[English] 日本語
Yorodumi
- PDB-1fsl: FERRIC SOYBEAN LEGHEMOGLOBIN COMPLEXED WITH NICOTINATE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fsl
TitleFERRIC SOYBEAN LEGHEMOGLOBIN COMPLEXED WITH NICOTINATE
ComponentsLEGHEMOGLOBIN A
KeywordsOXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN / NITROGEN FIXATION / MULTIGENE FAMILY
Function / homology
Function and homology information


response to nitrogen compound / nodulation / response to hydrogen sulfide / response to cobalt ion / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Leghaemoglobin, iron-binding site / Plant hemoglobins signature. / Leghaemoglobin / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Leghaemoglobin, iron-binding site / Plant hemoglobins signature. / Leghaemoglobin / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NICOTINIC ACID / Leghemoglobin A
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.3 Å
AuthorsEllis, P.J. / Guss, J.M. / Freeman, H.C.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Structure of ferric soybean leghemoglobin a nicotinate at 2.3 A resolution.
Authors: Ellis, P.J. / Appleby, C.A. / Guss, J.M. / Hunter, W.N. / Ollis, D.L. / Freeman, H.C.
#1: Journal: Aust.J.Chem. / Year: 1983
Title: Crystal Structure of Soybean Ferric Leghaemoglobin a Nicotinate at a Resolution of 3.3 Angstrom
Authors: Ollis, D.L. / Appleby, C.A. / Colman, P.M. / Cutten, A.E. / Guss, J.M. / Venkatappa, M.P. / Freeman, H.C.
History
DepositionDec 12, 1995Processing site: BNL
Revision 1.0Jun 26, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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: LEGHEMOGLOBIN A
B: LEGHEMOGLOBIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0006
Polymers30,5212
Non-polymers1,4794
Water1,26170
1
A: LEGHEMOGLOBIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0003
Polymers15,2601
Non-polymers7402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LEGHEMOGLOBIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0003
Polymers15,2601
Non-polymers7402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.690, 56.550, 57.800
Angle α, β, γ (deg.)90.00, 109.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.461976, 0.030242, 0.886377), (-0.021546, -0.999506, 0.022872), (0.886631, -0.008532, 0.4624)
Vector: -41.53064, 45.05125, 19.71374)

-
Components

#1: Protein LEGHEMOGLOBIN A


Mass: 15260.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: FE(III), PH 6.0 / Source: (natural) Glycine max (soybean) / Organ: ROOT NODULE / References: UniProt: P02238
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NIO / NICOTINIC ACID / Niacin


Mass: 123.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: other / Details: Ollis, D.L., (1983) Aust. J. Chem., 36, 451.

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: 1981 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→8 Å / Num. obs: 14153 / Observed criterion σ(I): 0 / Redundancy: 1.3 % / Rmerge(I) obs: 0.061
Reflection
*PLUS
Num. measured all: 18416

-
Processing

Software
NameVersionClassification
PROFFTrefinement
ENRAF-NONIUSdata reduction
PROTEIN(STEIGEMANN)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.3→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.158 --
obs-6877 49.5 %
Displacement parametersBiso mean: 12.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2168 0 172 70 2410
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.015
X-RAY DIFFRACTIONp_angle_d0.0160.015
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0250.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.591
X-RAY DIFFRACTIONp_mcangle_it1.031.5
X-RAY DIFFRACTIONp_scbond_it0.521
X-RAY DIFFRACTIONp_scangle_it0.941.5
X-RAY DIFFRACTIONp_plane_restr0.010.015
X-RAY DIFFRACTIONp_chiral_restr0.0780.15
X-RAY DIFFRACTIONp_singtor_nbd0.150.25
X-RAY DIFFRACTIONp_multtor_nbd0.1980.25
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1720.25
X-RAY DIFFRACTIONp_xyhbond_nbd0.1820.25
X-RAY DIFFRACTIONp_planar_tor2.23
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.158
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