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- PDB-3pi1: Crystallographic Structure of HbII-oxy from Lucina pectinata at pH 9.0 -

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Basic information

Entry
Database: PDB / ID: 3pi1
TitleCrystallographic Structure of HbII-oxy from Lucina pectinata at pH 9.0
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 speciesLucina pectinata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.002 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 1.1Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-58 kcal/mol
Surface area13290 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_556-y,-x,-z+11
Buried area11470 Å2
ΔGint-125 kcal/mol
Surface area25350 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_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area26880 Å2
ΔGint-245 kcal/mol
Surface area46770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.923, 75.923, 153.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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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) Lucina pectinata (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.: 224 / 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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 293 K / Method: capillary counterdiffusion / pH: 9
Details: Sodium Formate, pH 9.0, Capillary Counterdiffusion, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9075 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9075 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 29432 / Num. obs: 29432 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 7.78
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 1.943 / Rsym value: 0.512 / % possible all: 98.1
Cell measurementReflection used: 126200

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å19.51 Å
Translation3 Å19.51 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
SCALAdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
SCALEPACKdata scaling
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.002→19.509 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.27 / σ(F): 0.09 / Phase error: 23.96 / Stereochemistry target values: ML
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rfree0.2308 1329 4.97 %
Rwork0.1901 --
obs0.1921 26732 86.34 %
all-29432 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.558 Å2 / ksol: 0.42 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.9939 Å20 Å2-0 Å2
2--6.9939 Å20 Å2
3----13.9879 Å2
Refinement stepCycle: LAST / Resolution: 2.002→19.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2354 0 90 224 2668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152609
X-RAY DIFFRACTIONf_angle_d1.1173568
X-RAY DIFFRACTIONf_dihedral_angle_d16.108933
X-RAY DIFFRACTIONf_chiral_restr0.073370
X-RAY DIFFRACTIONf_plane_restr0.004453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0018-2.08190.4131170.28162470X-RAY DIFFRACTION78
2.0819-2.17650.25241340.2392675X-RAY DIFFRACTION83
2.1765-2.29110.27591270.22192640X-RAY DIFFRACTION82
2.2911-2.43440.25211530.21362732X-RAY DIFFRACTION85
2.4344-2.62190.2611490.21132851X-RAY DIFFRACTION88
2.6219-2.8850.2461610.20812898X-RAY DIFFRACTION90
2.885-3.30070.25541640.19652979X-RAY DIFFRACTION91
3.3007-4.1520.18751630.15233046X-RAY DIFFRACTION92
4.152-19.50990.19381610.16553112X-RAY DIFFRACTION89

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