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- PDB-1ch4: MODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA (F133V) -

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Basic information

Entry
Database: PDB / ID: 1ch4
TitleMODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA (F133V)
ComponentsMODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA
KeywordsOXYGEN TRANSPORT / CHIMERA PROTEIN / RESPIRATORY PROTEIN / HEME
Function / homology
Function and homology information


nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / 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 / 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 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / cytosol
Similarity search - Function
Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShirai, T. / Fujikake, M. / Yamane, T. / Inaba, K. / Ishimori, K. / Morishima, I.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of a protein with an artificial exon-shuffling, module M4-substituted chimera hemoglobin beta alpha, at 2.5 A resolution.
Authors: Shirai, T. / Fujikake, M. / Yamane, T. / Inaba, K. / Ishimori, K. / Morishima, I.
#1: Journal: Proteins / Year: 1998
Title: Design, Construction, Crystallization, and Preliminary X-Ray Studies of a Fine-Tuning Mutant (F133V) of Module-Substituted Chimera Hemoglobin
Authors: Shirai, T. / Fujikake, M. / Yamane, T. / Inaba, K. / Ishimori, K. / Morishima, I.
History
DepositionJun 11, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA
B: MODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA
C: MODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA
D: MODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,82712
Polymers63,2494
Non-polymers2,5788
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12980 Å2
ΔGint-118 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.870, 81.310, 55.110
Angle α, β, γ (deg.)90.00, 90.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.908143, -0.144029, -0.393105), (-0.137863, -0.783712, 0.605631), (-0.39531, 0.604194, 0.691867)
Vector: 36.64821, -4.80501, 10.26913)
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT IS THE CHIMERA-TETRAMER.

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Components

#1: Protein
MODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA


Mass: 15812.229 Da / Num. of mol.: 4 / Mutation: F133V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P68871*PLUS
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Details: Shirai, T., (1998) Proteins: Struct.,Funct., Genet., 32, 263.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 %(w/v)PEG40001reservoir
20.1 Msodium potassium phosphate1reservoir
30.600 mMprotein1drop
450 mMsodium phosphate1drop

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Oct 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 17766 / % possible obs: 91.2 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 5.6
Reflection shellResolution: 2.5→2.59 Å / % possible all: 82.5

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CN-HEMOGLOBIN H

Resolution: 2.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 3
Details: THIS PROTEIN WAS CONSTRUCTED BY REPLACING MODULE M4, 97(FG4)-146(HC3), OF BETA-SUBUNIT OF HUMAN HEMOGLOBIN WITH THE CORRESPONDING REGION, 92(FG4)-141(HC3), OF THE ALPHA-SUBUNIT. A POINT ...Details: THIS PROTEIN WAS CONSTRUCTED BY REPLACING MODULE M4, 97(FG4)-146(HC3), OF BETA-SUBUNIT OF HUMAN HEMOGLOBIN WITH THE CORRESPONDING REGION, 92(FG4)-141(HC3), OF THE ALPHA-SUBUNIT. A POINT MUTATION F133V(H11) WAS INTRODUCED TO INCREASE THE STABILITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 787 5 %RANDAM
Rwork0.188 ---
obs0.188 15212 81.4 %-
Displacement parametersBiso mean: 27.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 7 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4528 0 180 42 4750
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.646
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.475
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
Refine LS restraints NCSNCS model details: STRICT
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.906
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.475

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