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- PDB-1fhj: CRYSTAL STRUCTURE OF AQUOMET HEMOGLOBIN-I OF THE MANED WOLF (CHRY... -

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Basic information

Entry
Database: PDB / ID: 1fhj
TitleCRYSTAL STRUCTURE OF AQUOMET HEMOGLOBIN-I OF THE MANED WOLF (CHRYSOCYON BRACHYURUS) AT 2.0 RESOLUTION.
Components
  • HEMOGLOBIN (ALPHA CHAIN)
  • HEMOGLOBIN (BETA CHAIN)
KeywordsOXYGEN STORAGE/TRANSPORT / maned wolf / hemoglobin / metahemoglobin / OXYGEN STORAGE-TRANSPORT COMPLEX
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 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 alpha / Hemoglobin subunit beta / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesChrysocyon brachyurus (maned wolf)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFadel, V. / de Azevedo, W.F.
Citation
Journal: Protein Pept.Lett. / Year: 2003
Title: Crystal structure of hemoglobin from the maned wolf (Chrysocyon brachyurus) using synchrotron radiation.
Authors: Fadel, V. / Canduri, F. / Olivieri, J.R. / Smarra, A.L. / Colombo, M.F. / Bonilla-Rodriguez, G.O. / de Azevedo, W.F.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization, Preliminary X-ray Diffraction Analysis and Patterson Search of Oxyhemoglobin I from the Wolf (Chrysocyon brachiurus)
Authors: Smarra, A.L. / Fadel, V. / Dellamano, M. / Olivieri, J.R. / de Azevedo Jr., W.F. / Bonilla-Rodriguez, G.O.
History
DepositionAug 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 (ALPHA CHAIN)
B: HEMOGLOBIN (BETA CHAIN)
C: HEMOGLOBIN (ALPHA CHAIN)
D: HEMOGLOBIN (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0478
Polymers62,5814
Non-polymers2,4664
Water5,549308
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.184, 87.725, 133.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit has a complete tetramer formed by two alpha chains and two beta chains.

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Components

#1: Protein HEMOGLOBIN (ALPHA CHAIN)


Mass: 15270.329 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysocyon brachyurus (maned wolf) / References: UniProt: P01952, UniProt: P60523*PLUS
#2: Protein HEMOGLOBIN (BETA CHAIN)


Mass: 16020.366 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysocyon brachyurus (maned wolf) / References: UniProt: P02056, UniProt: P60526*PLUS
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: PEG 1500 30%, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.37
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 27, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37 Å / Relative weight: 1
ReflectionResolution: 1.864→72.548 Å / Num. all: 53941 / Num. obs: 50240 / % possible obs: 93.1 % / Observed criterion σ(I): 1 / Redundancy: 2.62 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.4
Reflection shellResolution: 1.86→1.9 Å / Redundancy: 2.38 % / Rmerge(I) obs: 0.583 / Num. unique all: 2799 / % possible all: 78.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN OXYHEMOGLOBIN pdb id 1HHO

1hho


Resolution: 1.8→10 Å / σ(F): 2 / σ(I): 0
Details: Refmac was also used for refinement. THE SIMULLATED ANNEALING METHOD (X-PLOR) AND MAXIMUM LIKELIHOOD METHOD (REFMAC) WAS EMPLOYED. Data was used to 1.8 angstroms, but with low completeness.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 10 -Fixed randomly for x-plor refinement and fixed the same reflections for the refmac refinement.
Rwork0.194 ---
all-53547 --
obs-50039 93.45 %-
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4420 0 172 308 4900
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.71
X-RAY DIFFRACTIONx_dihedral_angle_d21.171
X-RAY DIFFRACTIONx_improper_angle_d1.927

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