[English] 日本語
Yorodumi
- PDB-5ycr: X-Ray Structure of Enoyl-Acyl Carrier Protein Reductase from Baci... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ycr
TitleX-Ray Structure of Enoyl-Acyl Carrier Protein Reductase from Bacillus Anthracis with NAD+
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH] FabI
KeywordsOXIDOREDUCTASE / antibacterial / fabI
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / NADP+ binding / enoyl-[acyl-carrier-protein] reductase (NADH) activity / small molecule binding / catalytic complex / identical protein binding
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsKim, H.T.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural insights into the dimer-tetramer transition of FabI from Bacillus anthracis
Authors: Kim, H.T. / Kim, S. / Na, B.K. / Chung, J. / Hwang, E. / Hwang, K.Y.
History
DepositionSep 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
B: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
C: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
D: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,76123
Polymers111,6664
Non-polymers4,09519
Water11,331629
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21120 Å2
ΔGint-270 kcal/mol
Surface area35440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.566, 126.566, 185.742
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-516-

HOH

-
Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH] FabI / ENR / NADH-dependent enoyl-ACP reductase


Mass: 27916.555 Da / Num. of mol.: 4 / Mutation: no
Source method: isolated from a genetically manipulated source
Details: NAD+
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: fabI, BC_1216
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q81GI3, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 3.85 Å3/Da / Density % sol: 68.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1M Na acetate, pH 4.6, 2M AMS

-
Data collection

DiffractionMean temperature: 295 K / Ambient temp details: 100
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 123405 / % possible obs: 99.8 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.031 / Rsym value: 0.071 / Net I/σ(I): 31.3
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 4 / Num. unique obs: 6129 / CC1/2: 0.751 / Rpim(I) all: 0.169 / Rsym value: 0.495 / Χ2: 1.081 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QIO

2qio


Resolution: 1.96→41.037 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 18.7
RfactorNum. reflection% reflection
Rfree0.205 6192 5.02 %
Rwork0.1765 --
obs0.1779 123368 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→41.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7648 0 251 629 8528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087996
X-RAY DIFFRACTIONf_angle_d1.02610845
X-RAY DIFFRACTIONf_dihedral_angle_d14.1852963
X-RAY DIFFRACTIONf_chiral_restr0.0421256
X-RAY DIFFRACTIONf_plane_restr0.0041471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9602-1.98250.33322210.28693847X-RAY DIFFRACTION100
1.9825-2.00580.2961960.26543889X-RAY DIFFRACTION100
2.0058-2.03030.24822010.25063824X-RAY DIFFRACTION100
2.0303-2.0560.26962100.24623866X-RAY DIFFRACTION100
2.056-2.0830.2632240.23683866X-RAY DIFFRACTION100
2.083-2.11150.25812080.22693857X-RAY DIFFRACTION100
2.1115-2.14170.23281730.20693886X-RAY DIFFRACTION100
2.1417-2.17370.2321990.20353896X-RAY DIFFRACTION100
2.1737-2.20760.24622150.19323859X-RAY DIFFRACTION100
2.2076-2.24380.20252050.18023874X-RAY DIFFRACTION100
2.2438-2.28250.19971980.17623864X-RAY DIFFRACTION100
2.2825-2.3240.22742120.183887X-RAY DIFFRACTION100
2.324-2.36870.19851900.18113891X-RAY DIFFRACTION100
2.3687-2.41710.22962230.17733879X-RAY DIFFRACTION100
2.4171-2.46960.20932280.16823857X-RAY DIFFRACTION100
2.4696-2.5270.20672110.1723871X-RAY DIFFRACTION100
2.527-2.59020.18691860.16633920X-RAY DIFFRACTION100
2.5902-2.66030.2172140.16993903X-RAY DIFFRACTION100
2.6603-2.73850.20381960.15783896X-RAY DIFFRACTION100
2.7385-2.82690.19161870.16653889X-RAY DIFFRACTION100
2.8269-2.92790.18672260.16613900X-RAY DIFFRACTION100
2.9279-3.04510.21312100.16583914X-RAY DIFFRACTION100
3.0451-3.18360.18032010.17343898X-RAY DIFFRACTION100
3.1836-3.35140.18992390.1633917X-RAY DIFFRACTION100
3.3514-3.56130.18891950.16363936X-RAY DIFFRACTION100
3.5613-3.83610.18942130.16173946X-RAY DIFFRACTION100
3.8361-4.22170.16261890.14693996X-RAY DIFFRACTION100
4.2217-4.83180.17992000.14433957X-RAY DIFFRACTION100
4.8318-6.08440.18512080.17614047X-RAY DIFFRACTION100
6.0844-41.04610.21642140.18744144X-RAY DIFFRACTION99

+
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