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- PDB-1k1k: Structure of Mutant Human Carbonmonoxyhemoglobin C (beta E6K) at ... -

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Basic information

Entry
Database: PDB / ID: 1k1k
TitleStructure of Mutant Human Carbonmonoxyhemoglobin C (beta E6K) at 2.0 Angstrom Resolution in Phosphate Buffer.
Components
  • HEMOGLOBIN ALPHA CHAIN
  • HEMOGLOBIN BETA CHAIN
KeywordsOXYGEN STORAGE/TRANSPORT / mutant human hemoglobin C(betaE6K) / 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
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 Å
AuthorsDewan, J.C. / Taylor-Feeling, A. / Puius, Y.A. / Patskovska, L. / Patskovsky, Y. / Nagel, R.L. / Almo, S.C. / Hirsch, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of mutant human carbonmonoxyhemoglobin C (betaE6K) at 2.0 A resolution.
Authors: Dewan, J.C. / Feeling-Taylor, A. / Puius, Y.A. / Patskovska, L. / Patskovsky, Y. / Nagel, R.L. / Almo, S.C. / Hirsch, R.E.
History
DepositionSep 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Refinement description
Category: database_2 / software ...database_2 / software / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEMOGLOBIN ALPHA CHAIN
B: HEMOGLOBIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3306
Polymers31,0412
Non-polymers1,2894
Water2,036113
1
A: HEMOGLOBIN ALPHA CHAIN
B: HEMOGLOBIN BETA CHAIN
hetero molecules

A: HEMOGLOBIN ALPHA CHAIN
B: 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
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)54.16, 54.16, 195.3
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a tetramer generated from the dimer in the assymetric unit by the two fold axis: -y,-x,1/2-z.

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Components

#1: Protein HEMOGLOBIN ALPHA CHAIN


Mass: 15150.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: erythrocyte / Tissue: BLOOD / References: UniProt: P69905
#2: Protein HEMOGLOBIN BETA CHAIN


Mass: 15890.265 Da / Num. of mol.: 1 / Mutation: E6K / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: erythrocyte / Tissue: BLOOD / References: UniProt: P68871
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 310 K / Method: batch method / pH: 7.35
Details: potassium phosphate 1.75M, pH 7.35, batch method, temperature 310K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein11
21.75 Mpotassium phosphate11pH7.35

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Mar 8, 1995
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→22.55 Å / Num. all: 19382 / Num. obs: 19382 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.38 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.063
Reflection shellResolution: 2→2.09 Å / Num. unique all: 2135 / % possible all: 85.16
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 22.5 Å / % possible obs: 94 % / Num. measured all: 84880

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Processing

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

1hho


Resolution: 2→22.55 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Details: The side chain of beta K6 was added to the model in weak continuous density present at the 0.5 sigma level in a 2Fo-Fc map.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1906 -RANDOM
Rwork0.183 ---
all-19382 --
obs-19382 89.14 %-
Displacement parametersBiso mean: 24.9 Å2
Refinement stepCycle: LAST / Resolution: 2→22.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 90 113 2395
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.123
X-RAY DIFFRACTIONx_dihedral_angle_d21.82
X-RAY DIFFRACTIONx_improper_angle_d0.898
X-RAY DIFFRACTIONx_mcbond_it3.2741.5
X-RAY DIFFRACTIONx_mcangle_it4.0762
X-RAY DIFFRACTIONx_scbond_it5.0562
X-RAY DIFFRACTIONx_scangle_it6.8032.5
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection obs% reflection obs (%)
2-2.090.28732120.249213585.16
2.09-2.20.23991950.2304225290.12
2.2-2.340.25142550.218234892.7
2.34-2.520.2392400.2054237894.55
2.52-2.770.24992280.2015245295.93
2.77-3.170.26072420.1865251196.8
3.17-40.21532630.1501256198.09
4-22.550.22222710.1581274597.76
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramtophcsdx.pro
X-RAY DIFFRACTION2param19x.hemetoph19x.pro
X-RAY DIFFRACTION3tip3p.parametertoph19x.heme
X-RAY DIFFRACTION4tip3p.topology
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 22.5 Å / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.12
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.82
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.898

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