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- PDB-2gnv: Crystal structure of non-symbiotic plant hemoglobin from rice, B1... -

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Basic information

Entry
Database: PDB / ID: 2gnv
TitleCrystal structure of non-symbiotic plant hemoglobin from rice, B10 mutant F40L
ComponentsNon-symbiotic hemoglobin 1
KeywordsOXYGEN STORAGE/TRANSPORT / 2 ON 2 HELICAL FOLD / GLOBIN / HEME / IRON / HEMOGLOBIN / HEXACOORDINATE / NONSYMBIOTIC / RICE / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors; With a cytochrome as acceptor / response to nitrite / response to nitrate / response to nitric oxide / oxygen binding / oxidoreductase activity / heme binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Leghaemoglobin, iron-binding site / Plant hemoglobins signature. / Leghaemoglobin / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Leghaemoglobin, iron-binding site / Plant hemoglobins signature. / Leghaemoglobin / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Anaerobic nitrite reductase NSHB1
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHoy, J.A.
CitationJournal: Biochemistry / Year: 2006
Title: Role of Phenylalanine B10 in Plant Nonsymbiotic Hemoglobins
Authors: Smagghe, B.J. / Kundu, S. / Hoy, J.A. / Halder, P. / Weiland, T.R. / Savage, A. / Venugopal, A. / Goodman, M. / Premer, S. / Hargrove, M.S.
History
DepositionApr 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-symbiotic hemoglobin 1
B: Non-symbiotic hemoglobin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1948
Polymers36,6082
Non-polymers1,5856
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.286, 125.286, 56.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Non-symbiotic hemoglobin 1 / rHb1 / ORYsa GLB1a


Mass: 18304.221 Da / Num. of mol.: 2 / Mutation: F40L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: HB1, GLB1A / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O04986
#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-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.9M Ammonium Phosphate, 10mM Potassium Phosphate, 20% Sucrose, 3% Dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 12, 2002 / Details: OSMIC CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→111.803 Å / Num. all: 34568 / Num. obs: 32270 / Limit h max: 54 / Limit h min: 0 / Limit k max: 31 / Limit k min: 0 / Limit l max: 28 / Limit l min: -28 / Rmerge(I) obs: 0.065
Reflection shellResolution: 2→2.052 Å / Num. unique all: 1507

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D8U.pdb

1d8u


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.675 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.242 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1149 5 %RANDOM
Rwork0.201 ---
all0.203 22818 --
obs0.203 22761 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20.52 Å20 Å2
2--1.05 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2447 0 110 222 2779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222621
X-RAY DIFFRACTIONr_bond_other_d0.0060.022425
X-RAY DIFFRACTIONr_angle_refined_deg1.3832.0123558
X-RAY DIFFRACTIONr_angle_other_deg0.85335650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6365311
X-RAY DIFFRACTIONr_chiral_restr0.0770.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022867
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02509
X-RAY DIFFRACTIONr_nbd_refined0.2220.2716
X-RAY DIFFRACTIONr_nbd_other0.2360.22652
X-RAY DIFFRACTIONr_nbtor_other0.090.21395
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2148
X-RAY DIFFRACTIONr_metal_ion_refined0.0170.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3660.221
X-RAY DIFFRACTIONr_mcbond_it0.9491.51569
X-RAY DIFFRACTIONr_mcangle_it1.79122519
X-RAY DIFFRACTIONr_scbond_it2.131052
X-RAY DIFFRACTIONr_scangle_it3.5444.51039
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.345 68
Rwork0.276 1598
obs-1666

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