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- PDB-3wr1: Crystal structure of Cormorant (Phalacrocorax carbo) hemoglobin -

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Basic information

Entry
Database: PDB / ID: 3wr1
TitleCrystal structure of Cormorant (Phalacrocorax carbo) hemoglobin
Components
  • Hemoglobin subunit alpha-A
  • Hemoglobin subunit beta
KeywordsTRANSPORT PROTEIN / HEMOGLOBIN / HEME / Oxygen transport / IRON / METAL BINDING PROTEIN
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha-A / Hemoglobin subunit beta
Similarity search - Component
Biological speciesPhalacrocorax carbo (great cormorant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsJagadeesan, G. / Vinodh Kumar, V. / Peters, H.G. / Malathy, P. / Harikrishna Etti, S. / Gunasekaran, K. / Aravindhan, S.
CitationJournal: To be Published
Title: Crystal structure of Cormorant (Phalacrocorax carbo) hemoglobin
Authors: Jagadeesan, G. / Vinodh Kumar, V. / Peters, H.G. / Malathy, P. / Harikrishna Etti, S. / Gunasekaran, K. / Aravindhan, S.
History
DepositionFeb 9, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Other
Revision 1.2Jul 2, 2014Group: Other
Revision 1.3Sep 15, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _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.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha-A
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6644
Polymers31,4312
Non-polymers1,2332
Water181
1
A: Hemoglobin subunit alpha-A
B: Hemoglobin subunit beta
hetero molecules

A: Hemoglobin subunit alpha-A
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3298
Polymers62,8634
Non-polymers2,4664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area8970 Å2
ΔGint-71 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.640, 55.640, 153.381
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hemoglobin subunit alpha-A / / Alpha-A-globin / Hemoglobin alpha-A chain


Mass: 15300.681 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phalacrocorax carbo (great cormorant) / References: UniProt: P10780
#2: Protein Hemoglobin subunit beta / / Beta-globin / Hemoglobin beta chain


Mass: 16130.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phalacrocorax carbo (great cormorant) / References: UniProt: P10782
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG3350, 500mM NaCl, 10% Glycerol., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 11, 2014 / Details: Osmic Confocal MAX-FLUX mirror optics
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→13.08 Å / Num. obs: 2936 / % possible obs: 77.2 %
Reflection shellResolution: 3.5→13.08 Å / % possible all: 77.2

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FAW

1faw


Resolution: 3.5→13.08 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.787 / SU B: 40.994 / SU ML: 0.657 / Cross valid method: THROUGHOUT / ESU R Free: 0.976 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26513 282 9.6 %RANDOM
Rwork0.18785 ---
obs0.19582 2654 77.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.442 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.07 Å2-0 Å2
2--0.13 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 3.5→13.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 86 1 2304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192375
X-RAY DIFFRACTIONr_bond_other_d0.0020.022284
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9893250
X-RAY DIFFRACTIONr_angle_other_deg0.74935225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8615285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29323.72394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.92415375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022687
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02577
X-RAY DIFFRACTIONr_mcbond_it0.3990.9541146
X-RAY DIFFRACTIONr_mcbond_other0.3990.9531145
X-RAY DIFFRACTIONr_mcangle_it0.7421.4231429
X-RAY DIFFRACTIONr_mcangle_other0.7411.4241430
X-RAY DIFFRACTIONr_scbond_it0.1970.9351229
X-RAY DIFFRACTIONr_scbond_other0.1970.9361227
X-RAY DIFFRACTIONr_scangle_other0.4011.3881821
X-RAY DIFFRACTIONr_long_range_B_refined1.5357.412885
X-RAY DIFFRACTIONr_long_range_B_other1.5357.4092886
LS refinement shellResolution: 3.502→3.586 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 17 -
Rwork0.188 182 -
obs--80.24 %

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