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- PDB-7k4m: Crystal structure of MetAP2 Modified Hemoglobin S -

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Basic information

Entry
Database: PDB / ID: 7k4m
TitleCrystal structure of MetAP2 Modified Hemoglobin S
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / HEMOGLOBIN S / INHIBITOR / ANTISICKLING
Function / homology
Function and homology information


nitric oxide transport / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / hydrogen peroxide catabolic process / oxygen carrier activity ...nitric oxide transport / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / hydrogen peroxide catabolic process / oxygen carrier activity / 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 / peroxidase activity / blood microparticle / iron ion binding / heme binding / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsMusayev, F.N. / Safo, M.K. / Light, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)S10OD021756 United States
CitationJournal: Blood Adv / Year: 2021
Title: MetAP2 inhibition modifies hemoglobin S to delay polymerization and improves blood flow in sickle cell disease.
Authors: Demers, M. / Sturtevant, S. / Guertin, K.R. / Gupta, D. / Desai, K. / Vieira, B.F. / Li, W. / Hicks, A. / Ismail, A. / Goncalves, B.P. / Di Caprio, G. / Schonbrun, E. / Hansen, S. / Musayev, ...Authors: Demers, M. / Sturtevant, S. / Guertin, K.R. / Gupta, D. / Desai, K. / Vieira, B.F. / Li, W. / Hicks, A. / Ismail, A. / Goncalves, B.P. / Di Caprio, G. / Schonbrun, E. / Hansen, S. / Musayev, F.N. / Safo, M.K. / Wood, D.K. / Higgins, J.M. / Light, D.R.
History
DepositionSep 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta
I: Hemoglobin subunit alpha
J: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,91229
Polymers156,49510
Non-polymers6,41719
Water6,738374
1
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)65,17612
Polymers62,5984
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12010 Å2
ΔGint-117 kcal/mol
Surface area23050 Å2
MethodPISA
2
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
hetero molecules

E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,12010
Polymers62,5984
Non-polymers2,5226
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11200 Å2
ΔGint-104 kcal/mol
Surface area23940 Å2
MethodPISA
3
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta
I: Hemoglobin subunit alpha
J: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,17612
Polymers62,5984
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11430 Å2
ΔGint-110 kcal/mol
Surface area23080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.844, 53.846, 195.640
Angle α, β, γ (deg.)90.000, 91.730, 90.000
Int Tables number5
Space group name H-MI121

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Components

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


Mass: 15281.550 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein
Hemoglobin subunit beta


Mass: 16017.451 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Details: BETA_GLOBIN / Source: (natural) Homo sapiens (human) / References: UniProt: A0A481SHK9
#3: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 6.6 / Details: 0.2M Na acetate/0.1M Na cacodylate, 30% PEG-8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 18, 2018 / Details: Varimax-HF Arc Optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.5→29.07 Å / Num. obs: 49161 / % possible obs: 99.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 43.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.045 / Rrim(I) all: 0.096 / Net I/σ(I): 13.6 / Num. measured all: 215997 / Scaling rejects: 48
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.584.40.78144810.7770.4180.88999.8
2.58-2.684.444780.77599.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.03 Å29.3 Å
Translation7.03 Å29.3 Å

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Processing

Software
NameVersionClassification
CrysalisPro41_64.69adata collection
Aimless0.5.32data scaling
PHASER2.5.6phasing
PHENIX1.9-1692refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BBB

1bbb


Resolution: 2.5→29.067 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3228 2588 5.28 %
Rwork0.2387 46473 -
obs0.2433 49061 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.14 Å2 / Biso mean: 54.8417 Å2 / Biso min: 14.29 Å2
Refinement stepCycle: final / Resolution: 2.5→29.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10854 0 448 374 11676
Biso mean--51.81 47.35 -
Num. residues----1428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811675
X-RAY DIFFRACTIONf_angle_d1.38415985
X-RAY DIFFRACTIONf_chiral_restr0.0431749
X-RAY DIFFRACTIONf_plane_restr0.0061989
X-RAY DIFFRACTIONf_dihedral_angle_d15.9843951
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.54810.4561310.2982256199
2.5481-2.60.38871430.28912545100
2.6-2.65650.4421280.28972556100
2.6565-2.71830.38131380.29672573100
2.7183-2.78620.4821100.28472626100
2.7862-2.86150.46231400.29842567100
2.8615-2.94560.40691420.32182541100
2.9456-3.04060.40041460.31522531100
3.0406-3.14910.31911530.29142602100
3.1491-3.27510.3641830.26782498100
3.2751-3.42390.33281380.26012627100
3.4239-3.60410.42051540.2705256099
3.6041-3.82950.27961450.22172595100
3.8295-4.12440.33521110.2281259699
4.1244-4.5380.31521390.2087259899
4.538-5.19140.27971520.21522604100
5.1914-6.52840.31231660.23632612100
6.5284-29.0670.19311690.155268199

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