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- PDB-3pi3: Crystallographic Structure of HbII-oxy from Lucina pectinata at pH 5.0 -

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Basic information

Entry
Database: PDB / ID: 3pi3
TitleCrystallographic Structure of HbII-oxy from Lucina pectinata at pH 5.0
ComponentsHemoglobin II
KeywordsOXYGEN TRANSPORT / pH behavior / 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
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hemoglobin-2 / Hemoglobin II
Similarity search - Component
Biological speciesPhacoides pectinatus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsGavira, J.A. / Nieves-Marrero, C.A. / Ruiz-Martinez, C.R. / Estremera-Andujar, R.A. / Lopez-Garriga, J. / Garcia-Ruiz, J.M.
Citation
Journal: To be Published
Title: pH-dependence crystallographic studies of the oxygen carrier hemoglobin II from Lucina pectinata
Authors: Nieves-Marrero, C.A. / Ruiz-Martinez, C.R. / Estremera-Andujar, R.A. / Lopez-Garriga, J. / Garcia-Ruiz, J.M. / Gavira, J.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Two-step counterdiffusion protocol for the crystallization of heamoglobin II from Lucina pectinata in the pH range 4-9
Authors: Nieves-Marrero, C.A. / Ruiz-Martinez, C.R. / Estremera-Andujar, R.A. / Gonzalez-Ramirez, L.A. / Lopez-Garriga, J. / Gavira, J.A.
History
DepositionNov 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn_type.id / _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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,3806
Polymers34,0832
Non-polymers1,2974
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-58 kcal/mol
Surface area13160 Å2
MethodPISA
2
A: Hemoglobin II
B: Hemoglobin II
hetero molecules

A: Hemoglobin II
B: Hemoglobin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,76012
Polymers68,1664
Non-polymers2,5948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area11120 Å2
ΔGint-128 kcal/mol
Surface area25120 Å2
MethodPISA
3
A: Hemoglobin II
B: Hemoglobin II
hetero molecules

A: Hemoglobin II
B: Hemoglobin II
hetero molecules

A: Hemoglobin II
B: Hemoglobin II
hetero molecules

A: Hemoglobin II
B: Hemoglobin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,52024
Polymers136,3328
Non-polymers5,18816
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area26620 Å2
ΔGint-244 kcal/mol
Surface area45850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.973, 73.973, 153.194
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-215-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Hemoglobin II


Mass: 17041.557 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Phacoides pectinatus (invertebrata) / References: UniProt: Q86G74, UniProt: P41261*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.07 Å3/Da / Density % sol: 59.99 % / Mosaicity: 0.432 °
Crystal growTemperature: 293 K / Method: capillary counterdiffusion / pH: 5
Details: Sodium Formate, pH 5.0, Capillary Counterdiffusion, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.88506 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88506 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 31837 / Num. obs: 31837 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 28.569 Å2 / Rmerge(I) obs: 0.138 / Rsym value: 0.138 / Χ2: 1.092 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.029.50.42231041.2471100
2.02-2.19.50.30131151.2671100
2.1-2.29.50.23431381.1961100
2.2-2.319.70.19731391.091100
2.31-2.46100.17231361.0731100
2.46-2.6510.50.15231741.0921100
2.65-2.9111.20.13931611.0351100
2.91-3.3311.60.13132131.0031100
3.33-4.1911.60.12732481.0071100
4.19-2010.70.12834091.003198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å19.96 Å
Translation3 Å19.96 Å

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Processing

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

2olp


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2368 / WRfactor Rwork: 0.1985 / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.8738 / SU R Cruickshank DPI: 0.1338 / SU Rfree: 0.1276 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 1606 5.1 %RANDOM
Rwork0.1749 ---
obs0.1767 31770 99.88 %-
all-31770 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.83 Å2 / Biso mean: 32.0787 Å2 / Biso min: 11.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 90 237 2688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.010.0222666
X-RAY DIFFRACTIONf_angle_refined_deg1.1122.0453648
X-RAY DIFFRACTIONf_dihedral_angle_1_deg4.0855343
X-RAY DIFFRACTIONf_dihedral_angle_2_deg38.4924.622119
X-RAY DIFFRACTIONf_dihedral_angle_3_deg13.37815465
X-RAY DIFFRACTIONf_dihedral_angle_4_deg25.4031510
X-RAY DIFFRACTIONf_chiral_restr0.070.2381
X-RAY DIFFRACTIONf_gen_planes_refined0.0050.022032
X-RAY DIFFRACTIONf_mcbond_it3.6931.51566
X-RAY DIFFRACTIONf_mcangle_it5.28522532
X-RAY DIFFRACTIONf_scbond_it5.14931100
X-RAY DIFFRACTIONf_scangle_it7.1644.51094
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 122 -
Rwork0.238 2163 -
all-2285 -
obs--100 %

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