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- PDB-1g9v: HIGH RESOLUTION CRYSTAL STRUCTURE OF DEOXY HEMOGLOBIN COMPLEXED W... -

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Basic information

Entry
Database: PDB / ID: 1g9v
TitleHIGH RESOLUTION CRYSTAL STRUCTURE OF DEOXY HEMOGLOBIN COMPLEXED WITH A POTENT ALLOSTERIC EFFECTOR
Components
  • HEMOGLOBIN ALPHA CHAIN
  • HEMOGLOBIN BETA CHAIN
KeywordsOXYGEN STORAGE/TRANSPORT / Hemoglobin Tetramer / T state / Allosteric / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / organic acid binding / 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 / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / response to hydrogen peroxide / 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 / 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 domain profile. / Globin-like / Globin / Globin ...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 / Chem-RQ3 / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsSafo, M.K. / Moure, C.M. / Burnett, J.C. / Joshi, G.S. / Abraham, D.J.
CitationJournal: Protein Sci. / Year: 2001
Title: High-resolution crystal structure of deoxy hemoglobin complexed with a potent allosteric effector.
Authors: Safo, M.K. / Moure, C.M. / Burnett, J.C. / Joshi, G.S. / Abraham, D.J.
History
DepositionNov 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: 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)65,42212
Polymers62,0814
Non-polymers3,3418
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.20, 83.56, 53.86
Angle α, β, γ (deg.)90.00, 99.16, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly is a tetramer in the asymmetric unit

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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, 268 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-RQ3 / 2-{4-[(3,5-DIMETHYLANILINO)-CARBONYL-METHYL]-PHENOXY}-2-METHYLPROPIONIC ACID


Mass: 341.401 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23NO4 / Comment: chemotherapy*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.26 Å3/Da / Density % sol: 45.59 %
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
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 6, 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: 1.85→55 Å / Num. all: 44139 / Num. obs: 44139 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 20.26 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 6.9
Reflection shellResolution: 1.85→1.91 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3912 / % possible all: 85.1
Reflection
*PLUS
Lowest resolution: 55 Å / Num. measured all: 165826
Reflection shell
*PLUS
% possible obs: 85.1 % / Num. unique obs: 3912 / Num. measured obs: 14162

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TRUNCATEdata scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1HHB

1hhb
PDB Unreleased entry


Resolution: 1.85→55 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
Rfree0.208 2207 -random
Rwork0.177 ---
all0.179 44139 --
obs0.179 44139 100 %-
Displacement parametersBiso mean: 22.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.85→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 232 260 4876
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.67
X-RAY DIFFRACTIONx_dihedral_angle_d19.1
X-RAY DIFFRACTIONx_improper_angle_d1.43
LS refinement shellResolution: 1.85→1.93 Å
RfactorNum. reflection
Rfree0.348 486
Rwork0.328 -
obs-9721
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 55 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.43
LS refinement shell
*PLUS
Rfactor Rfree: 0.348 / Rfactor Rwork: 0.328 / Rfactor obs: 0.328

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