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- PDB-1ljw: Crystal Structure of Human Carbonmonoxy Hemoglobin at 2.16 A: A S... -

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Basic information

Entry
Database: PDB / ID: 1ljw
TitleCrystal Structure of Human Carbonmonoxy Hemoglobin at 2.16 A: A Snapshot of the Allosteric Transition
Components
  • hemoglobin alpha chain
  • hemoglobin beta chain
KeywordsOXYGEN STORAGE/TRANSPORT / Hemoglobin / R state / Allosteric / Carbonmonoxy / 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 / PHOSPHATE ION / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.16 Å
AuthorsSafo, M.K. / Burnett, J.C. / Musayev, F.N. / Nokuri, S. / Abraham, D.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of human carbonmonoxyhemoglobin at 2.16 A: a snapshot of the allosteric transition.
Authors: Safo, M.K. / Burnett, J.C. / Musayev, F.N. / Nokuri, S. / Abraham, D.J.
History
DepositionApr 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 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 / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4257
Polymers31,0412
Non-polymers1,3845
Water4,702261
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)64,84914
Polymers62,0814
Non-polymers2,76810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area12110 Å2
ΔGint-132 kcal/mol
Surface area23690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.566, 53.566, 192.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-343-

HOH

21A-344-

HOH

31A-449-

HOH

DetailsAsymmetric unit contains a dimer and the second dimer of the biological assembly is generate by the two fold axis: 1-Y, 1-X, 1/2-Z

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Components

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Protein , 2 types, 2 molecules AB

#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) / Tissue: blood / References: UniProt: P69905
#2: Protein hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 1 / 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, 266 molecules

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


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#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.: 261 / 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: 2.15 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 6.4
Details: Potassium phosphate, Sodium phosphate, toluene, hemoglobin, pH 6.4, LIQUID DIFFUSION, temperature 298K
Crystal grow
*PLUS
Method: batch method / Details: Perutz, M.F., (1968) J. Cryst. Growth, 2, 54.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140 mg/mlprotein11
23.4 Msodium potassium phosphate11pH6.4
32.35-2.65 Mphosphate11

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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: Feb 21, 2001 / 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: 2.16→60 Å / Num. all: 14444 / Num. obs: 14444 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 17.3
Reflection shellResolution: 2.16→2.26 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1229 / % possible all: 62.6
Reflection
*PLUS
Lowest resolution: 60 Å / Num. obs: 14441 / % possible obs: 90.2 % / Num. measured all: 44267
Reflection shell
*PLUS
% possible obs: 92.6 % / Num. unique obs: 1229 / Num. measured obs: 2856

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Processing

Software
NameClassification
bioteXdata collection
bioteXdata reduction
CNSrefinement
bioteXdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2HCO

2hco


Resolution: 2.16→60 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 718 -random
Rwork0.194 ---
all0.205 14444 --
obs0.205 14444 100 %-
Displacement parametersBiso mean: 34.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.18 Å
Refinement stepCycle: LAST / Resolution: 2.16→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 95 261 2548
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d19.8
X-RAY DIFFRACTIONx_improper_angle_d1.34
LS refinement shellResolution: 2.16→2.21 Å
RfactorNum. reflection% reflection
Rfree0.345 32 -
Rwork0.245 --
obs-718 60.4 %
Refinement
*PLUS
Lowest resolution: 60 Å / Num. reflection Rfree: 679 / % reflection Rfree: 5 % / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34
LS refinement shell
*PLUS
Lowest resolution: 2.22 Å / Rfactor Rwork: 0.235 / Rfactor obs: 0.235

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