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- PDB-1yff: STRUCTURE OF HUMAN CARBONMONOXYHEMOGLOBIN C (BETA E6K): TWO QUATE... -

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Basic information

Entry
Database: PDB / ID: 1yff
TitleSTRUCTURE OF HUMAN CARBONMONOXYHEMOGLOBIN C (BETA E6K): TWO QUATERNARY STATES (R2 and R3) IN ONE CRYSTAL
Components
  • Hemoglobin alpha chain
  • Hemoglobin beta chain
KeywordsOXYGEN STORAGE/TRANSPORT / CARBONMONOXY / LIGANDED / MUTANT HUMAN HEMOGLOBIN C(BETAE6K) / R2 STATE / R3 STATE / QUATERNARY CONFORMATION / HBC / COHBC / 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 / Late endosomal microautophagy / oxygen carrier activity / carbon dioxide transport / Heme signaling / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / regulation of blood pressure / platelet aggregation / oxygen binding / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPatskovska, L. / Patskovsky, Y. / Hirsch, R.E. / Almo, S.C.
CitationJournal: To be Published
Title: Mechanism of Quaternary Transitions in Human Liganded Hemoglobin
Authors: Patskovska, L. / Patskovsky, Y. / Hirsch, R.E. / Almo, S.C.
History
DepositionDec 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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
Remark 300BIOMELECULE BIOLOGICAL ASSEMBLY IS A TETRAMER COMPOSED OF TWO ALPHA-BETA HETERODIMERS. HOWEVER, THE ...BIOMELECULE BIOLOGICAL ASSEMBLY IS A TETRAMER COMPOSED OF TWO ALPHA-BETA HETERODIMERS. HOWEVER, THE ASYMMETRIC UNIT CONTAINS TWO FULL HEMOGLOBIN TETRAMERS AND THEY REPRESENTS TWO DIFFERENT QUATERNARY STATES. ONE TETRAMER (CHAINS A,B,C,D) REPRESENTS THE NOVEL (R3) QUATERNARY STATE, ANOTHER TETRAMER (CHAINS E,F,G,H) IS IDENTICAL TO THE R2 QUATERNARY STATE (PDB ENTRY 1M9P). THE R3 QUATERNARY STATE IS IN PART STABILIZED BY PHOSPHATE ANION BOUND WITHIN THE CENTRAL CAVITY
Remark 999SEQUENCE THE PROTEIN WAS NOT GENETICALLY MANIPULATED, BUT THE RESIDUE E6K OF CHAINS B,D,F AND H ARE ...SEQUENCE THE PROTEIN WAS NOT GENETICALLY MANIPULATED, BUT THE RESIDUE E6K OF CHAINS B,D,F AND H ARE ALLELIC VARIANTS OF HUMAN HEMOGLOBIN A.

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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
E: Hemoglobin alpha chain
F: Hemoglobin beta chain
G: Hemoglobin alpha chain
H: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,41325
Polymers124,1628
Non-polymers5,25117
Water9,026501
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)64,75413
Polymers62,0814
Non-polymers2,6739
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12630 Å2
ΔGint-118 kcal/mol
Surface area23380 Å2
MethodPISA
2
E: Hemoglobin alpha chain
F: Hemoglobin beta chain
G: Hemoglobin alpha chain
H: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,65912
Polymers62,0814
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11980 Å2
ΔGint-114 kcal/mol
Surface area23600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.320, 80.320, 179.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
DetailsBIOLOGICAL ASSEMBLY IS A TETRAMER COMPOSED OF TWO ALPHA-BETA HETERODIMERS. HOWEVER, THE ASYMMETRIC UNIT CONTAINS TWO FULL HEMOGLOBIN TETRAMERS AND THEY REPRESENTS TWO DIFFERENT QUATERNARY STATES. ONE TETRAMER (CHAINS A,B,C,D) REPRESENTS THE NOVEL (R3) QUATERNARY STATE, ANOTHER TETRAMER (CHAINS E,F,G,H) IS IDENTICAL TO THE R2 QUATERNARY STATE (PDB ENTRY 1M9P). THE R3 QUATERNARY STATE IS IN PART STABILIZED BY PHOSPHATE ANION BOUND WITHIN THE CENTRAL CAVITY

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#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: 15890.265 Da / Num. of mol.: 4 / Mutation: E6K / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 4 types, 518 molecules

#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: Chemical
ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CO
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 45.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 4000, SODIUM PHOSPHATE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 20, 2003 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 43129 / Num. obs: 43129 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.102 / Net I/σ(I): 5.4
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.7 / Num. unique all: 6383 / Rsym value: 0.34 / % possible all: 87.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
MOLREP(CCP4)phasing
CNS1refinement
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M9P
Resolution: 2.4→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff high rms absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1260 3 %RANDOM
Rwork0.228 ---
all0.24 43129 --
obs0.228 41813 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.272131 e/Å3
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å20 Å20 Å2
2--2.55 Å20 Å2
3----5.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8768 0 365 501 9634
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_improper_angle_d1.55
X-RAY DIFFRACTIONc_mcbond_it1.942
X-RAY DIFFRACTIONc_mcangle_it3.212.5
X-RAY DIFFRACTIONc_scbond_it3.023
X-RAY DIFFRACTIONc_scangle_it4.624
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.315 96 3 %
Rwork0.304 3141 -
obs-3141 73.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3HEM.PARAMHEM.TOP
X-RAY DIFFRACTION4CO.PARAMCO.TOP

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