[English] 日本語
Yorodumi
- PDB-4ggp: Crystal Structure of Selenomethionine containing Trans-2-Enoyl-Co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ggp
TitleCrystal Structure of Selenomethionine containing Trans-2-Enoyl-CoA Reductase from Treponema denticola
ComponentsTrans-2-enoyl-CoA reductase
KeywordsOXIDOREDUCTASE / Rossmann Fold / Reductase
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NAD+) / trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD binding / fatty acid biosynthetic process
Similarity search - Function
: / Trans-2-enoyl-CoA reductase / Enoyl reductase FAD binding domain / Trans-2-enoyl-CoA reductase catalytic domain, putative / Enoyl reductase FAD binding domain / Trans-2-enoyl-CoA reductase catalytic region / NAD(P)H binding domain of trans-2-enoyl-CoA reductase / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Trans-2-enoyl-CoA reductase [NADH]
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsBond-Watts, B.B. / Weeks, A.M. / Chang, M.C.Y.
CitationJournal: Biochemistry / Year: 2012
Title: Biochemical and Structural Characterization of the trans-Enoyl-CoA Reductase from Treponema denticola.
Authors: Bond-Watts, B.B. / Weeks, A.M. / Chang, M.C.
History
DepositionAug 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Trans-2-enoyl-CoA reductase
B: Trans-2-enoyl-CoA reductase
C: Trans-2-enoyl-CoA reductase
D: Trans-2-enoyl-CoA reductase


Theoretical massNumber of molelcules
Total (without water)177,5414
Polymers177,5414
Non-polymers00
Water9,818545
1
A: Trans-2-enoyl-CoA reductase


Theoretical massNumber of molelcules
Total (without water)44,3851
Polymers44,3851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Trans-2-enoyl-CoA reductase


Theoretical massNumber of molelcules
Total (without water)44,3851
Polymers44,3851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Trans-2-enoyl-CoA reductase


Theoretical massNumber of molelcules
Total (without water)44,3851
Polymers44,3851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Trans-2-enoyl-CoA reductase


Theoretical massNumber of molelcules
Total (without water)44,3851
Polymers44,3851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.580, 87.680, 91.990
Angle α, β, γ (deg.)106.248, 109.854, 98.335
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Trans-2-enoyl-CoA reductase


Mass: 44385.316 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola (bacteria) / Strain: ATCC 35405 / Gene: TDE_0597 / Plasmid: pET23a-His10-Tev / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q73Q47, acetoacetyl-CoA reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 0.1 M sodium citrate, pH 7.5, 25% PEG 6000, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979, 0.957
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2011
RadiationMonochromator: DOUBLE FLAT CRYSTAL, SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9571
ReflectionResolution: 2→20 Å / Num. obs: 114220 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 20.67
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 4.38 / % possible all: 96.1

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXAutoSolmodel building
AutoBuildmodel building
PHENIXAutoRefinerefinement
XDSdata reduction
XSCALEdata scaling
PHENIXAUTOSOLphasing
AUTOBUILDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→19.47 Å / SU ML: 0.2 / σ(F): 2 / Phase error: 23.48 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.2145 5182 5.065 %
Rwork0.1822 --
obs0.1838 103632 97.13 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.916 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12316 0 0 545 12861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412536
X-RAY DIFFRACTIONf_angle_d0.78316916
X-RAY DIFFRACTIONf_dihedral_angle_d12.7224696
X-RAY DIFFRACTIONf_chiral_restr0.0571872
X-RAY DIFFRACTIONf_plane_restr0.0032196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.07330.28691690.24983202X-RAY DIFFRACTION96
2.0733-2.09760.28061720.23883278X-RAY DIFFRACTION96
2.0976-2.12320.25311710.22943239X-RAY DIFFRACTION96
2.1232-2.150.2381710.22063263X-RAY DIFFRACTION97
2.15-2.17830.26261720.2143252X-RAY DIFFRACTION96
2.1783-2.20810.25591710.20923266X-RAY DIFFRACTION97
2.2081-2.23960.25851730.21963278X-RAY DIFFRACTION96
2.2396-2.2730.28281690.21213234X-RAY DIFFRACTION97
2.273-2.30840.27241750.20623326X-RAY DIFFRACTION97
2.3084-2.34620.23611700.20253212X-RAY DIFFRACTION97
2.3462-2.38660.27421730.20613289X-RAY DIFFRACTION97
2.3866-2.42990.23091710.19323263X-RAY DIFFRACTION97
2.4299-2.47660.24961740.19293295X-RAY DIFFRACTION97
2.4766-2.5270.20061700.1873233X-RAY DIFFRACTION97
2.527-2.58190.23171760.1873336X-RAY DIFFRACTION97
2.5819-2.64180.23071730.18593301X-RAY DIFFRACTION97
2.6418-2.70770.23461740.1933309X-RAY DIFFRACTION97
2.7077-2.78070.24721730.19433267X-RAY DIFFRACTION97
2.7807-2.86230.23431720.18453281X-RAY DIFFRACTION97
2.8623-2.95440.21721740.17783304X-RAY DIFFRACTION98
2.9544-3.05970.2241730.18343291X-RAY DIFFRACTION98
3.0597-3.18170.2031740.183293X-RAY DIFFRACTION98
3.1817-3.32580.19131740.18723305X-RAY DIFFRACTION98
3.3258-3.50030.23591730.17783302X-RAY DIFFRACTION98
3.5003-3.71830.19821740.17463300X-RAY DIFFRACTION98
3.7183-4.00320.18341750.16273318X-RAY DIFFRACTION98
4.0032-4.40210.19241720.15933280X-RAY DIFFRACTION97
4.4021-5.030.1891730.16053287X-RAY DIFFRACTION98
5.03-6.30330.19941760.18513344X-RAY DIFFRACTION98
6.3033-19.84780.17251750.16183302X-RAY DIFFRACTION98

+
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