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- PDB-1out: TROUT HEMOGLOBIN I -

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Basic information

Entry
Database: PDB / ID: 1out
TitleTROUT HEMOGLOBIN I
Components(HEMOGLOBIN I) x 2
KeywordsOXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN / ERYTHROCYTE
Function / homology
Function and homology information


haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily ...Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha-1 / Hemoglobin subunit beta-1
Similarity search - Component
Biological speciesOncorhynchus mykiss (rainbow trout)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsTame, J. / Wilson, J.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: The crystal structures of trout Hb I in the deoxy and carbonmonoxy forms.
Authors: Tame, J.R. / Wilson, J.C. / Weber, R.E.
History
DepositionJun 21, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 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_ref_seq_dif / 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_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMOGLOBIN I
B: HEMOGLOBIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2424
Polymers31,0092
Non-polymers1,2332
Water3,117173
1
A: HEMOGLOBIN I
B: HEMOGLOBIN I
hetero molecules

A: HEMOGLOBIN I
B: HEMOGLOBIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4848
Polymers62,0184
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
Unit cell
Length a, b, c (Å)63.280, 63.280, 312.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein HEMOGLOBIN I


Mass: 15110.572 Da / Num. of mol.: 1 / Mutation: CHAIN A, DEL(D32,K33)
Source method: isolated from a genetically manipulated source
Details: DEOXY / Source: (gene. exp.) Oncorhynchus mykiss (rainbow trout) / Tissue: BLOOD / References: UniProt: P02019
#2: Protein HEMOGLOBIN I


Mass: 15898.425 Da / Num. of mol.: 1 / Mutation: CHAIN A, DEL(D32,K33)
Source method: isolated from a genetically manipulated source
Details: DEOXY / Source: (gene. exp.) Oncorhynchus mykiss (rainbow trout) / References: UniProt: P02142
#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.: 173 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.91 Å3/Da / Density % sol: 55 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMbis-Tris-HCl11
215 %PEG800011

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionNum. obs: 17315 / % possible obs: 84.9 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.049

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Processing

Software
NameClassification
PROLSQrefinement
MOSFLMdata reduction
RefinementResolution: 2.3→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.247 -5 %
Rwork0.162 --
obs-14704 -
Displacement parametersBiso mean: 23.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 90 173 2450
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.025
X-RAY DIFFRACTIONp_angle_d0.030.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.0634
X-RAY DIFFRACTIONp_mcangle_it4.5476
X-RAY DIFFRACTIONp_scbond_it7.5998
X-RAY DIFFRACTIONp_scangle_it9.64110
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.0960.12
X-RAY DIFFRACTIONp_singtor_nbd0.1920.3
X-RAY DIFFRACTIONp_multtor_nbd0.2750.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1810.3
X-RAY DIFFRACTIONp_planar_tor2.77
X-RAY DIFFRACTIONp_staggered_tor19.9920
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor31.78530
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: 'PROLSQ (CCP4)' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS

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