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- PDB-1c7d: DEOXY RHB1.2 (RECOMBINANT HEMOGLOBIN) -

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Basic information

Entry
Database: PDB / ID: 1c7d
TitleDEOXY RHB1.2 (RECOMBINANT HEMOGLOBIN)
Components
  • PROTEIN (DEOXYHEMOGLOBIN (ALPHA CHAIN))
  • PROTEIN (DEOXYHEMOGLOBIN (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 / 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
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBrucker, E.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Genetically crosslinked hemoglobin: a structural study.
Authors: Brucker, E.A.
#1: Journal: Structure / Year: 1997
Title: Structures of a Hemoglobin-Based Blood Substitute: Insights Into the Function of Allosteric Proteins
Authors: Kroeger, K.S. / Kundrot, C.E.
#2: Journal: Nature / Year: 1992
Title: A Human Recombinant Haemoglobin 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
DepositionFeb 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 3, 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 1.5Aug 9, 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: PROTEIN (DEOXYHEMOGLOBIN (ALPHA CHAIN))
B: PROTEIN (DEOXYHEMOGLOBIN (BETA CHAIN))
D: PROTEIN (DEOXYHEMOGLOBIN (BETA CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7707
Polymers62,3043
Non-polymers2,4664
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10680 Å2
ΔGint-109 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.144, 83.282, 53.928
Angle α, β, γ (deg.)90.00, 99.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (DEOXYHEMOGLOBIN (ALPHA CHAIN))


Mass: 30428.895 Da / Num. of mol.: 1 / Mutation: V1M,142G,143G
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 PROTEIN (DEOXYHEMOGLOBIN (BETA CHAIN))


Mass: 15937.343 Da / Num. of mol.: 2 / Mutation: V1M,N108K
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 / Heme B


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


Mass: 18.015 Da / Num. of mol.: 244 / 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: 1.84 Å3/Da / Density % sol: 33.3 %
Crystal growpH: 6.5 / Details: PERUTZ, J.CRYST.GROWTH 2(1968)54-56, pH 6.5
Crystal grow
*PLUS
Method: batch method / pH: 7
Components of the solutions
*PLUS
Conc.: 10 mM / Common name: ammonium phosphate

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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: Dec 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: 1.8→30 Å / Num. obs: 45959 / % possible obs: 90.2 % / Redundancy: 2.91 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.86 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 4.42 / % possible all: 87.4
Reflection
*PLUS
Redundancy: 2.9 % / Num. measured all: 133741
Reflection shell
*PLUS
% possible obs: 87.4 % / Redundancy: 2.9 % / Mean I/σ(I) obs: 4.4

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Processing

Software
NameClassification
XDSdata scaling
XSCALEdata scaling
SHELXmodel building
SHELXL-97refinement
XDSdata reduction
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ABY

1aby


Resolution: 1.8→8 Å / Num. parameters: 19271 / Num. restraintsaints: 28895 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 2156 4.739 %RANDOM
all0.189 45496 --
obs0.1879 -90.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4802
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4396 0 172 244 4812
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.015
X-RAY DIFFRACTIONs_similar_dist0.02
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.034
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.07
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.188 / Lowest resolution: 8 Å / Num. reflection obs: 45496 / % reflection Rfree: 4.7 % / Rfactor obs: 0.189 / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_chiral_restr / Dev ideal: 0.034

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