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

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Basic information

Entry
Database: PDB / ID: 6oty
TitleCrystallographic Structure of (HbII-HbIII)-O2 from Lucina pectinata at pH 4.0
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 / Hemoglobin-2 / Hemoglobin-3 / Hemoglobin II
Similarity search - Component
Biological speciesPhacoides pectinatus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.3Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-58 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.429, 74.429, 152.100
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.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 4 / Details: Sodium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 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: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.598→50 Å / Num. obs: 13907 / % possible obs: 99.5 % / Redundancy: 7.7 % / Net I/σ(I): 22.8
Reflection shellResolution: 2.598→2.64 Å / Num. unique obs: 784334

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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: 2.598→33.862 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.98
RfactorNum. reflection% reflection
Rfree0.2349 673 4.89 %
Rwork0.1807 --
obs0.1835 13773 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 183.34 Å2 / Biso mean: 77.7341 Å2 / Biso min: 36.32 Å2
Refinement stepCycle: final / Resolution: 2.598→33.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 86 32 2512
Biso mean--72.14 73.49 -
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 (%)
2.5977-2.79810.35241340.29492510264498
2.7981-3.07960.28661230.243425912714100
3.0796-3.52480.31260.213925982724100
3.5248-4.43930.21621350.160426222757100
4.4393-33.86470.20151550.15462779293499
Refinement TLS params.Method: refined / Origin x: 24.2556 Å / Origin y: -27.4411 Å / Origin z: -24.6733 Å
111213212223313233
T0.4645 Å20.0271 Å20.0456 Å2-0.4712 Å20.0784 Å2--0.4346 Å2
L1.3359 °2-0.7366 °20.2994 °2-3.5839 °20.5358 °2--3.0995 °2
S0.0275 Å °-0.0237 Å °0.0774 Å °-0.1298 Å °0.1556 Å °0.3383 Å °-0.3369 Å °-0.3684 Å °-0.171 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 151
2X-RAY DIFFRACTION1allA500 - 501
3X-RAY DIFFRACTION1allB501 - 152
4X-RAY DIFFRACTION1allB500
5X-RAY DIFFRACTION1allW3 - 130

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