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- PDB-1d8u: CRYSTAL STRUCTURE OF NON-SYMBIOTIC PLANT HEMOGLOBIN FROM RICE -

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Basic information

Entry
Database: PDB / ID: 1d8u
TitleCRYSTAL STRUCTURE OF NON-SYMBIOTIC PLANT HEMOGLOBIN FROM RICE
ComponentsNON-SYMBIOTIC HEMOGLOBIN
KeywordsOXYGEN STORAGE/TRANSPORT / GLOBIN / BIS-HISTIDYL / HEME PROTEIN / 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
PROTOPORPHYRIN IX CONTAINING FE / Anaerobic nitrite reductase NSHB1
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsHargrove, M. / Brucker, E.A. / Stec, B. / Olson, J.S. / Phillips Jr., G.N.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystal structure of a nonsymbiotic plant hemoglobin.
Authors: Hargrove, M.S. / Brucker, E.A. / Stec, B. / Sarath, G. / Arredondo-Peter, R. / Klucas, R.V. / Olson, J.S. / Phillips Jr., G.N.
History
DepositionOct 26, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 14, 2019Group: Data collection / Category: computing
Revision 1.6Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: NON-SYMBIOTIC HEMOGLOBIN
B: NON-SYMBIOTIC HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1724
Polymers36,9392
Non-polymers1,2332
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.800, 126.800, 55.500
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


Mass: 18469.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Organ: ROOT / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 3.49 Å3/Da / Density % sol: 64.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: AMMONIUM PHOSPHATE, SUCROSE, POTASSIUM PHOSPHATE, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.2 Mammonium phosphate1reservoir
220 %sucrose1reservoir
310 mMpotassium phosphate1drop
42.2 mMprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.74
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Aug 21, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 19025 / % possible obs: 87.8 % / Observed criterion σ(I): 0 / Redundancy: 8.06 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.7 / Net I/σ(I): 13.7
Reflection shellResolution: 2.35→2.42 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.271 / % possible all: 0.7
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. obs: 21422 / % possible obs: 80 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.69
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / % possible obs: 46 % / Num. unique obs: 1634 / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
CNSrefinement
X-PLOR3.1refinement
PHASESphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.35→50 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1879 -1 SET RANDOM
Rwork0.208 ---
obs-19025 87.8 %-
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 0 86 203 2865
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.11
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: 'XPLOR 3.1 AND CNS' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_plane_restr1.85
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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