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- PDB-1j3z: Direct observation of photolysis-induced tertiary structural chan... -

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Basic information

Entry
Database: PDB / ID: 1j3z
TitleDirect observation of photolysis-induced tertiary structural changes in human haemoglobin; Crystal structure of alpha(Fe-CO)-beta(Ni) hemoglobin (laser unphotolysed)
Components
  • Hemoglobin alpha Chain
  • Hemoglobin beta Chain
KeywordsOXYGEN STORAGE/TRANSPORT / Tertiary structure changes / Crystal photolysis / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


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 ...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 / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / response to hydrogen peroxide / carbon dioxide transport / 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
BUT-2-ENEDIAL / CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / PROTOPORPHYRIN IX CONTAINING NI(II) / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAdachi, S. / Park, S.-Y. / Tame, J.R.H. / Shiro, Y. / Shibayama, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Direct observation of photolysis-induced tertiary structural changes in hemoglobin
Authors: Adachi, S. / Park, S.-Y. / Tame, J.R.H. / Shiro, Y. / Shibayama, N.
History
DepositionFeb 21, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_chiral / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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: Hemoglobin alpha Chain
B: Hemoglobin beta Chain
C: Hemoglobin alpha Chain
D: Hemoglobin beta Chain
E: Hemoglobin alpha Chain
F: Hemoglobin beta Chain
G: Hemoglobin alpha Chain
H: Hemoglobin beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,38622
Polymers124,1628
Non-polymers5,22314
Water24,0501335
1
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)64,69311
Polymers62,0814
Non-polymers2,6127
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12120 Å2
ΔGint-101 kcal/mol
Surface area23120 Å2
MethodPISA
2
E: Hemoglobin alpha Chain
F: Hemoglobin beta Chain
G: Hemoglobin alpha Chain
H: Hemoglobin beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,69311
Polymers62,0814
Non-polymers2,6127
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12040 Å2
ΔGint-97 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.057, 93.702, 99.209
Angle α, β, γ (deg.)90.00, 101.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Hemoglobin alpha Chain


Mass: 15150.353 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein
Hemoglobin beta Chain


Mass: 15890.198 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 5 types, 1349 molecules

#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-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#5: Chemical
ChemComp-HNI / PROTOPORPHYRIN IX CONTAINING NI(II)


Mass: 619.336 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32N4NiO4
#6: Chemical ChemComp-2FU / BUT-2-ENEDIAL


Mass: 84.073 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1335 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 293 K / pH: 6.6
Details: PEG 4000, 50mM citrate-ammonium buffer, SMALL TUBES, temperature 293K, pH 6.60
Crystal grow
*PLUS
pH: 6.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11-2 %(w/v)CO-saturated11
218 %(w/v)PEG335011
30.15 M11K2SO4
45 mMhomocysteine11
550 mMcitrate-ammonium11pH6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 20, 2002 / Details: MONOCHROMATOR
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 144674 / % possible obs: 94.4 % / Observed criterion σ(I): 26 / Redundancy: 3 % / Rmerge(I) obs: 0.035
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.096 / % possible all: 83.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 437187
Reflection shell
*PLUS
% possible obs: 83.9 %

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.505 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.196 7181 5 %RANDOM
Rwork0.159 ---
obs0.161 144674 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å2-0.42 Å2
2---0.59 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8768 0 364 1335 10467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0219430
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2962.03212908
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.87651140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.21468
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027060
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.24859
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2942
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.2112
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.274
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6681.55716
X-RAY DIFFRACTIONr_mcangle_it1.29129140
X-RAY DIFFRACTIONr_scbond_it2.20233714
X-RAY DIFFRACTIONr_scangle_it3.4654.53768
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.217 440
Rwork0.176 8934
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.312

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