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- PDB-4rom: Deoxyhemoglobin in complex with imidazolylacryloyl derivatives -

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Basic information

Entry
Database: PDB / ID: 4rom
TitleDeoxyhemoglobin in complex with imidazolylacryloyl derivatives
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / allosteric / sickle cell disease / hemoglobin / high-affinity / low-affinity / oxygen / oxygen carrying
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 / 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
Chem-3U8 / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsOmar, A.M. / Mahran, M.A. / Ghatge, M.N. / Chowdhury, N. / Bamane, F.H.A. / El-Araby, M.E. / Abdulmalik, O. / Safo, M.K.
CitationJournal: Org.Biomol.Chem. / Year: 2015
Title: Identification of a novel class of covalent modifiers of hemoglobin as potential antisickling agents.
Authors: Omar, A.M. / Mahran, M.A. / Ghatge, M.S. / Chowdhury, N. / Bamane, F.H. / El-Araby, M.E. / Abdulmalik, O. / Safo, M.K.
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,41312
Polymers62,0814
Non-polymers3,3328
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12460 Å2
ΔGint-135 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.985, 78.922, 53.264
Angle α, β, γ (deg.)90.00, 98.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Hemoglobin subunit ... , 2 types, 4 molecules ACBD

#1: Protein Hemoglobin subunit alpha / / Alpha-globin / Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: blood / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / / Beta-globin / Hemoglobin beta chain / LVV-hemorphin-7 / Spinorphin


Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: blood / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 4 types, 557 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-3U8 / 4-{2-chloro-4-[3-(1H-imidazol-2-yl)propanoyl]phenoxy}butanoic acid


Mass: 336.770 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17ClN2O4
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE 3U8 LIGAND IS ATTACHED TO N ATOM OF VAL 1 TO FORM A COVALENT LINKAGE. THE LIGAND 3U8 REPRESENTS ...THE 3U8 LIGAND IS ATTACHED TO N ATOM OF VAL 1 TO FORM A COVALENT LINKAGE. THE LIGAND 3U8 REPRESENTS THE FINAL BOUND PRODUCT. THE STARTING MATERIAL FOR 3U8 LIGAND 4-{2-CHLORO-4-[(2E)-3-(1H-IMIDAZOL-2-yl)PROP-2-ENOYL]PHENOXY}BUTANOIC ACID HAS A DOUBLE BOND BETWEEN C18 AND C19 ATOM GROUPS

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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: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 6.8
Details: 3.2 M sulfate/phosphate precipitant, pH 6.8, LIQUID DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 12, 2014 / Details: mirrors
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→33.75 Å / Num. all: 40041 / Num. obs: 37044 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.64 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 22.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 5 / Num. unique all: 3482 / % possible all: 87.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→33.18 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1308218.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1856 5 %RANDOM
Rwork0.213 ---
obs0.213 37014 92.3 %-
all-37014 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.7894 Å2 / ksol: 0.381806 e/Å3
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.64 Å20 Å2-0.04 Å2
2--13.49 Å20 Å2
3----8.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→33.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 228 549 5161
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.342 218 5 %
Rwork0.306 4143 -
obs-4143 87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2water_rep.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3param19x_t.heme&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4k15&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5k15&_1_TOPOLOGY_INFILE_5

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