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- PDB-1vwt: T STATE HUMAN HEMOGLOBIN [ALPHA V96W], ALPHA AQUOMET, BETA DEOXY -

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Basic information

Entry
Database: PDB / ID: 1vwt
TitleT STATE HUMAN HEMOGLOBIN [ALPHA V96W], ALPHA AQUOMET, BETA DEOXY
Components(HEMOGLOBIN) x 2
KeywordsOXYGEN TRANSPORT / HEMOGLOBIN / HUMAN / MUTANT / ALPHA-(V96W) / DEOXY / DEOXY HEMOGLOBIN / MET HEMOGLOBIN
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 / DIFFERENCE FOURIER / Resolution: 1.9 Å
AuthorsPuius, Y.A. / Zou, M. / Ho, N.T. / Ho, C. / Almo, S.C.
Citation
Journal: Biochemistry / Year: 1998
Title: Novel water-mediated hydrogen bonds as the structural basis for the low oxygen affinity of the blood substitute candidate rHb(alpha 96Val-->Trp).
Authors: Puius, Y.A. / Zou, M. / Ho, N.T. / Ho, C. / Almo, S.C.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: A Novel Low Oxygen Affinity Recombinant Hemoglobin (Alpha96Val--> Trp): Switching Quaternary Structure without Changing the Ligation State
Authors: Kim, H.W. / Shen, T.J. / Sun, D.P. / Ho, N.T. / Madrid, M. / Ho, C.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Production of Unmodified Human Adult Hemoglobin in Escherichia Coli
Authors: Shen, T.J. / Ho, N.T. / Simplaceanu, V. / Zou, M. / Green, B.N. / Tam, M.F. / Ho, C.
History
DepositionMar 20, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)64,91310
Polymers62,2554
Non-polymers2,6586
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
ΔGint-140 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.271, 83.416, 53.799
Angle α, β, γ (deg.)90.00, 99.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HEMOGLOBIN / R HB (ALPHA 96 VAL -> TRP)


Mass: 15237.433 Da / Num. of mol.: 2 / Mutation: CHAIN A, C, V96W
Source method: isolated from a genetically manipulated source
Details: ALPHA AQUOMET, BETA DEOXY / Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Cell: ERYTHROCYTE / Plasmid: PHE2 / Production host: Escherichia coli (E. coli) / References: UniProt: P69905
#2: Protein HEMOGLOBIN / R HB (ALPHA 96 VAL -> TRP)


Mass: 15890.198 Da / Num. of mol.: 2 / Mutation: CHAIN A, C, V96W
Source method: isolated from a genetically manipulated source
Details: ALPHA AQUOMET, BETA DEOXY / Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Cell: ERYTHROCYTE / Plasmid: PHE2 / 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.: 243 / 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: 2.25 Å3/Da / Density % sol: 45.28 %

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 39687 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.067
Reflection shellResolution: 1.9→1.99 Å / % possible all: 75.8

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1DXU

1dxu


Resolution: 1.9→25 Å / σ(F): 0 / Details: ISOTROPIC SOLVENT MASK
RfactorNum. reflection% reflection
Rwork0.169 --
obs0.169 39687 91.3 %
Displacement parametersBiso mean: 21.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 184 241 4823
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.227 4102 -
obs--75.8 %

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