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- PDB-1a4f: BAR-HEADED GOOSE HEMOGLOBIN (OXY FORM) -

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Basic information

Entry
Database: PDB / ID: 1a4f
TitleBAR-HEADED GOOSE HEMOGLOBIN (OXY FORM)
Components
  • HEMOGLOBIN (ALPHA CHAIN)
  • HEMOGLOBIN (BETA CHAIN)
KeywordsOXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN / ERYTHROCYTE
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hemoglobin subunit alpha-A / Hemoglobin subunit beta
Similarity search - Component
Biological speciesAnser indicus (Bar-headed goose)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, J. / Gu, X.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: The crystal structure of a high oxygen affinity species of haemoglobin (bar-headed goose haemoglobin in the oxy form).
Authors: Zhang, J. / Hua, Z. / Tame, J.R. / Lu, G. / Zhang, R. / Gu, X.
History
DepositionJan 29, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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.process_site / _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_conn.ptnr2_label_seq_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 (ALPHA CHAIN)
B: HEMOGLOBIN (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9736
Polymers31,6762
Non-polymers1,2974
Water1,946108
1
A: HEMOGLOBIN (ALPHA CHAIN)
B: HEMOGLOBIN (BETA CHAIN)
hetero molecules

A: HEMOGLOBIN (ALPHA CHAIN)
B: HEMOGLOBIN (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,94512
Polymers63,3514
Non-polymers2,5948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)81.590, 81.590, 107.280
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 (ALPHA CHAIN)


Mass: 15361.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Anser indicus (Bar-headed goose) / References: UniProt: P01990
#2: Protein HEMOGLOBIN (BETA CHAIN)


Mass: 16313.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Anser indicus (Bar-headed goose) / References: UniProt: P02118
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.71 Å3/Da / Density % sol: 54 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG60001drop
250 mMpotassium phosphate1drop
325 mg/mlprotein1drop
41 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Type: PHOTON FACTORY / Wavelength: 1
DetectorDetector: FILM / Date: Jul 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. obs: 24887 / % possible obs: 87.2 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.051
Reflection
*PLUS
Num. measured all: 92268

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Processing

Software
NameClassification
AUTOMRmodel building
PROLSQrefinement
WEISdata reduction
AUTOMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / σ(F): 0 / Details: THE OVERALL GEOMETRY IS RELATIVELY POOR.
RfactorNum. reflection% reflection
Rwork0.198 --
obs-2488 87.12 %
Displacement parametersBiso mean: 29.4 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 90 108 2448
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.015
X-RAY DIFFRACTIONp_angle_d0.0520.025
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0750.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it5.8884
X-RAY DIFFRACTIONp_mcangle_it7.4126
X-RAY DIFFRACTIONp_scbond_it10.396
X-RAY DIFFRACTIONp_scangle_it13.0710
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.2630.15
X-RAY DIFFRACTIONp_singtor_nbd0.2230.3
X-RAY DIFFRACTIONp_multtor_nbd0.260.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd00.3
X-RAY DIFFRACTIONp_planar_tor2.997
X-RAY DIFFRACTIONp_staggered_tor24.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor39.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS

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