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- PDB-1fsl: FERRIC SOYBEAN LEGHEMOGLOBIN COMPLEXED WITH NICOTINATE -

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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 / nucleus / cytosol
Similarity search - Function
Leghaemoglobin, iron-binding site / Plant hemoglobins signature. / Leghaemoglobin / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily ...Leghaemoglobin, iron-binding site / Plant hemoglobins signature. / Leghaemoglobin / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NICOTINIC ACID / Leghemoglobin 3
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)

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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


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


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


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

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Experimental details

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Experiment

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

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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.

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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

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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

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