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- PDB-1o1m: Deoxy hemoglobin (A-GLYGLYGLY-C:V1M,L29F,H58Q B,D:V1M,V67W) -

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Basic information

Entry
Database: PDB / ID: 1o1m
TitleDeoxy hemoglobin (A-GLYGLYGLY-C:V1M,L29F,H58Q 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 / Heme signaling / Late endosomal microautophagy / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / response to hydrogen peroxide / 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: 1.85 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 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_database_remark ...database_2 / pdbx_database_remark / 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 / _pdbx_database_remark.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE HUMAN HEMOGLOBIN HAS TWO ALPHA CHAINS WHICH ARE CALLED CHAINS A AND C IN OTHER PDB FILES. ...SEQUENCE HUMAN HEMOGLOBIN HAS TWO ALPHA CHAINS WHICH ARE CALLED CHAINS A AND C IN OTHER PDB FILES. IN THIS ENTRY THE C-TERMINUS OF THE ALPHA-1 CHAIN AND THE N-TERMINUS OF THE ALPHA-2 CHAIN ARE GENETICALLY LINKED BY THREE GLYCINE RESIDUES TO FORM ONE COVALENTLY LINKED POLYPEPTIDE CHAIN. THESE THREE RESIDUES ARE HIGHLY DISORDERED, I.E. NOT DEFINED IN ELECTRON DENSITY. ALSO, THE INITIAL RESIDUE OF THE ALPHA-2 CHAIN, JUST AFTER THE GLYCINE LINKER, IS THE NATIVE VALINE, NOT A METHIONINE. THEREFORE, THE THREE GLYCINE LINKER IS NOT INCLUDED IN THESE COORDINATES, AND THE INITIAL RESIDUE OF THE ALPHA CHAIN(S) IS MODELED AS AN ALANINE.

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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
D: Hemoglobin Beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0197
Polymers62,5533
Non-polymers2,4664
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-108 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.481, 83.642, 53.516
Angle α, β, γ (deg.)90.00, 98.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemoglobin Alpha chain / DEOXYHEMOGLOBIN ALPHA CHAIN


Mass: 30533.941 Da / Num. of mol.: 1 / Mutation: V1M, L29F, H58Q
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.: 339 / 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: 1.85 Å3/Da / Density % sol: 33.5 %
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: 1.85→30 Å / Num. obs: 43765 / % possible obs: 92.7 % / Redundancy: 2.51 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 24.7
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 5.01 / % possible all: 93.7

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Processing

Software
NameClassification
SHELXL-97refinement
XSCALEdata scaling
CNSrefinement
XDSdata scaling
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1C7C

1c7c


Resolution: 1.85→8 Å / Num. parameters: 19681 / Num. restraintsaints: 23153 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2210 5.107 %RANDOM
all0.2 41057 --
obs0.198 -87 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91(1973) 201-228
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4895
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4407 0 172 339 4918
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.015
X-RAY DIFFRACTIONs_similar_dist0.005
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.037
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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