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- PDB-4c0n: Crystal structure of non symbiotic plant hemoglobin AHb3 (GLB3) f... -

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Basic information

Entry
Database: PDB / ID: 4c0n
TitleCrystal structure of non symbiotic plant hemoglobin AHb3 (GLB3) from Arabidopsis thaliana
Components2-ON-2 HEMOGLOBIN
KeywordsOXYGEN TRANSPORT / 2-OVER-2 FOLD
Function / homology
Function and homology information


response to auxin / oxygen transport / oxygen carrier activity / oxygen binding / response to hypoxia / heme binding / metal ion binding
Similarity search - Function
Two-on-two hemoglobin-3 / Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / HYDROXIDE ION / Two-on-two hemoglobin-3
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsHough, M.A. / Reeder, B.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The Structure of a Class 3 Nonsymbiotic Plant Haemoglobin from Arabidopsis Thaliana Reveals a Novel N-Terminal Helical Extension
Authors: Reeder, B.J. / Hough, M.A.
History
DepositionAug 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-ON-2 HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8934
Polymers20,2241
Non-polymers6693
Water2,072115
1
A: 2-ON-2 HEMOGLOBIN
hetero molecules

A: 2-ON-2 HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7858
Polymers40,4472
Non-polymers1,3386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation19_666-x+5/4,-z+5/4,-y+5/41
Buried area5010 Å2
ΔGint-82.6 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.373, 123.373, 123.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-1152-

CL

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Components

#1: Protein 2-ON-2 HEMOGLOBIN / NON-SYMBIOTIC PLANT HEMOGLOBIN AHB3


Mass: 20223.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q67XG0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.88 Å3/Da / Density % sol: 68.3 % / Description: NONE
Crystal growpH: 8.2 / Details: 1.6 M AMMONIUM SULFATE, 0.1 M TRIS PH 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2013 / Details: MIRRORS
RadiationMonochromator: SI DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.77→50.3 Å / Num. obs: 31454 / % possible obs: 99 % / Observed criterion σ(I): -10 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.4
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.77→50.42 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.765 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 1574 5 %RANDOM
Rwork0.18574 ---
obs0.18675 29824 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.274 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.77→50.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1228 0 45 115 1388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191371
X-RAY DIFFRACTIONr_bond_other_d0.0020.021243
X-RAY DIFFRACTIONr_angle_refined_deg1.511.9721877
X-RAY DIFFRACTIONr_angle_other_deg0.88832861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5075168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0124.80577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17515233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.865158
X-RAY DIFFRACTIONr_chiral_restr0.1040.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021633
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02365
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0282.522625
X-RAY DIFFRACTIONr_mcbond_other2.022.514624
X-RAY DIFFRACTIONr_mcangle_it3.033.783787
X-RAY DIFFRACTIONr_mcangle_other3.0323.791788
X-RAY DIFFRACTIONr_scbond_it2.2742.627746
X-RAY DIFFRACTIONr_scbond_other2.2672.627744
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4563.8661082
X-RAY DIFFRACTIONr_long_range_B_refined5.57620.6641757
X-RAY DIFFRACTIONr_long_range_B_other5.48520.3361717
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 120 -
Rwork0.359 2197 -
obs--99.83 %

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