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- PDB-1fn3: CRYSTAL STRUCTURE OF NICKEL RECONSTITUTED HEMOGLOBIN-A CASE FOR P... -

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Basic information

Entry
Database: PDB / ID: 1fn3
TitleCRYSTAL STRUCTURE OF NICKEL RECONSTITUTED HEMOGLOBIN-A CASE FOR PERMANENT, T-STATE HEMOGLOBIN
Components
  • HEMOGLOBIN ALPHA CHAIN
  • HEMOGLOBIN BETA CHAIN
KeywordsOXYGEN STORAGE/TRANSPORT / PERMANENT T-STATE / METAL ION COORDINATION / SUBUNIT INEQUIVALENCE / SPECTROSCOPY / CRYSTALLOGRAPHY. / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / response to hydrogen peroxide / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / inflammatory response / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. ...Hemoglobin, pi / 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 NI(II) / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsVenkateshrao, S. / Deepthi, S. / Pattabhi, V. / Manoharan, P.T.
Citation
Journal: CURR.SCI. / Year: 2003
Title: Crystal Structure of Nickel Reconstituted Hemoglobin - A Case for Permanent, T-State Hemoglobin
Authors: Venkateshrao, S. / Deepthi, S. / Pattabhi, V. / Manoharan, P.T.
#1: Journal: Protein Sci. / Year: 2000
Title: Oxygen Binding by Alpha(Fe2+)2Beta(Ni2+)2 Hemoglobin Crystals
Authors: Bruno, S. / Bettati, S. / Manfredini, M. / Mozzarelli, A. / Bolognesi, M. / Deriu, D. / Rosano, C. / Tsuneshige, A. / Yonetani, T. / Henry, E.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: High Resolution Crystal Structures and Comparisons of T-State Deoxyhaemoglobin and Two Liganded T-State Haemoglobins:T(Alpha-Oxy)Haemoglobin and T(met)Haemoglobin
Authors: Liddington, R. / Derewenda, Z. / Dodson, E. / Hubbard, R. / Dodson, G.
#3: Journal: J.Mol.Biol. / Year: 1990
Title: Structure of Deoxy Quaternary Hemoglobin with Liganded Beta Subunits
Authors: Luisi, B. / Liddington, B. / Fermi, G. / Shibayama, N.
History
DepositionAug 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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.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_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)64,5588
Polymers62,0814
Non-polymers2,4774
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.520, 96.138, 65.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HEMOGLOBIN ALPHA CHAIN


Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein HEMOGLOBIN BETA CHAIN


Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871
#3: Chemical
ChemComp-HNI / PROTOPORPHYRIN IX CONTAINING NI(II)


Mass: 619.336 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32N4NiO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growpH: 7.2 / Details: pH 7.20
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %(w/v)PEG800011
24 %Hb solution11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.48→19.81 Å / Num. obs: 19946 / % possible obs: 91.37 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.1549 / Net I/σ(I): 3.04
Reflection shellResolution: 2.48→2.6 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.7552 / Mean I/σ(I) obs: 0.07 / % possible all: 71.5
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 19.8 Å / % possible obs: 91.4 % / Redundancy: 3.8 % / Num. measured all: 75819 / Rmerge(I) obs: 0.155

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Processing

Software
NameClassification
XDSdata scaling
AUTOMARdata reduction
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1THB

1thb


Resolution: 2.48→8 Å / Cross valid method: FREE R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.324 118 4.098 %RANDOM
Rwork0.242 ---
all0.4 19334 --
obs0.244 2888 --
Refinement stepCycle: LAST / Resolution: 2.48→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 172 38 4594
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg2.242
Refinement
*PLUS
Highest resolution: 2.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg2.241
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.059
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.627

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