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- PDB-3pi4: Crystallographic Structure of HbII-oxy from Lucina pectinata at pH 4.0 -

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Basic information

Entry
Database: PDB / ID: 3pi4
TitleCrystallographic Structure of HbII-oxy from Lucina pectinata at pH 4.0
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 / Hemoglobin-2 / Hemoglobin II
Similarity search - Component
Biological speciesPhacoides pectinatus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.17 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 1.1Nov 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)35,3164
Polymers34,0832
Non-polymers1,2332
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-61 kcal/mol
Surface area12420 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)70,6328
Polymers68,1664
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10660 Å2
ΔGint-134 kcal/mol
Surface area23460 Å2
MethodPISA
3
A: Hemoglobin II
B: Hemoglobin II
hetero molecules

A: Hemoglobin II
B: Hemoglobin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6328
Polymers68,1664
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area11330 Å2
ΔGint-123 kcal/mol
Surface area22790 Å2
MethodPISA
4
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)141,26416
Polymers136,3328
Non-polymers4,9328
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 area25430 Å2
ΔGint-269 kcal/mol
Surface area42820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.237, 72.237, 146.288
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) 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 293 K / Method: capillary counterdiffusion / pH: 4
Details: Sodium Formate, pH 4.0, 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
ReflectionResolution: 3.17→20 Å / Num. all: 6617 / Num. obs: 6617 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.145 / Rsym value: 0.145 / Net I/σ(I): 8.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.3 Å19.38 Å
Translation3.3 Å19.38 Å

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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: 3.17→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.876 / Occupancy max: 1 / Occupancy min: 0.45 / SU B: 23.019 / SU ML: 0.397 / Cross valid method: THROUGHOUT / ESU R Free: 0.59 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28708 309 4.7 %RANDOM
Rwork0.19576 ---
obs0.19978 6277 93.99 %-
all-6586 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2--0.73 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 3.17→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2339 0 86 6 2431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212512
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5632.0443430
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5095306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.26224.818110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.76915399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.561157
X-RAY DIFFRACTIONr_chiral_restr0.0960.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211919
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6521.51512
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25322413
X-RAY DIFFRACTIONr_scbond_it1.47731000
X-RAY DIFFRACTIONr_scangle_it2.5294.51015
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.174→3.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.498 10 -
Rwork0.232 255 -
obs--53.21 %

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