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- PDB-1buw: CRYSTAL STRUCTURE OF S-NITROSO-NITROSYL HUMAN HEMOGLOBIN A -

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Basic information

Entry
Database: PDB / ID: 1buw
TitleCRYSTAL STRUCTURE OF S-NITROSO-NITROSYL HUMAN HEMOGLOBIN A
Components(PROTEIN (HEMOGLOBIN)) x 2
KeywordsOXYGEN STORAGE/TRANSPORT / OXYGEN TRANSPORT AND VASODILATION / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


haptoglobin binding / : / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex ...haptoglobin binding / : / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / peroxidase activity / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / 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 family profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / Hemoglobin subunit beta / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.9 Å
AuthorsChan, N.-L. / Rogers, P.H. / Arnone, A.
CitationJournal: Biochemistry / Year: 1998
Title: Crystal structure of the S-nitroso form of liganded human hemoglobin.
Authors: Chan, N.L. / Rogers, P.H. / Arnone, A.
History
DepositionSep 6, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (HEMOGLOBIN)
B: PROTEIN (HEMOGLOBIN)
C: PROTEIN (HEMOGLOBIN)
D: PROTEIN (HEMOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,72512
Polymers62,1394
Non-polymers2,5868
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11150 Å2
ΔGint-118 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.100, 101.200, 61.100
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: (0.202601, -0.326635, 0.923181), (-0.333979, -0.909257, -0.248414), (0.920549, -0.257994, -0.293305)
Vector: 39.80348, 43.16976, 33.84707)

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Components

#1: Protein PROTEIN (HEMOGLOBIN) / S-NITROSO-NITROSYLHB


Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: OUDATED BLOOD DRAWN FROM HEALTHY NON-SMOKER. / Source: (natural) Homo sapiens (human) / Cell: RED BLOOD CELL / References: UniProt: P69905
#2: Protein PROTEIN (HEMOGLOBIN) / S-NITROSO-NITROSYLHB


Mass: 15919.196 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: OUDATED BLOOD DRAWN FROM HEALTHY NON-SMOKER. / Source: (natural) Homo sapiens (human) / Cell: RED BLOOD CELL / References: UniProt: P02023, UniProt: P68871*PLUS
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS STRUCTURE PROVIDES THE FIRST DIRECT VISUALIZATION OF AN S-NITROSYLATED PROTEIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49.06 %
Crystal growpH: 5.8
Details: 1% PROTEIN 100 MM SODIUM CACODYLATE, PH 5.8 16% PEG 6000
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Silva, M.M., (1992) J. Biol. Chem., 267, 17248.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 %protein solution1reservoir
2100 mMcacodylate1reservoirtitrating sodium cacodylate with HCl to pH5.8
316 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Apr 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→20 Å / Num. obs: 55671 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rsym value: 0.07 / Net I/σ(I): 17
Reflection shellResolution: 1.77→1.9 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.25 / % possible all: 77
Reflection
*PLUS
% possible obs: 93 % / Num. measured all: 273695 / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1BBB

1bbb


Resolution: 1.9→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.244 5063 10 %EVERY 10TH REFLECTION
Rwork0.184 ---
obs0.184 55671 93 %-
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4342 0 180 196 4718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
Software
*PLUS
Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.010.01
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_planar_d0.0370.03
X-RAY DIFFRACTIONx_plane_restr0.010.01
X-RAY DIFFRACTIONx_chiral_restr0.1190.08

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