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- PDB-3dhr: Crystal Structure Determination of Methemoglobin from Pigeon at 2... -

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Basic information

Entry
Database: PDB / ID: 3dhr
TitleCrystal Structure Determination of Methemoglobin from Pigeon at 2 Angstrom Resolution (Columba livia)
Components
  • Hemoglobin subunit alpha-A
  • Hemoglobin subunit beta
KeywordsOXYGEN STORAGE / OXYGEN TRANSPORT / AVIAN HEMOGLOBIN / METHEMOGLOBIN / TRICLINIC / Heme / Iron / Metal-binding / Transport
Function / homology
Function and homology information


haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding ...haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / 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 / Hemoglobin subunit beta / Hemoglobin subunit alpha-A
Similarity search - Component
Biological speciesColumba livia (rock pigeon)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSathya Moorthy, P. / Neelagandan, K. / Balasubramanian, M. / Ponnuswamy, M.N.
CitationJournal: To be Published
Title: Purification, Crystallization and X-ray Diffraction Studies of Pigeon Hemoglobin
Authors: Sathya Moorthy, P. / Neelagandan, K. / Balasubramanian, M. / Ponnuswamy, M.N.
History
DepositionJun 18, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2016Group: Other
Revision 1.3Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: Hemoglobin subunit alpha-A
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha-A
D: Hemoglobin subunit beta
E: Hemoglobin subunit alpha-A
F: Hemoglobin subunit beta
G: Hemoglobin subunit alpha-A
H: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,81716
Polymers125,8858
Non-polymers4,9328
Water3,873215
1
A: Hemoglobin subunit alpha-A
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha-A
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4088
Polymers62,9434
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Hemoglobin subunit alpha-A
F: Hemoglobin subunit beta
G: Hemoglobin subunit alpha-A
H: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4088
Polymers62,9434
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Hemoglobin subunit alpha-A
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7044
Polymers31,4712
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-50 kcal/mol
Surface area13640 Å2
MethodPISA
4
C: Hemoglobin subunit alpha-A
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7044
Polymers31,4712
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-46 kcal/mol
Surface area13870 Å2
MethodPISA
5
E: Hemoglobin subunit alpha-A
F: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7044
Polymers31,4712
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-51 kcal/mol
Surface area13730 Å2
MethodPISA
6
G: Hemoglobin subunit alpha-A
H: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7044
Polymers31,4712
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-50 kcal/mol
Surface area13950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.659, 65.322, 103.733
Angle α, β, γ (deg.)78.78, 89.90, 65.30
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Hemoglobin subunit alpha-A / Hemoglobin alpha-A chain / Alpha-A-globin


Mass: 15295.683 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Columba livia (rock pigeon) / Cell: Red blood cells (RBC) / References: UniProt: P21871
#2: Protein
Hemoglobin subunit beta / Hemoglobin beta chain / Beta-globin


Mass: 16175.591 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Columba livia (rock pigeon) / Cell: Red blood cells (RBC) / References: UniProt: P11342
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 30% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 79185 / Redundancy: 1.75 % / Net I/σ(I): 6.83
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.71 %

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
AUTOMARdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FAW

1faw


Resolution: 2→19.99 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.346 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27597 7956 10.1 %RANDOM
Rwork0.24334 ---
obs0.24663 71134 91.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.187 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8828 0 344 215 9387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0229431
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9332.05612899
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87751136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79424.027375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.413151500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.561532
X-RAY DIFFRACTIONr_chiral_restr0.0650.21405
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027076
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1790.24344
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2890.26409
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.040.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3961.55848
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.59129072
X-RAY DIFFRACTIONr_scbond_it0.5234107
X-RAY DIFFRACTIONr_scangle_it0.834.53811
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 563 -
Rwork0.303 5125 -
obs--89.49 %

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