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- PDB-1rvw: R STATE HUMAN HEMOGLOBIN [ALPHA V96W], CARBONMONOXY -

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Basic information

Entry
Database: PDB / ID: 1rvw
TitleR STATE HUMAN HEMOGLOBIN [ALPHA V96W], CARBONMONOXY
Components(HEMOGLOBIN) x 2
KeywordsOXYGEN TRANSPORT / HEMOGLOBIN / HUMAN / MUTANT / ALPHA-(V96W) / CARBONMONOXY
Function / homology
Function and homology information


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 ...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 / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.5 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn_type.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 1.5Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMOGLOBIN
B: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5127
Polymers31,1282
Non-polymers1,3845
Water45025
1
A: HEMOGLOBIN
B: HEMOGLOBIN
hetero molecules

A: HEMOGLOBIN
B: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,02314
Polymers62,2554
Non-polymers2,76810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)54.282, 54.282, 194.122
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-142-

PO4

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 15237.433 Da / Num. of mol.: 1 / Mutation: CHAIN A, V96W
Source method: isolated from a genetically manipulated source
Details: CARBONMONXY HEMES / 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.: 1 / Mutation: CHAIN A, V96W
Source method: isolated from a genetically manipulated source
Details: CARBONMONXY HEMES / Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Cell: ERYTHROCYTE / Plasmid: PHE2 / Production host: Escherichia coli (E. coli) / References: UniProt: P68871

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Non-polymers , 4 types, 30 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal grow
*PLUS
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

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: 2.5→25 Å / Num. obs: 9340 / % possible obs: 86.7 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065
Reflection shellResolution: 2.5→2.61 Å / % possible all: 75.7
Reflection shell
*PLUS
% possible obs: 75.7 % / Num. unique obs: 993

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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 1HHO

1hho


Resolution: 2.5→25 Å / σ(F): 0 / Details: ISOTROPIC SOLVENT MASK
RfactorNum. reflection% reflection
Rwork0.167 --
obs0.167 9340 86.7 %
Displacement parametersBiso mean: 33.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 95 25 2319
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.3
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: 2.5→2.61 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.241 993 -
obs--75.7 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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