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- PDB-1ouu: CARBONMONOXY TROUT HEMOGLOBIN I -

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Basic information

Entry
Database: PDB / ID: 1ouu
TitleCARBONMONOXY TROUT 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha-1 / Hemoglobin subunit beta-1
Similarity search - Component
Biological speciesOncorhynchus mykiss (rainbow trout)
MethodX-RAY DIFFRACTION / Resolution: 2.5 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 3, 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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
C: HEMOGLOBIN I
D: HEMOGLOBIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,59612
Polymers62,0184
Non-polymers2,5788
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12890 Å2
ΔGint-118 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.200, 79.800, 122.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99715, 0.04061, -0.06359), (0.03969, -0.43447, -0.89981), (-0.06417, -0.89977, 0.43162)31.13336, 99.7356, 63.99959
2given(-0.99753, 0.05148, -0.04784), (0.02018, -0.44225, -0.89666), (-0.06732, -0.89541, 0.44012)30.20762, 100.33498, 63.57013

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Components

#1: Protein HEMOGLOBIN I


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


Mass: 15898.425 Da / Num. of mol.: 2 / Mutation: CHAIN A, C, DEL(D32,K33)
Source method: isolated from a genetically manipulated source
Details: CARBONMONOXY / Source: (gene. exp.) Oncorhynchus mykiss (rainbow trout) / Tissue: BLOOD / References: UniProt: P02142
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 49 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %(w/v)PEG40001drop
250 mMTris-HCl1drop
310 mg/mlprotein1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 22054 / % possible obs: 74.1 % / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Rmerge(I) obs: 0.065

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Processing

Software
NameClassification
PROLSQrefinement
XDSdata reduction
RefinementResolution: 2.5→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.286 -5 %
Rwork0.162 --
obs-16338 -
Displacement parametersBiso mean: 29.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4374 0 180 163 4717
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.025
X-RAY DIFFRACTIONp_angle_d0.0330.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.014
X-RAY DIFFRACTIONp_mcangle_it4.5396
X-RAY DIFFRACTIONp_scbond_it7.28
X-RAY DIFFRACTIONp_scangle_it9.43310
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1120.13
X-RAY DIFFRACTIONp_singtor_nbd0.1990.3
X-RAY DIFFRACTIONp_multtor_nbd0.2730.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1870.3
X-RAY DIFFRACTIONp_planar_tor2.1943
X-RAY DIFFRACTIONp_staggered_tor22.63620
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor34.31530
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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