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- PDB-1o1k: Deoxy hemoglobin (A,C:V1M; B,D:V1M,V67W) -

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Basic information

Entry
Database: PDB / ID: 1o1k
TitleDeoxy hemoglobin (A,C:V1M; B,D:V1M,V67W)
Components
  • Hemoglobin Alpha chain
  • Hemoglobin Beta chain
KeywordsOXYGEN STORAGE/TRANSPORT / HEME / OXYGEN DELIVERY VEHICLE / BLOOD SUBSTITUTE / 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 / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / 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 / Late endosomal microautophagy / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / response to hydrogen peroxide / 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 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 / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBrucker, E.A.
Citation
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Genetically Crosslinked Hemoglobin: A Structural Study
Authors: Brucker, E.A.
#2: Journal: NAT.BIOTECHNOL. / Year: 1998
Title: Rate of Reaction with Nitric Oxide Determines the Hypertensive Effect of Cell-Free Hemoglobin
Authors: Doherty, D.H. / Doyle, M.P. / Curry, S.R. / Vali, R.J. / Fattor, T.J. / Olson, J.S. / Lemon, D.D.
#3: Journal: Nature / Year: 1992
Title: A Human Recombinant Hemoglobin Designed for Use as a Blood Substitute
Authors: Looker, D. / Abbot-Brown, D. / Cozart, P. / Durfee, S. / Hoffman, S. / Mathews, A.J. / Miller-Roehrich, J. / Shoemaker, S. / Trimble, S. / Fermi, G. / Komiyama, N.H. / Nagai, K. / Stetler, G.L.
History
DepositionNov 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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.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_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

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)64,8498
Polymers62,3844
Non-polymers2,4664
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11140 Å2
ΔGint-101 kcal/mol
Surface area23580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.470, 83.627, 53.644
Angle α, β, γ (deg.)90.00, 99.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemoglobin Alpha chain / DEOXYHEMOGLOBIN ALPHA CHAIN


Mass: 15182.419 Da / Num. of mol.: 2 / Mutation: V1M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: RED BLOOD CELL / Production host: Escherichia coli (E. coli) / References: UniProt: P69905
#2: Protein Hemoglobin Beta chain / DEOXYHEMOGLOBIN BETA CHAIN


Mass: 16009.343 Da / Num. of mol.: 2 / Mutation: V1M, V67W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: RED BLOOD CELL / Production host: Escherichia coli (E. coli) / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.11 Å3/Da / Density % sol: 41.23 %
Crystal growpH: 6.5 / Details: pH 6.50

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 15, 1998 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 26599 / % possible obs: 71 % / Redundancy: 2.17 % / Biso Wilson estimate: 5.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 3.68 / % possible all: 75.9

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Processing

Software
NameClassification
XDSdata scaling
XSCALEdata scaling
CNSrefinement
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C7C

1c7c


Resolution: 2→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1185 4.854 %random
Rwork0.216 ---
obs-24412 66.2 %-
Displacement parametersBiso mean: 18.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-8 Å
Luzzati sigma a0.3 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 172 202 4760
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.521.5
X-RAY DIFFRACTIONc_mcangle_it3.232
X-RAY DIFFRACTIONc_scbond_it3.862
X-RAY DIFFRACTIONc_scangle_it5.232.5
Refine LS restraints NCSNCS model details: RESTRAINED / Rms dev position: 0.028 Å
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.33 158 4.779 %
Rwork0.3 3148 -
obs--72.6 %

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