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- PDB-6otw: Crystallographic Structure of (HbII-HbIII)-O2 from Lucina pectina... -

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Basic information

Entry
Database: PDB / ID: 6otw
TitleCrystallographic Structure of (HbII-HbIII)-O2 from Lucina pectinata at pH 5.0
Components
  • Hemoglobin II
  • Hemoglobin III
KeywordsOXYGEN TRANSPORT / hemeprotein
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin-2 / Hemoglobin-3 / Hemoglobin II
Similarity search - Component
Biological speciesPhacoides pectinatus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.447 Å
AuthorsMarchany-Rivera, D. / Smith, C.A. / Rodriguez-Perez, J.D. / Lopez-Garriga, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Inorg.Biochem. / Year: 2020
Title: Lucina pectinata oxyhemoglobin (II-III) heterodimer pH susceptibility.
Authors: Marchany-Rivera, D. / Smith, C.A. / Rodriguez-Perez, J.D. / Lopez-Garriga, J.
History
DepositionMay 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemoglobin II
B: Hemoglobin III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8314
Polymers34,5982
Non-polymers1,2332
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-58 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.300, 74.300, 152.299
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Hemoglobin II


Mass: 17146.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phacoides pectinatus (invertebrata) / Production host: Phacoides pectinatus (invertebrata) / References: UniProt: Q86G74, UniProt: P41261*PLUS
#2: Protein Hemoglobin III / Hemoglobin-3 / Hb III


Mass: 17450.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phacoides pectinatus (invertebrata) / Production host: Phacoides pectinatus (invertebrata) / References: UniProt: P41262
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.05 Å3/Da / Density % sol: 59.66 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 5 / Details: sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.19499 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.19499 Å / Relative weight: 1
ReflectionResolution: 2.447→50 Å / Num. obs: 16508 / % possible obs: 97.5 % / Redundancy: 6.9 % / Net I/σ(I): 26.7
Reflection shellResolution: 2.447→2.49 Å / Num. unique obs: 262087

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PT8

3pt8


Resolution: 2.447→33.228 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.17
RfactorNum. reflection% reflection
Rfree0.2481 799 4.98 %
Rwork0.1899 --
obs0.1927 16058 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 167.83 Å2 / Biso mean: 75.2282 Å2 / Biso min: 36.77 Å2
Refinement stepCycle: final / Resolution: 2.447→33.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2413 0 86 38 2537
Biso mean--65.68 69.01 -
Num. residues----303
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4468-2.60.3581190.30582451257096
2.6-2.80070.35471420.26822458260097
2.8007-3.08240.3471270.24332514264197
3.0824-3.52790.27541400.21792516265698
3.5279-4.44320.22311300.16752567269798
4.4432-33.2310.20591410.16172753289499
Refinement TLS params.Method: refined / Origin x: -9.6945 Å / Origin y: 12.9284 Å / Origin z: 24.5415 Å
111213212223313233
T0.5056 Å20.0424 Å20.1041 Å2-0.4817 Å20.0588 Å2--0.4226 Å2
L3.9661 °2-0.4274 °20.604 °2-1.3975 °20.5177 °2--2.7431 °2
S0.1878 Å °0.0363 Å °0.3298 Å °0.0509 Å °0.0164 Å °0.0422 Å °-0.293 Å °-0.2687 Å °-0.1882 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 500
2X-RAY DIFFRACTION1allA501
3X-RAY DIFFRACTION1allB1 - 500
4X-RAY DIFFRACTION1allB501
5X-RAY DIFFRACTION1allW2 - 40
6X-RAY DIFFRACTION1allD2 - 47

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