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- PDB-1lfl: DEOXY HEMOGLOBIN (90% RELATIVE HUMIDITY) -

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Basic information

Entry
Database: PDB / ID: 1lfl
TitleDEOXY HEMOGLOBIN (90% RELATIVE HUMIDITY)
Components
  • Hemoglobin alpha chain
  • Hemoglobin beta chain
KeywordsOXYGEN STORAGE/TRANSPORT / HEMOGLOBIN / T State / HUMIDITY / ENVIRONMENT / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / 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 / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / regulation of blood pressure / 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 / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
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 / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsBiswal, B.K. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structures of human oxy- and deoxyhaemoglobin at different levels of humidity: variability in the T state.
Authors: Biswal, B.K. / Vijayan, M.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of human oxyhaemoglobin at 2.1 A resolution
Authors: Shaanan, B.
#2: Journal: J.Mol.Biol. / Year: 1984
Title: The crystal structure of human deoxyhaemoglobin at 1.74 A resolution
Authors: Fermi, G. / Perutz, M.F. / Shaanan, B. / Fourme, R.
#3: Journal: J.Biol.Chem. / Year: 1992
Title: A Third Quaternary Structure of Human Hemoglobin a at 1.7-Angstroms Resolution
Authors: Silva, M.M. / Rogers, P.H. / Arnone, A.
History
DepositionApr 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
P: Hemoglobin alpha chain
Q: Hemoglobin beta chain
R: Hemoglobin alpha chain
S: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,09416
Polymers124,1628
Non-polymers4,9328
Water3,063170
1
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)64,5478
Polymers62,0814
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11110 Å2
ΔGint-106 kcal/mol
Surface area23570 Å2
MethodPISA
2
P: Hemoglobin alpha chain
Q: Hemoglobin beta chain
R: Hemoglobin alpha chain
S: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5478
Polymers62,0814
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11160 Å2
ΔGint-106 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.300, 82.900, 76.300
Angle α, β, γ (deg.)90.00, 99.30, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 4 / 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.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 6.7 / Details: phosphate buffer, pH 6.7, LIQUID DIFFUSION at 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.7 Å / Num. obs: 25510 / Biso Wilson estimate: 30.7 Å2

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementResolution: 2.7→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 192934.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1233 4.8 %RANDOM
Rwork0.19 ---
obs0.19 25510 84.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.6142 Å2 / ksol: 0.296282 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å24.87 Å2
2--2.43 Å20 Å2
3----1.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8768 0 344 170 9282
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_improper_angle_d1.08
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 146 4.5 %
Rwork0.232 3132 -
obs--65.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP

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