[English] 日本語
Yorodumi
- PDB-1e1l: STRUCTURE OF ADRENODOXIN REDUCTASE IN COMPLEX WITH NADP obtained ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1e1l
TitleSTRUCTURE OF ADRENODOXIN REDUCTASE IN COMPLEX WITH NADP obtained by cocrystallisation
ComponentsADRENODOXIN REDUCTASE
KeywordsOXIDOREDUCTASE / NADP / ELECTRON TRANSFERASE / FLAVOENZYME
Function / homology
Function and homology information


adrenodoxin-NADP+ reductase / : / : / steroid biosynthetic process / cholesterol metabolic process / electron transport chain / flavin adenine dinucleotide binding / NADP binding / mitochondrial inner membrane / mitochondrion
Similarity search - Function
Ferredoxin-NADP+ reductase, adrenodoxin-type / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / NAD(P)-binding Rossmann-like Domain / Rossmann fold ...Ferredoxin-NADP+ reductase, adrenodoxin-type / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADPH:adrenodoxin oxidoreductase, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZiegler, G.A. / Schulz, G.E.
Citation
Journal: Biochemistry / Year: 2000
Title: Crystal Structures of Adrenodoxin Reductase in Complex with Nadp+ and Nadph Suggesting a Mechanism for the Electron Transfer of an Enzyme Family
Authors: Ziegler, G.A. / Schulz, G.E.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: The Structure of Adrenodoxin Reductase of Mitochondrial P450 Systems: Electron Transfer for Steroid Biosynthesis
Authors: Ziegler, G.A. / Vonrhein, C. / Hanukoglu, I. / Schulz, G.E.
#2: Journal: FEBS Lett. / Year: 1999
Title: Chaperone-Assisted Expression of Authentic Bovine Adrenodoxin Reductase in Escherichia Coli
Authors: Vonrhein, C. / Schmidt, U. / Ziegler, G.A. / Schweiger, S. / Hanukoglu, I. / Schulz, G.E.
History
DepositionMay 9, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADRENODOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8893
Polymers50,3601
Non-polymers1,5292
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.500, 62.800, 85.300
Angle α, β, γ (deg.)90.00, 108.20, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ADRENODOXIN REDUCTASE


Mass: 50360.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COFACTOR FAD IS NON-COVALENTLY BOUND COFACTOR NADP+ IS NON-COVALENTLY BOUND
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Tissue: STEROIDOGENIC TISSUES / Cellular location: MITOCHONDRIAL MATRIX / Organ: ADRENAL CORTEX / Organelle: MITOCHONDRIA / Plasmid: PET22B3-AR242 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08165, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST 32 RESIDUES OF SWISS-PROT SEQUENCE REFER TO A MITOCHONDRIAL LEADER SEQUENCE THAT WAS DELETED ...FIRST 32 RESIDUES OF SWISS-PROT SEQUENCE REFER TO A MITOCHONDRIAL LEADER SEQUENCE THAT WAS DELETED WHEN CLONED. THE FIRST 5 RESIDUES OF THE MATURE PROTEIN WERE NOT SEEN IN THE DENSITY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 57 %
Crystal growpH: 6.5
Details: DROPLET: 4 MG/ML PROTEIN, 8% PEG8000, 5% GLYCEROL, 100 MM CALCIUM ACETATE, 50 MM SODIUM-CACODYLATE PH 6.5. RESERVOIR: 12 % PEG8000, 100 MM CALCIUM ACETATE, 50 MM SODIUM CACODYLATE PH 6.5, 0.05 MM NADP+.
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
25 %glycerol1drop
38 %(w/v)PEG80001drop
450 mMsodium cacodylate1dropBuffer C
5100 mMcalcium acetate1dropBufferC
712 %(w/v)PEG80001reservoir
6Buffer C1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.847
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1999 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.847 Å / Relative weight: 1
ReflectionResolution: 2.25→29.7 Å / Num. obs: 28171 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.059 / Net I/σ(I): 8.7
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.306 / % possible all: 99.1

-
Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CJC

1cjc


Resolution: 2.3→15 Å / SU B: 8.7 / SU ML: 0.2 / σ(F): 0 / ESU R: 0.33 / ESU R Free: 0.25
Details: SOME SIDECHAINS ON THE SURFACE OF THE NADP-DOMAIN ARE NOT VISIBLE IN THE ELECTRON DENSITY THEY WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1284 5 %RANDOM
Rwork0.219 ---
obs-25684 98.7 %-
Displacement parametersBiso mean: 59.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 101 109 3715
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.034
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2
X-RAY DIFFRACTIONp_mcangle_it3.18
X-RAY DIFFRACTIONp_scbond_it2.14
X-RAY DIFFRACTIONp_scangle_it3.3
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 59 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.9

+
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