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- PDB-1bzz: HEMOGLOBIN (ALPHA V1M) MUTANT -

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Basic information

Entry
Database: PDB / ID: 1bzz
TitleHEMOGLOBIN (ALPHA V1M) MUTANT
Components
  • PROTEIN (HEMOGLOBIN ALPHA CHAIN)
  • PROTEIN (HEMOGLOBIN BETA CHAIN)
KeywordsOXYGEN STORAGE/TRANSPORT / OXYGEN TRANSPORT / OXYGEN STORAGE-TRANSPORT COMPLEX
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
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.59 Å
AuthorsKavanaugh, J.S. / Arnone, A.
CitationJournal: Biochemistry / Year: 1999
Title: Structural and functional properties of human hemoglobins reassembled after synthesis in Escherichia coli.
Authors: Hui, H.L. / Kavanaugh, J.S. / Doyle, M.L. / Wierzba, A. / Rogers, P.H. / Arnone, A. / Holt, J.M. / Ackers, G.K. / Noble, R.W.
History
DepositionNov 4, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 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 1.4Aug 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 (HEMOGLOBIN ALPHA CHAIN)
B: PROTEIN (HEMOGLOBIN BETA CHAIN)
C: PROTEIN (HEMOGLOBIN ALPHA CHAIN)
D: PROTEIN (HEMOGLOBIN BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6118
Polymers62,1454
Non-polymers2,4664
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11380 Å2
ΔGint-107 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.300, 83.600, 53.800
Angle α, β, γ (deg.)90.00, 99.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.952619, 0.302211, -0.034444), (0.30337, 0.93582, -0.179465), (-0.022003, -0.181411, -0.983161)17.30281, 4.92311, 81.66702
2given(-0.952619, 0.302211, -0.034444), (0.30337, 0.93582, -0.179465), (-0.022003, -0.181411, -0.983161)17.30281, 4.92311, 81.66702

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Components

#1: Protein PROTEIN (HEMOGLOBIN ALPHA CHAIN)


Mass: 15182.419 Da / Num. of mol.: 2 / Mutation: V1M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: SYNTHETIC ALPHA GLOBIN GENE; / Cell: RED BLOOD CELL / Gene: HUMAN ALPHA GLOBIN / Gene (production host): HUMAN ALPHA GLOBIN / Production host: Escherichia coli (E. coli) / References: UniProt: P69905
#2: Protein PROTEIN (HEMOGLOBIN BETA CHAIN)


Mass: 15890.198 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: SYNTHETIC ALPHA GLOBIN GENE / Cell: RED BLOOD CELL / Gene: HUMAN ALPHA GLOBIN / Gene (production host): HUMAN ALPHA GLOBIN / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.19 Å3/Da / Density % sol: 44 %
Description: HBA STRUCTURE IN PDB FILE 1BZ0 WAS USED AS THE STARTING MODEL FOR RIGID BODY REFINEMENT WITH X-PLOR FOLLOWED BY LEAST-SQUARES REFINEMENT WITH PROLSQ.
Crystal growpH: 7
Details: 2.3 M AMMONIUM SULFATE 0.3 M AMMONIUM PHOSPHATE PH 6.5 10 MM FERROUS CITRATE, pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: microdialysis
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: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Sep 25, 1992
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.59→25 Å / Num. obs: 64636 / % possible obs: 88.7 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.0477 / Rsym value: 0.05477 / Net I/σ(I): 16.6
Reflection shellResolution: 1.59→1.72 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.1532 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.1532 / % possible all: 73.4
Reflection
*PLUS
Num. measured all: 448711
Reflection shell
*PLUS
% possible obs: 73.4 %

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: HBA STRUCTURE, PDB FILE 1BZ0.

1bz0


Resolution: 1.59→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE STARTING MODEL FOR REFINEMENT WAS THE HBA STRUCTURE IN PDB FILE 1BZ0. RIGID BODY REFINEMENT WITH X-PLOR WAS FOLLOWED BY LEAST-SQUARES REFINEMENT WITH PROLSQ
RfactorNum. reflection% reflectionSelection details
Rfree0.214 5777 10 %OTHER REFLECTIONS COMMON WITH THE TEST SET FOR PDB FILE 1BZ0 WERE SELECTED FOR THE TEST SET
Rwork0.163 ---
all-64010 --
obs-57534 88.7 %-
Displacement parametersBiso mean: 20.42 Å2
Refinement stepCycle: LAST / Resolution: 1.59→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 172 198 4756
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.01
X-RAY DIFFRACTIONp_angle_d0.0340.015
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0540.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.7572
X-RAY DIFFRACTIONp_mcangle_it3.8913
X-RAY DIFFRACTIONp_scbond_it8.6074
X-RAY DIFFRACTIONp_scangle_it12.3076
X-RAY DIFFRACTIONp_plane_restr0.0150.01
X-RAY DIFFRACTIONp_chiral_restr0.1560.08
X-RAY DIFFRACTIONp_singtor_nbd0.1720.2
X-RAY DIFFRACTIONp_multtor_nbd0.1620.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.150.2
X-RAY DIFFRACTIONp_planar_tor3.35
X-RAY DIFFRACTIONp_staggered_tor19.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.325
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_mcbond_it2
X-RAY DIFFRACTIONp_scbond_it4
X-RAY DIFFRACTIONp_mcangle_it3
X-RAY DIFFRACTIONp_scangle_it6

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