[English] 日本語
Yorodumi
- PDB-1dfi: X-RAY STRUCTURE OF ESCHERICHIA COLI ENOYL REDUCTASE WITH BOUND NAD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dfi
TitleX-RAY STRUCTURE OF ESCHERICHIA COLI ENOYL REDUCTASE WITH BOUND NAD
ComponentsENOYL ACYL CARRIER PROTEIN REDUCTASE
KeywordsOXIDOREDUCTASE / LIPID BIOSYNTHESIS
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid biosynthetic process / catalytic complex / protein homotetramerization / response to antibiotic ...enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid biosynthetic process / catalytic complex / protein homotetramerization / response to antibiotic / protein-containing complex / identical protein binding / membrane / cytosol
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 / Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, ISOMORPHOUS REPLACEMENT / Resolution: 2.09 Å
AuthorsBaldock, C. / Rafferty, J.B. / Rice, D.W.
Citation
Journal: Science / Year: 1996
Title: A mechanism of drug action revealed by structural studies of enoyl reductase.
Authors: Baldock, C. / Rafferty, J.B. / Sedelnikova, S.E. / Baker, P.J. / Stuitje, A.R. / Slabas, A.R. / Hawkes, T.R. / Rice, D.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization of Escherichia Coli Enoyl Reductase and its Complex with Diazaborine
Authors: Baldock, C. / Rafferty, J.B. / Sedelnikova, S.E. / Bithell, S. / Stuitje, A.R. / Slabas, A.R. / Rice, D.W.
History
DepositionJan 16, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENOYL ACYL CARRIER PROTEIN REDUCTASE
B: ENOYL ACYL CARRIER PROTEIN REDUCTASE
C: ENOYL ACYL CARRIER PROTEIN REDUCTASE
D: ENOYL ACYL CARRIER PROTEIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7018
Polymers111,0474
Non-polymers2,6544
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19060 Å2
ΔGint-109 kcal/mol
Surface area30540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.000, 81.200, 79.000
Angle α, β, γ (deg.)90.00, 92.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.795, 0.159, -0.585), (0.158, -0.986, -0.053), (-0.585, -0.05, -0.809)14.51, -0.98, 44.24
2given(-0.812, 0.025, 0.583), (0.018, -0.997, 0.068), (0.583, 0.066, 0.81)19.05, -1.09, -6.12
3given(-0.984, -0.175, -0.001), (-0.175, 0.984, -0.009), (0.002, -0.008, -1)33.13, 3.1, 38.1

-
Components

#1: Protein
ENOYL ACYL CARRIER PROTEIN REDUCTASE / ENR


Mass: 27761.730 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PENVM5 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P29132, UniProt: P0AEK4*PLUS, 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 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growpH: 5 / Details: 12% PEG 400, PH 5.0 ACETATE, 10MM NAD
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Details: Baldock, C., (1996) Acta Crystallogr.,Sect.D, 52, 1181.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mM1dropNaPO4
31 mMdithiothreitol1drop
410 mMNAD+1drop
512 %PEG4001reservoir
6100 mMacetate1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.08→26.35 Å / Num. obs: 51902 / % possible obs: 93.1 % / Redundancy: 2.2 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 8.2
Reflection shellResolution: 2.08→2.14 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 4.6 / % possible all: 71.4
Reflection
*PLUS
Num. measured all: 113658

-
Processing

Software
NameClassification
CCP4model building
TNTrefinement
MOSFLMdata reduction
Agrovatadata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, ISOMORPHOUS REPLACEMENT
Starting model: BRASSICA NAPUS ENR (PDB ENTRY 1ENO)

1eno


Resolution: 2.09→10 Å / Stereochemistry target values: ENGH AND HUBER
Details: ASN A 155, ASN A 157, ASN B 155, ASN B 157 ARE THE RESIDUES EITHER SIDE OF THE CATALYTIC TYROSINE AND HAVE DIHEDRAL ANGLES WHICH LIE OUTSIDE THEIR EXPECTED RANGE. THIS IS THOUGHT TO ALLOW ...Details: ASN A 155, ASN A 157, ASN B 155, ASN B 157 ARE THE RESIDUES EITHER SIDE OF THE CATALYTIC TYROSINE AND HAVE DIHEDRAL ANGLES WHICH LIE OUTSIDE THEIR EXPECTED RANGE. THIS IS THOUGHT TO ALLOW THE TYROSINE SIDE-CHAIN TO OCCUPY THE CORRECT POSITION WITH RESPECT TO THE POSITION OF THE NICOTINAMIDE RING.
RfactorNum. reflection% reflection
Rwork0.162 --
all-52346 -
obs-52346 93 %
Solvent computationBsol: 275.1 Å2 / ksol: 0.85 e/Å3
Refinement stepCycle: LAST / Resolution: 2.09→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7336 0 176 327 7839
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01376482
X-RAY DIFFRACTIONt_angle_deg1.503103363
X-RAY DIFFRACTIONt_dihedral_angle_d16.46145040
X-RAY DIFFRACTIONt_incorr_chiral_ct2
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0121684
X-RAY DIFFRACTIONt_gen_planes0.01811289
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.188770
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0124
X-RAY DIFFRACTIONt_plane_restr0.0189

+
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