
D: CrmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,3048
Polymers114,4392
Non-polymers8656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11600 Å2
ΔGint-52 kcal/mol
Surface area36740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.874, 83.858, 88.438
Angle α, β, γ (deg.)106.660, 109.250, 94.840
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYVALVALAA6 - 5216 - 521
21GLYGLYVALVALBB6 - 5216 - 521
12GLYGLYLEULEUAA6 - 5226 - 522
22GLYGLYLEULEUCC6 - 5226 - 522
13SERSERLEULEUAA5 - 5225 - 522
23SERSERLEULEUDD5 - 5225 - 522
14GLYGLYLEULEUBB6 - 5226 - 522
24GLYGLYLEULEUCC6 - 5226 - 522
15GLYGLYVALVALBB6 - 5216 - 521
25GLYGLYVALVALDD6 - 5216 - 521
16GLYGLYLEULEUCC6 - 5226 - 522
26GLYGLYLEULEUDD6 - 5226 - 522

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: Chemical
ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Sodium acetate, 0.1M TRIS pH 8.5, 32% PEG3350, 2% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.928
11-K, -H, -L20.072
ReflectionResolution: 2.46→50.51 Å / Num. obs: 75400 / % possible obs: 97.3 % / Redundancy: 3.5 % / CC1/2: 0.947 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.098 / Net I/σ(I): 6.8 / Num. measured all: 262030 / Scaling rejects: 650
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.46-2.513.40.6272.31494343960.590.38196.3
12.3-50.513.80.1213.322785930.9750.06995.2

-
Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimless0.3.11data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
Aimlessdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→50.51 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.2325 / WRfactor Rwork: 0.2019 / FOM work R set: 0.8235 / SU B: 16.99 / SU ML: 0.192 / SU R Cruickshank DPI: 0.1731 / SU Rfree: 0.0607 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 3750 5 %RANDOM
Rwork0.2065 ---
obs0.2081 71589 88.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.44 Å2 / Biso mean: 19.832 Å2 / Biso min: 6.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20.02 Å2-6.18 Å2
2---2.96 Å2-4.37 Å2
3---4.16 Å2
Refinement stepCycle: final / Resolution: 2.46→50.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15836 0 128 278 16242
Biso mean--35.53 24.62 -
Num. residues----2049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01916222
X-RAY DIFFRACTIONr_bond_other_d0.0040.0215651
X-RAY DIFFRACTIONr_angle_refined_deg0.8191.97221962
X-RAY DIFFRACTIONr_angle_other_deg0.68335807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.50852041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35922.855767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.939152697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.18915180
X-RAY DIFFRACTIONr_chiral_restr0.0610.22506
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218431
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023741
X-RAY DIFFRACTIONr_mcbond_it1.2521.8878188
X-RAY DIFFRACTIONr_mcbond_other1.2521.8878187
X-RAY DIFFRACTIONr_mcangle_it2.0542.82910221
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
11A62648
12B62648
21A62586
22C62586
31A62544
32D62544
41B62434
42C62434
51B62566
52D62566
61C62214
62D62214
LS refinement shellResolution: 2.46→2.46 Å / Total num. of bins used: 20

+
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