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- PDB-2r50: The crystal structure of nonsymbiotic corn hemoglobin 1 -

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Basic information

Entry
Database: PDB / ID: 2r50
TitleThe crystal structure of nonsymbiotic corn hemoglobin 1
ComponentsNon-symbiotic hemoglobin
KeywordsMETAL BINDING PROTEIN / corn hemoglobin / plant hemoglobin / nonsymbiotic hemoglobin / Heme / Iron / Metal-binding
Function / homology
Function and homology information


oxygen binding / heme binding / metal ion binding
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
ACETIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Non-symbiotic hemoglobin
Similarity search - Component
Biological speciesZea mays subsp. parviglumis (Balsas teosinte)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSmagghe, B.J. / Hoy, J.A. / Hargrove, M.S.
CitationJournal: To be Published
Title: The crystal structure of nonsymbiotic corn hemoglobin 1
Authors: Smagghe, B.J. / Hoy, J.A. / Hargrove, M.S.
History
DepositionSep 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
C: Non-symbiotic hemoglobin
D: Non-symbiotic hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,28415
Polymers73,2184
Non-polymers3,06611
Water10,521584
1
A: Non-symbiotic hemoglobin
D: Non-symbiotic hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0947
Polymers36,6092
Non-polymers1,4855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
MethodPISA
2
B: Non-symbiotic hemoglobin
C: Non-symbiotic hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1908
Polymers36,6092
Non-polymers1,5816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.754, 89.734, 157.424
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Non-symbiotic hemoglobin / Hbt / ZEAmp GLB1


Mass: 18304.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays subsp. parviglumis (Balsas teosinte)
Species: Zea mays / Strain: subsp. parviglumis / Gene: HB, GLB1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* DE3 / References: UniProt: Q9M593
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Sodium Acetate, 0.2M Ammonium Sulfate, 20% PEG MME 1900, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 23, 2004 / Details: Osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→80 Å / Num. obs: 35371 / % possible obs: 99.6 % / Redundancy: 6.67 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.3
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 5.24 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6.4 / Num. unique all: 2504 / % possible all: 97.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
AMoREphasing
REFMAC5.1.24refinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1D8U

1d8u


Resolution: 2.2→79.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.762 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1873 5 %RANDOM
Rwork0.201 ---
obs0.203 35371 99.63 %-
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: 38.837 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2--1.19 Å20 Å2
3----2.49 Å2
Refinement stepCycle: LAST / Resolution: 2.2→79.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4579 0 197 592 5368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224890
X-RAY DIFFRACTIONr_bond_other_d0.0080.024543
X-RAY DIFFRACTIONr_angle_refined_deg1.7792.0176626
X-RAY DIFFRACTIONr_angle_other_deg1.052310540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.645576
X-RAY DIFFRACTIONr_chiral_restr0.1110.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025351
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02993
X-RAY DIFFRACTIONr_nbd_refined0.2320.21428
X-RAY DIFFRACTIONr_nbd_other0.2530.25248
X-RAY DIFFRACTIONr_nbtor_other0.0940.22573
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2390.2266
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.215
X-RAY DIFFRACTIONr_mcbond_it1.3691.52906
X-RAY DIFFRACTIONr_mcangle_it2.4924618
X-RAY DIFFRACTIONr_scbond_it3.25431984
X-RAY DIFFRACTIONr_scangle_it5.2214.52008
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.319 126
Rwork0.264 2504
all-2630

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