[English] 日本語
Yorodumi
- PDB-1afr: STEAROYL-ACYL CARRIER PROTEIN DESATURASE FROM CASTOR SEEDS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1afr
TitleSTEAROYL-ACYL CARRIER PROTEIN DESATURASE FROM CASTOR SEEDS
ComponentsDELTA9 STEAROYL-ACYL CARRIER PROTEIN DESATURASE
KeywordsOXIDOREDUCTASE / FATTY ACID DESATURASE / FATTY ACID BIOSYNTHESIS / BINUCLEAR IRON CENTER / ELECTRON TRANSFER
Function / homology
Function and homology information


stearoyl-[acyl-carrier-protein] 9-desaturase / stearoyl-[acp] desaturase activity / acyl-[acyl-carrier-protein] desaturase activity / chloroplast / fatty acid biosynthetic process / metal ion binding
Similarity search - Function
Fatty acid desaturase type 2, conserved site / Fatty acid desaturases family 2 signature. / Fatty acid desaturase, type 2 / Fatty acid desaturase / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Stearoyl-[acyl-carrier-protein] 9-desaturase, chloroplastic
Similarity search - Component
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR, NCS / Resolution: 2.4 Å
AuthorsLindqvist, Y. / Huang, W. / Schneider, G.
Citation
Journal: EMBO J. / Year: 1996
Title: Crystal structure of delta9 stearoyl-acyl carrier protein desaturase from castor seed and its relationship to other di-iron proteins.
Authors: Lindqvist, Y. / Huang, W. / Schneider, G. / Shanklin, J.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Preliminary Crystallographic Data for Stearoyl-Acyl Carrier Protein Desaturase from Castor Seed
Authors: Schneider, G. / Lindqvist, Y. / Shanklin, J. / Somerville, C.
History
DepositionMar 13, 1997Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: DELTA9 STEAROYL-ACYL CARRIER PROTEIN DESATURASE
B: DELTA9 STEAROYL-ACYL CARRIER PROTEIN DESATURASE
C: DELTA9 STEAROYL-ACYL CARRIER PROTEIN DESATURASE
D: DELTA9 STEAROYL-ACYL CARRIER PROTEIN DESATURASE
E: DELTA9 STEAROYL-ACYL CARRIER PROTEIN DESATURASE
F: DELTA9 STEAROYL-ACYL CARRIER PROTEIN DESATURASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,19518
Polymers238,5246
Non-polymers67012
Water9,692538
1
A: DELTA9 STEAROYL-ACYL CARRIER PROTEIN DESATURASE
F: DELTA9 STEAROYL-ACYL CARRIER PROTEIN DESATURASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7326
Polymers79,5082
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-65 kcal/mol
Surface area27190 Å2
MethodPISA
2
B: DELTA9 STEAROYL-ACYL CARRIER PROTEIN DESATURASE
C: DELTA9 STEAROYL-ACYL CARRIER PROTEIN DESATURASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7326
Polymers79,5082
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-66 kcal/mol
Surface area27070 Å2
MethodPISA
3
D: DELTA9 STEAROYL-ACYL CARRIER PROTEIN DESATURASE
E: DELTA9 STEAROYL-ACYL CARRIER PROTEIN DESATURASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7326
Polymers79,5082
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-66 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.200, 147.800, 198.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9996, 0.020006, 0.02001), (0.020105, 0.999786, 0.004782), (-0.01991, 0.005182, -0.999788)74.17559, -1.439, 57.51155
2given(0.99976, -0.021591, -0.003601), (-0.01386, -0.497084, -0.867592), (0.016942, 0.867434, -0.497264)-54.5699, 32.33702, 36.88653
3given(-0.999525, 0.021604, 0.021956), (0.008235, -0.499442, 0.866308), (0.029681, 0.866078, 0.499027)101.57135, -17.70161, 8.03085
4given(0.999815, -0.018222, -0.006207), (-0.003828, -0.50418, 0.86359), (-0.018866, -0.863406, -0.504156)-27.14411, -16.72521, 47.60679
5given(-0.999983, -0.001201, 0.005636), (-0.004307, -0.49411, -0.869389), (0.003829, -0.869399, 0.494096)129.67854, 31.7986, 18.15608

-
Components

#1: Protein
DELTA9 STEAROYL-ACYL CARRIER PROTEIN DESATURASE / FATTY ACID DESATURASE


Mass: 39754.074 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Tissue: SEEDSSeed / Organ: SEED / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P22337, EC: 1.14.99.6
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.52 Å3/Da / Density % sol: 57 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16-9 mg/mlenzyme1drop
20.04 Mcacodylate1drop
3100 mMmagnesium acetate1drop
437.5 mMammonium sulfate1drop
51 mM1dropLiCl
60.5 mM1dropKCl
70.1 %beta-octylglucoside1drop
86-7.5 %PEG40001drop
90.08 Mcacodylate1reservoir
10200 mMmagnesium acetate1reservoir
1175 mMammonium sulfate1reservoir
122 mM1reservoirLiCl
131 mM1reservoirKCl
140.2 %beta-octylglucoside1reservoir
1512-15 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 79674 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075
Reflection
*PLUS
Num. measured all: 403539

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: SIR, NCS / Resolution: 2.4→7 Å / Isotropic thermal model: RESTRAINED
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1928 -RANDOM
Rwork0.22 ---
obs0.22 77044 87 %-
Displacement parametersBiso mean: 59.7 Å2
Refine analyzeLuzzati d res low obs: 7 Å
Refinement stepCycle: LAST / Resolution: 2.4→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16776 0 12 538 17326
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.34
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINED
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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