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- PDB-5e83: CRYSTAL STRUCTURE OF CARBONMONOXY HEMOGLOBIN S (LIGANDED SICKLE C... -

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Basic information

Entry
Database: PDB / ID: 5.0E+83
TitleCRYSTAL STRUCTURE OF CARBONMONOXY HEMOGLOBIN S (LIGANDED SICKLE CELL HEMOGLOBIN) COMPLEXED WITH GBT440, CO-CRYSTALLIZATION EXPERIMENT
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / MUTANT HUMAN HEMOGLOBIN S[BETAE6V] / R2 QUATERNARY STATE
Function / homology
Function and homology information


cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid 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 / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / 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 / ficolin-1-rich granule lumen / blood microparticle / 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 domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-5L7 / CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Unknown ligand / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPatskovska, L. / Patskovsky, Y. / Bonanno, J.B. / Almo, S.C.
CitationJournal: Br.J.Haematol. / Year: 2016
Title: GBT440 increases haemoglobin oxygen affinity, reduces sickling and prolongs RBC half-life in a murine model of sickle cell disease.
Authors: Oksenberg, D. / Dufu, K. / Patel, M.P. / Chuang, C. / Li, Z. / Xu, Q. / Silva-Garcia, A. / Zhou, C. / Hutchaleelaha, A. / Patskovska, L. / Patskovsky, Y. / Almo, S.C. / Sinha, U. / Metcalf, B.W. / Archer, D.R.
History
DepositionOct 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Aug 29, 2018Group: Data collection / Database references / Structure summary
Category: entity / struct_ref_seq_dif / Item: _entity.pdbx_mutation / _struct_ref_seq_dif.details
Revision 1.5Sep 27, 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 / struct_conn
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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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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)65,30217
Polymers62,0214
Non-polymers3,28113
Water7,188399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.777, 59.104, 170.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 143
2114C1 - 143
1124B1 - 148
2124D1 - 148

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.189167, 0.981702, 0.021821), (0.981764, -0.189512, 0.014997), (0.018858, 0.018586, -0.999649)11.52547, -14.73523, 42.12014

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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 / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / / Beta-globin / Hemoglobin beta chain


Mass: 15860.216 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 6 types, 412 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-5L7 / 2-methyl-3-({2-[1-(propan-2-yl)-1H-pyrazol-5-yl]pyridin-3-yl}methoxy)phenol


Mass: 323.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.17 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.1M HEPES, 25% PEG4000, PH 7.4, 40 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2013 / Details: MIRRORS
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 56423 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rsym value: 0.063 / Net I/σ(I): 12.4
Reflection shellResolution: 1.8→1.82 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3 / Rejects: 0 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NEJ

1nej


Resolution: 1.8→41.71 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 6.791 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 1719 3.1 %RANDOM
Rwork0.1773 ---
obs0.1783 53969 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 126.52 Å2 / Biso mean: 40.129 Å2 / Biso min: 18.28 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å2-0 Å20 Å2
2--4.58 Å20 Å2
3----3.22 Å2
Refinement stepCycle: final / Resolution: 1.8→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 255 400 5035
Biso mean--37.96 43.46 -
Num. residues----574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194824
X-RAY DIFFRACTIONr_bond_other_d0.0010.024554
X-RAY DIFFRACTIONr_angle_refined_deg1.122.0156608
X-RAY DIFFRACTIONr_angle_other_deg0.728310452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5385586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98223.855179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67715714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3341512
X-RAY DIFFRACTIONr_chiral_restr0.090.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215437
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021142
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2166MEDIUM POSITIONAL0.475
1A2166MEDIUM THERMAL3.482
2B2301MEDIUM POSITIONAL0.545
2B2301MEDIUM THERMAL3.632
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 120 -
Rwork0.266 3900 -
all-4020 -
obs--98.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9867-0.16531.03372.4549-0.1663.2647-0.0743-0.13620.05880.22960.0849-0.0959-0.2990.1396-0.01060.3505-0.0083-0.01410.0283-0.00360.260223.8577.82236.269
22.6204-0.13790.25871.9389-0.58913.38470.0126-0.0688-0.16780.02020.00930.3441-0.1326-0.8178-0.02190.30040.09880.04290.2715-0.01250.38560.8797.68128.535
31.883-0.04020.07032.05360.412.89430.04010.54390.1072-0.2001-0.0096-0.0994-0.55020.2848-0.03050.3199-0.04850.02310.2894-0.01660.255224.3057.646.152
42.3721-0.25730.69691.58480.12943.8706-0.06430.1251-0.48490.2280.08430.0330.5521-0.053-0.020.32340.0320.01150.1291-0.12920.414119.803-14.93113.784
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 141
2X-RAY DIFFRACTION1A201 - 203
3X-RAY DIFFRACTION2B1 - 146
4X-RAY DIFFRACTION2B201 - 202
5X-RAY DIFFRACTION3C1 - 141
6X-RAY DIFFRACTION3C201 - 202
7X-RAY DIFFRACTION4D1 - 146
8X-RAY DIFFRACTION4D201 - 202

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