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- PDB-1k0y: X-ray Crystallographic Analyses of Symmetrical Allosteric Effecto... -

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Basic information

Entry
Database: PDB / ID: 1k0y
TitleX-ray Crystallographic Analyses of Symmetrical Allosteric Effectors of Hemoglobin. Compounds Designed to Link Primary and Secondary Binding Sites
Components
  • hemoglobin alpha chain
  • hemoglobin beta chain
KeywordsOXYGEN STORAGE/TRANSPORT / hemoglobin / allosteric / T state / deoxy / 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
Chem-CNO / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.87 Å
AuthorsSafo, M.K. / Boyiri, T. / Burnett, J.C. / Danso-Danquah, R. / Moure, C.M. / Joshi, G.S. / Abraham, D.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: X-ray crystallographic analyses of symmetrical allosteric effectors of hemoglobin: compounds designed to link primary and secondary binding sites.
Authors: Safo, M.K. / Boyiri, T. / Burnett, J.C. / Danso-Danquah, R. / Moure, C.M. / Joshi, G.S. / Abraham, D.J.
History
DepositionSep 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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)65,83612
Polymers62,0814
Non-polymers3,7558
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14430 Å2
ΔGint-143 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.28, 83.79, 53.80
Angle α, β, γ (deg.)90.0, 99.33, 90.0
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

#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) / Tissue: blood / 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) / Tissue: blood / References: UniProt: P68871

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Non-polymers , 4 types, 265 molecules

#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CNO / 2-{4-[(3{2-[4-(1-CARBOXY-1-METHYL-ETHOXY)-PHENYL]-ACETYLAMINO}-PHENYLCARBAMOYL)-METHYL]-PHENOXY}-2-METHYL-PROPIONIC ACID


Mass: 548.584 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H32N2O8
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 6.5
Details: Ammonium sulfate, ammonium phosphate, ferrous citrate, pH 6.5, LIQUID DIFFUSION, temperature 298K
Crystal grow
*PLUS
Method: batch method / Details: Safo, M.K., (2001) Protein Sci, 10, 951.
Components of the solutions
*PLUS
Conc.: 3.6 M / Common name: sulfate/phosphate

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 22, 1997 / Details: mirrors
RadiationMonochromator: MSC Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→53 Å / Num. all: 42624 / Num. obs: 42624 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 24.16 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 8.6
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3287 / % possible all: 73.8
Reflection
*PLUS
Lowest resolution: 53 Å / Num. measured all: 119063
Reflection shell
*PLUS
% possible obs: 73.8 % / Num. unique obs: 3287 / Num. measured obs: 8433

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
bioteXdata reduction
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1HHB

1hhb
PDB Unreleased entry


Resolution: 1.87→53 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh and Huber
Details: Anomalous data used for refinement. Bulk solvent correction used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.189 2131 -random
Rwork0.163 ---
all0.164 42624 --
obs0.164 42624 100 %-
Displacement parametersBiso mean: 22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.87→53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 262 257 4903
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.66
X-RAY DIFFRACTIONx_dihedral_angle_d19
X-RAY DIFFRACTIONx_improper_angle_d1.36
LS refinement shellResolution: 1.87→1.96 Å
RfactorNum. reflection% reflection
Rfree0.286 233 -
Rwork0.275 --
obs-4639 69.6 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 53 Å / σ(F): 0 / Rfactor obs: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.73
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36
LS refinement shell
*PLUS
Rfactor Rfree: 0.286 / Rfactor Rwork: 0.275

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