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- PDB-3pi2: Crystallographic Structure of HbII-oxy from Lucina pectinata at pH 8.0 -

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Basic information

Entry
Database: PDB / ID: 3pi2
TitleCrystallographic Structure of HbII-oxy from Lucina pectinata at pH 8.0
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 domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / 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: 1.85 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 1.1Dec 21, 2016Group: Non-polymer description
Revision 1.2Oct 16, 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_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.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)35,4267
Polymers34,0832
Non-polymers1,3435
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-57 kcal/mol
Surface area12920 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)70,85214
Polymers68,1664
Non-polymers2,68610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area11660 Å2
ΔGint-126 kcal/mol
Surface area24560 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)141,70428
Polymers136,3328
Non-polymers5,37220
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 area27300 Å2
ΔGint-245 kcal/mol
Surface area45150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.706, 74.706, 152.646
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-317-

HOH

21B-395-

HOH

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Components

#1: Protein Hemoglobin II / Lucina pectinata


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: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 293 K / Method: capillary counterdiffusion / pH: 8
Details: Sodium Formate, pH 8.0, 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 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9075 Å / Relative weight: 1
ReflectionAv R equivalents: 0.069 / Number: 317299
ReflectionResolution: 1.85→20 Å / Num. all: 37050 / Num. obs: 37050 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 25.911
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 4.347 / Rsym value: 0.491 / % possible all: 100
Cell measurementReflection used: 317299

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.34 / SU B: 2.682 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 1864 5 %RANDOM
Rwork0.1835 ---
obs0.185 37050 98.35 %-
all-37050 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.89 Å2 / Biso mean: 31.6376 Å2 / Biso min: 16.29 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2--1.07 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 93 268 2717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222675
X-RAY DIFFRACTIONr_bond_other_d0.0010.022
X-RAY DIFFRACTIONr_angle_refined_deg2.2052.0413665
X-RAY DIFFRACTIONr_angle_other_deg2.04433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3615340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.28225.085118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17815451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.198157
X-RAY DIFFRACTIONr_chiral_restr0.1740.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022065
X-RAY DIFFRACTIONr_mcbond_it1.5391.51598
X-RAY DIFFRACTIONr_mcbond_other0.181.51
X-RAY DIFFRACTIONr_mcangle_it2.4622579
X-RAY DIFFRACTIONr_scbond_it4.06331077
X-RAY DIFFRACTIONr_scangle_it5.494.51078
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 128 -
Rwork0.25 2578 -
all-2706 -
obs--99.93 %

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