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- PDB-1gbu: DEOXY (BETA-(C93A,C112G)) HUMAN HEMOGLOBIN -

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Basic information

Entry
Database: PDB / ID: 1gbu
TitleDEOXY (BETA-(C93A,C112G)) HUMAN HEMOGLOBIN
Components(HEMOGLOBIN) x 2
KeywordsOXYGEN TRANSPORT / HEMOGLOBIN / HUMAN / MUTANT / BETA-(C93A / C112G) / DEOXY / DEOXY HEMOGLOBIN
Function / homology
Function and homology information


Heme assimilation / 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 ...Heme assimilation / 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 / erythrocyte development / endocytic vesicle lumen / blood vessel diameter maintenance / oxygen carrier activity / hydrogen peroxide catabolic process / 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 / Cytoprotection by HMOX1 / Late endosomal microautophagy / 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
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsVasquez, G.B. / Ji, X. / Fronticelli, C. / Gilliland, G.L.
CitationJournal: Biophys.J. / Year: 1999
Title: Cysteines beta93 and beta112 as probes of conformational and functional events at the human hemoglobin subunit interfaces.
Authors: Vasquez, G.B. / Karavitis, M. / Ji, X. / Pechik, I. / Brinigar, W.S. / Gilliland, G.L. / Fronticelli, C.
History
DepositionJan 4, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software / Item: _pdbx_database_status.process_site / _software.name
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 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMOGLOBIN
B: HEMOGLOBIN
C: HEMOGLOBIN
D: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,58310
Polymers61,9254
Non-polymers2,6586
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11620 Å2
ΔGint-130 kcal/mol
Surface area23350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.020, 82.940, 53.830
Angle α, β, γ (deg.)90.00, 99.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HEMOGLOBIN / T[BETA-(C93A / C112G)]


Mass: 15150.353 Da / Num. of mol.: 2 / Mutation: CHAIN B, D, C93A, C112G
Source method: isolated from a genetically manipulated source
Details: DEOXY / Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD
Description: THE BETA CHAINS WERE RECOMBINANT, BUT THE ALPHA CHAINS WERE PURIFIED FROM OUTDATED BLOOD OBTAINED FROM THE BLOOD BANK OF THE UNIVERSITY OF MARYLAND
Cell: ERYTHROCYTE / Organ: BLOOD / Plasmid: PJK05 / Production host: Escherichia coli (E. coli) / References: UniProt: P69905
#2: Protein HEMOGLOBIN / T[BETA-(C93A / C112G)]


Mass: 15812.042 Da / Num. of mol.: 2 / Mutation: CHAIN B, D, C93A, C112G
Source method: isolated from a genetically manipulated source
Details: DEOXY / Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD
Description: THE BETA CHAINS WERE RECOMBINANT, BUT THE ALPHA CHAINS WERE PURIFIED FROM OUTDATED BLOOD OBTAINED FROM THE BLOOD BANK OF THE UNIVERSITY OF MARYLAND
Cell: ERYTHROCYTE / Organ: BLOOD / Plasmid: PJK05 / 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.3 % / Description: THE TOTAL NUMBER OF REFLECTIONS IS 131074.
Crystal grow
*PLUS
pH: 6.5 / Method: unknown / Details: Perutz, M.F., (1968) J. Crystal Growth, 2, 54.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 Mammonium sulfate11
22 M11(NH4)H2PO4
32 M11(NH4)2HPO4

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 20, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→6 Å / Num. obs: 41926 / % possible obs: 82.7 % / Observed criterion σ(I): 1 / Redundancy: 3.13 % / Rsym value: 0.08 / Net I/σ(I): 1.1
Reflection
*PLUS
Observed criterion σ(I): 1.1 / Redundancy: 3.1 % / Num. measured all: 131074 / Rmerge(I) obs: 0.08

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Processing

Software
NameClassification
PROLSQrefinement
GPRLSArefinement
XENGENdata reduction
RefinementResolution: 1.8→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.167 --
obs-41926 82.7 %
Displacement parametersBiso mean: 20.51 Å2
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 174 454 5006
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0380.036
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0450.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.981
X-RAY DIFFRACTIONp_mcangle_it1.4651.5
X-RAY DIFFRACTIONp_scbond_it1.8811.5
X-RAY DIFFRACTIONp_scangle_it2.7792
X-RAY DIFFRACTIONp_plane_restr0.0240.03
X-RAY DIFFRACTIONp_chiral_restr0.2330.2
X-RAY DIFFRACTIONp_singtor_nbd0.1910.3
X-RAY DIFFRACTIONp_multtor_nbd0.1840.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2280.3
X-RAY DIFFRACTIONp_planar_tor3.55
X-RAY DIFFRACTIONp_staggered_tor18.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor3215
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
σ(F): 2 / Rfactor obs: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04

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