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- PDB-1a00: HEMOGLOBIN (VAL BETA1 MET, TRP BETA37 TYR) MUTANT -

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Basic information

Entry
Database: PDB / ID: 1a00
TitleHEMOGLOBIN (VAL BETA1 MET, TRP BETA37 TYR) MUTANT
Components
  • HEMOGLOBIN (ALPHA CHAIN)
  • HEMOGLOBIN (BETA CHAIN)
KeywordsOXYGEN TRANSPORT
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 / ISOMORPHOUS WITH DEOXYHEMOGLOBIN A / Resolution: 2 Å
AuthorsKavanaugh, J.S. / Arnone, A.
Citation
Journal: Biochemistry / Year: 1998
Title: High-resolution crystal structures of human hemoglobin with mutations at tryptophan 37beta: structural basis for a high-affinity T-state,.
Authors: Kavanaugh, J.S. / Weydert, J.A. / Rogers, P.H. / Arnone, A.
#1: Journal: Biochemistry / Year: 1992
Title: High-Resolution X-Ray Study of Deoxyhemoglobin Rothschild 37 Beta Trp-->Arg: A Mutation that Creates an Intersubunit Chloride-Binding Site
Authors: Kavanaugh, J.S. / Rogers, P.H. / Case, D.A. / Arnone, A.
History
DepositionDec 8, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: 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
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 2, 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 (ALPHA CHAIN)
B: HEMOGLOBIN (BETA CHAIN)
C: HEMOGLOBIN (ALPHA CHAIN)
D: HEMOGLOBIN (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5658
Polymers62,0994
Non-polymers2,4664
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11230 Å2
ΔGint-105 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.100, 112.000, 63.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.95067, -0.05056, 0.30605), (-0.0512, -0.99867, -0.00594), (0.30594, -0.01002, -0.952)
Vector: 5.59928, 90.78605, -20.34795)

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Components

#1: Protein HEMOGLOBIN (ALPHA CHAIN)


Mass: 15150.353 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: RED BLOOD CELL / Gene: HUMAN BETA GLOBIN / Organ: BLOOD / Gene (production host): HUMAN BETA GLOBIN / Production host: Escherichia coli (E. coli) / References: UniProt: P69905
#2: Protein HEMOGLOBIN (BETA CHAIN)


Mass: 15899.228 Da / Num. of mol.: 2 / Mutation: V1M, W37Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: RED BLOOD CELL / Gene: HUMAN BETA GLOBIN / Organ: BLOOD / Gene (production host): HUMAN BETA 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.: 216 / 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: 2.32 Å3/Da / Density % sol: 47 %
Description: BV1M STRUCTURE IN ENTRY 1A0Z WAS USED AS THE STARTING MODEL FOR RIGID BODY REFINEMENT WITH X-PLOR FOLLOWED BY LEAST-SQUARES REFINEMENT WITH PROLSQ.
Crystal growpH: 7
Details: 10.5% PEG 6000 10 MM POTASSIUM PHOSPHATE PH 7.0 100 MM POTASSIUM CHLORIDE 3 MM SODIUM DITHIONITE
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMpotassium phosphate11
2100 mM11KCl
33 mMsodium dithionite11
410.0 %PEG600011
510 mg/mlhemoglobin11

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Oct 31, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 40226 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 8.6
Reflection shellResolution: 2→2.15 Å / Redundancy: 3 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 2.24 / Rsym value: 0.191 / % possible all: 86.3
Reflection
*PLUS
Num. measured all: 237463

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Processing

Software
NameClassification
PROLSQrefinement
SDMSdata reduction
SDMSdata scaling
RefinementMethod to determine structure: ISOMORPHOUS WITH DEOXYHEMOGLOBIN A
Starting model: BV1M STRUCTURE, PDB ENTRY 1A0Z.

1a0z


Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE STARTING MODEL FOR REFINEMENT WAS THE BV1M STRUCTURE IN PDB ENTRY 1A0Z.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 3470 10 %RANDOM
Rwork0.169 ---
all-44641 --
obs-34844 97.1 %-
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 172 216 4770
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.01
X-RAY DIFFRACTIONp_angle_d0.030.015
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0490.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.62
X-RAY DIFFRACTIONp_mcangle_it3.53
X-RAY DIFFRACTIONp_scbond_it8.84
X-RAY DIFFRACTIONp_scangle_it12.36
X-RAY DIFFRACTIONp_plane_restr0.0130.01
X-RAY DIFFRACTIONp_chiral_restr0.1430.08
X-RAY DIFFRACTIONp_singtor_nbd0.1720.2
X-RAY DIFFRACTIONp_multtor_nbd0.1680.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1750.2
X-RAY DIFFRACTIONp_planar_tor2.85
X-RAY DIFFRACTIONp_staggered_tor20.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.425
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS

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