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

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Basic information

Entry
Database: PDB / ID: 6otx
TitleCrystallographic Structure of (HbII-HbIII)-O2 from Lucina pectinata at pH 7.0
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-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hemoglobin-2 / Hemoglobin-3 / Hemoglobin II
Similarity search - Component
Biological speciesPhacoides pectinatus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.539 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)35,8956
Polymers34,5982
Non-polymers1,2974
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-53 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.736, 74.736, 152.571
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: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 7 / 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: 2.539→50 Å / Num. obs: 15012 / % possible obs: 99.6 % / Redundancy: 10 % / Net I/σ(I): 36.6
Reflection shellResolution: 2.54→2.58 Å / Num. unique obs: 784334

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PT8

3pt8


Resolution: 2.539→33.558 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.82
RfactorNum. reflection% reflection
Rfree0.2488 747 5.02 %
Rwork0.1922 --
obs0.1952 14867 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 201.81 Å2 / Biso mean: 82.7208 Å2 / Biso min: 44.76 Å2
Refinement stepCycle: final / Resolution: 2.539→33.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2413 0 90 39 2542
Biso mean--73.28 79.57 -
Num. residues----303
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5395-2.73550.36911430.29072691283498
2.7355-3.01060.32521450.262227812926100
3.0106-3.44580.29991420.231828012943100
3.4458-4.33990.25431530.17828342987100
4.3399-33.56110.20531640.163330133177100
Refinement TLS params.Method: refined / Origin x: -9.7797 Å / Origin y: 12.9466 Å / Origin z: 24.5872 Å
111213212223313233
T0.7825 Å20.0259 Å20.1069 Å2-0.4319 Å20.0437 Å2--0.502 Å2
L3.4836 °2-0.5934 °20.0537 °2-1.2043 °20.4247 °2--2.3332 °2
S0.1965 Å °0.1268 Å °0.2948 Å °0.2367 Å °-0.0705 Å °0.0554 Å °-0.2808 Å °-0.2645 Å °-0.1058 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 151
2X-RAY DIFFRACTION1allA500 - 501
3X-RAY DIFFRACTION1allB1 - 152
4X-RAY DIFFRACTION1allB500 - 501
5X-RAY DIFFRACTION1allD1 - 42

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