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- PDB-1m9p: Crystalline Human Carbonmonoxy Hemoglobin C Exhibits The R2 Quate... -

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Basic information

Entry
Database: PDB / ID: 1m9p
TitleCrystalline Human Carbonmonoxy Hemoglobin C Exhibits The R2 Quaternary State at Neutral pH In The Presence of Polyethylene Glycol: The 2.1 Angstrom Resolution Crystal Structure
Components
  • Hemoglobin alpha chain
  • Hemoglobin beta chain
KeywordsOXYGEN STORAGE/TRANSPORT / Mutant human hemoglobin C(beta E6K) / R2 quaternary state of human hemoglobin / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPatskovska, L.N. / Patskovsky, Y.V. / Almo, S.C. / Hirsch, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: COHbC and COHbS crystallize in the R2 quaternary state at neutral pH in the presence of PEG 4000.
Authors: Patskovska, L.N. / Patskovsky, Y.V. / Almo, S.C. / Hirsch, R.E.
History
DepositionJul 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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.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 400COMPOUND THE QUATERNARY STRUCTURE OF THIS PDB ENTRY SUPERIMPOSES UPON THE R2 QUATERNARY STATE OF ...COMPOUND THE QUATERNARY STRUCTURE OF THIS PDB ENTRY SUPERIMPOSES UPON THE R2 QUATERNARY STATE OF COHBA (PDB ID 1BBB), BUT NOT UPON THE R QUATERNARY CONFORMATION OF OUR COHBC STRUCTURE OBTAINED IN CONCENTRATED PHOSPHATE BUFFER AT PH 7.35 (PDB ID 1K1K) OR UPON R-STATE COHBA(PDB ID 1HHO).
Remark 999SEQUENCE Author states the protein was not genetically manipulated, but the residue E6K of chains B ...SEQUENCE Author states the protein was not genetically manipulated, but the residue E6K of chains B and D 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,65912
Polymers62,0814
Non-polymers2,5788
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
ΔGint-116 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.00, 58.70, 175.20
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer in the assymetric unit.

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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 / Details: blood erythrocytes / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein Hemoglobin beta chain


Mass: 15890.265 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: blood erythrocytes / 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.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 21% Polyethylene glycol, 0.150M HEPES-Na, chloride anion traces, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 298 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-20 mg/mlprotein1reservoir
20.1 Msodium HEPES1reservoir
320-21 %PEG40001reservoir
430 mg/mlprotein1drop
50.1 Msodium HEPES1droppH7.1
625 %PEG40001drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
ROTATING ANODERIGAKU21.5418
ROTATING ANODERIGAKU31.5418
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEJun 27, 2001
RIGAKU RAXIS IV2IMAGE PLATENov 28, 2001
RIGAKU RAXIS IV3IMAGE PLATENov 30, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1graphiteSINGLE WAVELENGTHMx-ray1
2graphiteSINGLE WAVELENGTHMx-ray1
3graphiteSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 32840 / Num. obs: 31220 / % possible obs: 90 % / Observed criterion σ(I): 0.1 / Redundancy: 20.1 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.1
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 1.54 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1935 / % possible all: 56.9
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / % possible obs: 90 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BBB

1bbb


Resolution: 2.1→8 Å / Data cutoff high absF: 10000 / Data cutoff high rms absF: 10000 / Data cutoff low absF: 0.1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1423 5.04 %RANDOM
Rwork0.231 ---
all-30567 --
obs-28245 83.36 %-
Displacement parametersBiso mean: 51.72 Å2
Baniso -1Baniso -2Baniso -3
1--1.093 Å20 Å20 Å2
2---2.437 Å20 Å2
3---3.531 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 180 437 5001
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.764
X-RAY DIFFRACTIONx_dihedral_angle_d22.06
X-RAY DIFFRACTIONx_improper_angle_d1.858
X-RAY DIFFRACTIONx_mcbond_it2.52
X-RAY DIFFRACTIONx_mcangle_it57
X-RAY DIFFRACTIONx_scbond_it34
X-RAY DIFFRACTIONx_scangle_it710
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection obs% reflection obs (%)
2.1-2.190.3774914.90.3754175242.03
2.19-2.310.3711450.3622279967.24
2.31-2.450.37491530.337334379.27
2.45-2.630.33461840.3375357285.7
2.63-2.880.35582060.3294395793.77
2.88-3.280.33262010.2763416597.88
3.28-4.040.24842140.1941425199.39
4.04-80.20012290.16440699.77
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1param19x.hemetoph19.pep
X-RAY DIFFRACTION2protein_rep.paramtoph19x.heme
X-RAY DIFFRACTION3tophcsdx.pro
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.06
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.858

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