[English] 日本語
Yorodumi
- PDB-6oz1: Crystal structure of the adenylation (A) domain of the carboxylat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6oz1
TitleCrystal structure of the adenylation (A) domain of the carboxylate reductase (CAR) GR01_22995 from Mycobacterium chelonae
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / adenylation domain / carboxylate reductase
Function / homology
Function and homology information


phosphopantetheine binding
Similarity search - Function
Thioester reductase-like domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site ...Thioester reductase-like domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / SUCCINIC ACID / Oxidoreductase
Similarity search - Component
Biological speciesMycobacterium chelonae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsStogios, P.J. / Evdokimova, E. / Di Leo, R. / Fedorchuk, T. / Khusnutdinova, A. / Yakunin, A.F. / Savchenko, A.
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: One-Pot Biocatalytic Transformation of Adipic Acid to 6-Aminocaproic Acid and 1,6-Hexamethylenediamine Using Carboxylic Acid Reductases and Transaminases.
Authors: Fedorchuk, T.P. / Khusnutdinova, A.N. / Evdokimova, E. / Flick, R. / Di Leo, R. / Stogios, P. / Savchenko, A. / Yakunin, A.F.
History
DepositionMay 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,02417
Polymers70,3511
Non-polymers1,67316
Water11,422634
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.325, 90.580, 172.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Oxidoreductase / GR01_22995


Mass: 70351.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium chelonae (bacteria) / Gene: GR01_22995 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A0E3TT64

-
Non-polymers , 6 types, 650 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 mg/mL protein, 2.5 mM adipic acid, 1 mM AMP-PNP and the reservoir solution 1.5 M lithium sulfate and 0.1 M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. obs: 66954 / % possible obs: 98.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 41.24 Å2 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.027 / Net I/σ(I): 30.26
Reflection shellResolution: 1.97→2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 1 / Num. unique obs: 2702 / CC1/2: 0.635 / Rpim(I) all: 0.395 / % possible all: 81.2

-
Processing

Software
NameVersionClassification
PHENIX(1.15_3448: ???)refinement
HKL-3000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MSD

5msd


Resolution: 1.97→29.909 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.32
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 2000 2.99 %RANDOM
Rwork0.1823 ---
obs0.1835 66873 98.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.97→29.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4957 0 97 634 5688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015166
X-RAY DIFFRACTIONf_angle_d1.0587047
X-RAY DIFFRACTIONf_dihedral_angle_d20.5391896
X-RAY DIFFRACTIONf_chiral_restr0.061801
X-RAY DIFFRACTIONf_plane_restr0.007915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.01650.28471180.27783799X-RAY DIFFRACTION82
2.0165-2.0710.26571400.23694576X-RAY DIFFRACTION99
2.071-2.13190.24481430.22354608X-RAY DIFFRACTION100
2.1319-2.20070.25861430.2084664X-RAY DIFFRACTION100
2.2007-2.27930.21971430.19224641X-RAY DIFFRACTION100
2.2793-2.37060.23141430.19874662X-RAY DIFFRACTION100
2.3706-2.47840.25191450.20094675X-RAY DIFFRACTION100
2.4784-2.6090.23821440.19914664X-RAY DIFFRACTION100
2.609-2.77240.25241440.19744679X-RAY DIFFRACTION100
2.7724-2.98620.22591450.19274693X-RAY DIFFRACTION100
2.9862-3.28640.25581450.18764711X-RAY DIFFRACTION100
3.2864-3.76120.21421460.1674760X-RAY DIFFRACTION100
3.7612-4.73570.18531470.1494767X-RAY DIFFRACTION100
4.7357-29.90.21951540.18454974X-RAY DIFFRACTION100
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)
13.40581.5321-2.29090.6832-0.95571.4555-0.17981.10340.0360.02640.2673-0.0423-0.1213-0.5566-0.09610.7040.1979-0.06650.89510.0680.5962-15.718428.5191-43.2832
21.91550.2627-0.28452.05540.17942.51870.1665-0.20870.22840.0277-0.23530.2971-0.1402-0.40360.06120.31860.04220.0460.4382-0.13470.3376-19.388924.7307-9.9311
35.48015.59732.91846.6783.18461.6487-0.24930.48040.2196-0.67170.0620.1457-0.4050.07950.16760.42320.13930.06750.4048-0.0250.2739-11.16226.8671-27.0195
41.13411.04-0.07781.62840.22260.62420.0917-0.0492-0.15390.0986-0.1277-0.17710.01980.00160.0380.30520.0547-0.0380.32030.01110.2596-1.58413.6617-31.8405
54.44890.61470.06043.24310.39363.16340.3285-0.4802-0.73560.8696-0.2831-0.82760.23280.1575-0.06020.5596-0.0697-0.17270.39460.11520.57544.0403-2.9284-23.4243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 267 )
3X-RAY DIFFRACTION3chain 'A' and (resid 268 through 304 )
4X-RAY DIFFRACTION4chain 'A' and (resid 305 through 561 )
5X-RAY DIFFRACTION5chain 'A' and (resid 562 through 641 )

+
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