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- PDB-3pt8: Structure of HbII-III-CN from Lucina pectinata at pH 5.0 -

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Basic information

Entry
Database: PDB / ID: 3pt8
TitleStructure of HbII-III-CN from Lucina pectinata at pH 5.0
Components
  • Hemoglobin II
  • Hemoglobin III
KeywordsOXYGEN TRANSPORT / oxygen carrier
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
CYANIDE ION / FORMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin III / Hemoglobin-2 / Hemoglobin-3 / Hemoglobin II
Similarity search - Component
Biological speciesLucina pectinata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.762 Å
AuthorsGavira, J.A. / Ruiz-Martinez, C.R. / Nieves-Marrero, C.A. / Estremera-Andujar, R.A. / Lopez-Garriga, J. / Garcia-Ruiz, J.M.
CitationJournal: To be Published
Title: New Crystallographic Structure of HbII-III-Oxy and CN forms from Lucina pectinata.
Authors: Ruiz-Martinez, C.R. / Nieves-Marrero, C.A. / Estremera-Andujar, R.A. / Lopez-Garriga, J. / Garcia-Ruiz, J.M. / Gavira, J.A.
History
DepositionDec 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)36,11311
Polymers34,5062
Non-polymers1,6079
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-14 kcal/mol
Surface area14330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.231, 74.231, 152.302
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemoglobin II


Mass: 17041.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lucina pectinata (invertebrata) / Strain: HbII / Tissue: ctenidia / References: UniProt: Q86G74, UniProt: P41261*PLUS
#2: Protein Hemoglobin III


Mass: 17463.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lucina pectinata (invertebrata) / Strain: HbIII / Tissue: ctenidia / References: UniProt: A7UAU9, UniProt: P41262*PLUS

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Non-polymers , 5 types, 231 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE AUTHORS STATE THAT THE OBSERVED SEQUENCE DOES NOT MATCH THE DEPOSITED ONE FOR THE HBIII MONOMER (CHAIN B)

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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: 3.04 Å3/Da / Density % sol: 59.54 % / Mosaicity: 0.479 °
Crystal growTemperature: 293 K / pH: 5
Details: Capillary Counterdiffusion, Sodium Formate, pH 5.0, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9075 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9075 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 42684 / Num. obs: 42684 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13 % / Biso Wilson estimate: 25.51 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Χ2: 0.99 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.8110.80.46334101.08179.2
1.81-1.8911.80.3742601.039199.8
1.89-1.97120.25943091.0471100
1.97-2.0712.40.18143141.071100
2.07-2.2130.13543311.0231100
2.2-2.3713.60.11143420.971100
2.37-2.6114.20.09643660.9311100
2.61-2.9914.40.08643960.9311100
2.99-3.7614.20.0844501199.7
3.76-2012.80.0845060.877195.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å19.98 Å
Translation3.5 Å19.98 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OLP

2olp


Resolution: 1.762→19.982 Å / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.8487 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 2148 5.04 %RANDOM
Rwork0.197 ---
all0.1984 42611 --
obs0.1984 42611 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.505 Å2 / ksol: 0.435 e/Å3
Displacement parametersBiso max: 84.79 Å2 / Biso mean: 30.3434 Å2 / Biso min: 14.52 Å2
Baniso -1Baniso -2Baniso -3
1-3.0716 Å20 Å2-0 Å2
2--3.0716 Å20 Å2
3----6.1432 Å2
Refinement stepCycle: LAST / Resolution: 1.762→19.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 111 222 2729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072747
X-RAY DIFFRACTIONf_angle_d0.7983753
X-RAY DIFFRACTIONf_chiral_restr0.055387
X-RAY DIFFRACTIONf_plane_restr0.003475
X-RAY DIFFRACTIONf_dihedral_angle_d14.1921019
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.762-1.82490.25412150.25213920413599
1.8249-1.89790.26222170.226939974214100
1.8979-1.98420.24742120.224339974209100
1.9842-2.08870.23632330.212139894222100
2.0887-2.21950.2352160.204340144230100
2.2195-2.39060.24982090.201940814290100
2.3906-2.63060.24132190.202440414260100
2.6306-3.01020.25292160.196440814297100
3.0102-3.78830.19272050.176941464351100
3.7883-19.9830.20362060.18684197440396

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