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- PDB-3mju: Crystal structure determination of pigeon (columba livia) haemogl... -

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Basic information

Entry
Database: PDB / ID: 3mju
TitleCrystal structure determination of pigeon (columba livia) haemoglobin at 3.5 angstrom resolution
Components
  • Hemoglobin subunit alpha-A
  • Hemoglobin subunit beta
KeywordsOxygen Storage / Oxygen Transport / Avian Hemoglobin / High oxygen affinity / Inositol penta phosphate
Function / homology
Function and homology information


hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle ...hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / 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 / Globin-like superfamily ...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 / PHASER / Resolution: 3.5 Å
AuthorsSathya Moorthy, P. / Balasubramanian, M. / Thenmozhi, M. / Ponnuswamy, M.N.
CitationJournal: To be Published
Title: Crystal structure determination of pigeon (columba livia) haemoglobin at 3.5 angstrom resolution
Authors: Sathya Moorthy, P. / Balasubramanian, M. / Thenmozhi, M. / Ponnuswamy, M.N.
History
DepositionApr 13, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Dec 18, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.oper_expression
Revision 1.4Nov 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_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.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.ptnr3_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5734
Polymers31,3402
Non-polymers1,2332
Water362
1
A: Hemoglobin subunit alpha-A
B: Hemoglobin subunit beta
hetero molecules

A: Hemoglobin subunit alpha-A
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1468
Polymers62,6804
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)82.061, 82.061, 106.095
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 15164.487 Da / Num. of mol.: 1 / 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.: 1 / 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.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. all: 7172 / Num. obs: 4263 / % possible obs: 96.2 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 1 / Redundancy: 6.01 % / Rsym value: 0.2346 / Net I/σ(I): 1.8
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 6.14 % / Mean I/σ(I) obs: 0.7 / Rsym value: 0.3389 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0102refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: PHASER
Starting model: PDB ENTRY 1A4F

1a4f


Resolution: 3.5→27.99 Å / Cor.coef. Fo:Fc: 0.841 / Cor.coef. Fo:Fc free: 0.703 / SU B: 38.62 / SU ML: 0.615 / Cross valid method: THROUGHOUT / ESU R Free: 0.843 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31199 444 9.4 %RANDOM
Rwork0.23605 ---
obs0.24327 4263 95.57 %-
all-4263 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 3.5→27.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 86 2 2301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222370
X-RAY DIFFRACTIONr_angle_refined_deg1.4152.0523241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2335285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5842495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.3115377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.559158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211776
X-RAY DIFFRACTIONr_mcbond_it0.4371.51422
X-RAY DIFFRACTIONr_mcangle_it0.82222276
X-RAY DIFFRACTIONr_scbond_it0.8243948
X-RAY DIFFRACTIONr_scangle_it1.4974.5965
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 29 -
Rwork0.203 307 -
obs--99.12 %

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