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- PDB-4c44: Crystal Structure of Truncated Plant Hemoglobin from Arabidopsis ... -

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Basic information

Entry
Database: PDB / ID: 4c44
TitleCrystal Structure of Truncated Plant Hemoglobin from Arabidopsis thaliana
Components2-ON-2 HEMOGLOBIN
KeywordsOXYGEN BINDING
Function / homology
Function and homology information


response to auxin / oxygen transport / oxygen carrier activity / oxygen binding / response to hypoxia / heme binding / metal ion binding / plasma membrane
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 / Two-on-two hemoglobin-3
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMukhi, N. / Dhindwal, S. / Kumar, P. / Kaur, J. / Kundu, S.
CitationJournal: To be Published
Title: X-Ray Crystallographic Structural Characteristics of Truncated Hemoglobin from Arabidopsis Thaliana
Authors: Mukhi, N. / Dhindwal, S. / Kumar, P. / Kaur, J. / Kundu, S.
History
DepositionAug 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,8633
Polymers20,2241
Non-polymers6392
Water66737
1
A: 2-ON-2 HEMOGLOBIN
hetero molecules

A: 2-ON-2 HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7266
Polymers40,4472
Non-polymers1,2794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_454-x-1/4,z+1/4,y-1/41
Buried area4840 Å2
ΔGint-73.4 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.085, 122.085, 122.085
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-2013-

HOH

21A-2029-

HOH

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Components

#1: Protein 2-ON-2 HEMOGLOBIN / 2-ON-2 HEMOGLOBIN (GLB3) / AT4G32690 / HEMOGLOBIN 3


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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 4.09 Å3/Da / Density % sol: 69.98 % / Description: NONE
Crystal growDetails: 1.2M SODIUM POTASSIUM TARTARATE TETRAHYDRATE, 0.1M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 9881 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.68 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.24
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NGK

1ngk


Resolution: 2.65→43.2 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.427 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 504 5.3 %RANDOM
Rwork0.20269 ---
obs0.20519 9020 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.82 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.65→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1227 0 44 37 1308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191307
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9731778
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3475149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02824.79573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.74815213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.182157
X-RAY DIFFRACTIONr_chiral_restr0.1130.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211038
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.2733.873599
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.8375.794747
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8563.984707
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 34 -
Rwork0.283 649 -
obs--100 %

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