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Basic information

Entry
Database: PDB / ID: 1hdb
TitleANALYSIS OF THE CRYSTAL STRUCTURE, MOLECULAR MODELING AND INFRARED SPECTROSCOPY OF THE DISTAL BETA-HEME POCKET VALINE67(E11)-THREONINE MUTATION OF HEMOGLOBIN
Components(HEMOGLOBIN (DEOXY) BETA-V67T) x 2
KeywordsOXYGEN TRANSPORT / HUMAN HEMOGLOBIN / DEOXY-BETA-V67T
Function / homology
Function and homology information


: / haptoglobin binding / organic acid binding / nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex ...: / haptoglobin binding / organic acid binding / 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 / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / peroxidase activity / response to hydrogen peroxide / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / 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 alpha / Hemoglobin subunit beta / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsPechik, I. / Ji, X. / Fronticelli, C. / Gilliland, G.L.
Citation
Journal: Biochemistry / Year: 1996
Title: Crystallographic, molecular modeling, and biophysical characterization of the valine beta 67 (E11)-->threonine variant of hemoglobin.
Authors: Pechik, I. / Ji, X. / Fidelis, K. / Karavitis, M. / Moult, J. / Brinigar, W.S. / Fronticelli, C. / Gilliland, G.L.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Oxygen Affinity Modulation by the N-Termini of the Beta-Chains in Human and Bovine Hemoglobin
Authors: Fronticelli, C. / Pechik, I. / Brinigar, W.S. / Gryczynski, Z. / Gilliland, G.L.
History
DepositionApr 14, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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 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 (DEOXY) BETA-V67T
B: HEMOGLOBIN (DEOXY) BETA-V67T
C: HEMOGLOBIN (DEOXY) BETA-V67T
D: HEMOGLOBIN (DEOXY) BETA-V67T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,74310
Polymers62,0854
Non-polymers2,6586
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11670 Å2
ΔGint-133 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.540, 83.190, 54.020
Angle α, β, γ (deg.)90.00, 99.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HEMOGLOBIN (DEOXY) BETA-V67T / HBV67T


Mass: 15150.353 Da / Num. of mol.: 2 / Mutation: CHAIN B, D, V67T
Source method: isolated from a genetically manipulated source
Details: ALPHA-BETA-ALPHA-BETA TETRAMER / Source: (gene. exp.) Homo sapiens (human) / Gene: BETA-GLOBIN CDNA FUSED TO A / Plasmid: PJK05 (FRONTICELLI ET AL. 1 / Gene (production host): BETA-GLOBIN CDNA FUSED TO A / Production host: Escherichia coli (E. coli) / Strain (production host): AR120 / References: UniProt: P01922, UniProt: P69905*PLUS
#2: Protein HEMOGLOBIN (DEOXY) BETA-V67T / HBV67T


Mass: 15892.171 Da / Num. of mol.: 2 / Mutation: CHAIN B, D, V67T
Source method: isolated from a genetically manipulated source
Details: ALPHA-BETA-ALPHA-BETA TETRAMER / Source: (gene. exp.) Homo sapiens (human) / Gene: BETA-GLOBIN CDNA FUSED TO A / Plasmid: PJK05 (FRONTICELLI ET AL. 1 / Gene (production host): BETA-GLOBIN CDNA FUSED TO A / Production host: Escherichia coli (E. coli) / Strain (production host): AR120 / References: UniProt: P02023, UniProt: P68871*PLUS
#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.: 434 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal grow
*PLUS
pH: 6.5 / Method: batch method / Details: Perutz, M.F., (1968) J.Crystal Growth, 2, 54.
Components of the solutions
*PLUS
IDConc.Crystal-IDSol-IDChemical formula
14 M11(NH4)2SO4
22 M11(NH4)H2PO4
32 M11(NH4)HPO4

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Data collection

DetectorDate: Jul 4, 1994
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 27163 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 2.75 %
Reflection
*PLUS
Highest resolution: 2.2 Å / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
GPRLSArefinement
XENGENdata reduction
RefinementResolution: 2.2→6 Å / σ(F): 2 /
RfactorNum. reflection
obs0.149 21669
Displacement parametersBiso mean: 21.43 Å2
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 182 434 5000
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.025
X-RAY DIFFRACTIONp_angle_d0.0380.036
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.6761
X-RAY DIFFRACTIONp_mcangle_it1.141.5
X-RAY DIFFRACTIONp_scbond_it1.2791.5
X-RAY DIFFRACTIONp_scangle_it2.0312
X-RAY DIFFRACTIONp_plane_restr0.0230.03
X-RAY DIFFRACTIONp_chiral_restr0.1810.2
X-RAY DIFFRACTIONp_singtor_nbd0.1860.3
X-RAY DIFFRACTIONp_multtor_nbd0.1870.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1740.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.55
X-RAY DIFFRACTIONp_staggered_tor17.415
X-RAY DIFFRACTIONp_orthonormal_tor31.715
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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