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- PDB-3d4x: Crystal structure determination of cat (Felis silvestris catus) h... -

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Basic information

Entry
Database: PDB / ID: 3d4x
TitleCrystal structure determination of cat (Felis silvestris catus) hemoglobin at 2.2 angstrom resolution
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta-A/B
KeywordsOxygen storage / Oxygen transport / Felis silvestris catus / Monoclinic / Hemoglobin / low oxygen affinity / allosteric mechanism / Heme / Iron / Transport
Function / homology
Function and homology information


hemoglobin alpha binding / cellular oxidant detoxification / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / 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-like / Globin / Globin / Globin domain profile. ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / 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 subunit alpha / Hemoglobin subunit beta-A/B
Similarity search - Component
Biological speciesFelis silvestris catus (domestic cat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBalasubramanian, M. / Sathya Moorthy, P. / Neelagandan, K. / Ponnuswamy, M.N.
Citation
Journal: To be Published
Title: Crystal structure determination of cat (Felis silvestris catus) hemoglobin at 2.2 angstrom resolution
Authors: Balasubramanian, M. / Sathya Moorthy, P. / Neelagandan, K. / Ponnuswamy, M.N.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization of sheep (Ovis aries) and goat (Capra hircus) haemoglobins under unbuffered low-salt conditions
Authors: Neelagandan, K. / Sathya Moorthy, P. / Balasubramanian, M. / Ponnuswamy, M.N.
#2: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Purification, crystallization and preliminary crystallographic study of low oxygen-affinity haemoglobin from cat (Felis silvestris catus) in two different crystal forms
Authors: Balasubramanian, M. / Sathya Moorthy, P. / Neelagandan, K. / Ponnuswamy, M.N.
#3: Journal: Protein Pept.Lett. / Year: 2009
Title: Preliminary Crystallographic Study of Hemoglobin from Buffalo (Bubalus bubalis): A Low Oxygen Affinity Species
Authors: Balasubramanian, M. / Sathya Moorthy, P. / Neelagandan, K. / Ponnuswamy, M.N.
#4: Journal: Protein Pept.Lett. / Year: 2009
Title: Purification, Crystallization and Preliminary X-Ray Diffraction Studies on Goat (Capra hircus) Hemoglobin - A Low Oxygen Affinity Species
Authors: Sathya Moorthy, P. / Neelagandan, K. / Balasubramanian, M. / Ponnuswamy, M.N.
History
DepositionMay 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2016Group: Other
Revision 1.3Dec 18, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.4Nov 1, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,9078
Polymers62,4414
Non-polymers2,4664
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10850 Å2
ΔGint-115 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.045, 74.195, 72.272
Angle α, β, γ (deg.)90.00, 102.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15328.458 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Felis silvestris catus (domestic cat) / Cell: RED BLOOD CELLS / Tissue: blood / References: UniProt: P07405
#2: Protein Hemoglobin subunit beta-A/B / Hemoglobin beta-A/B chain / Beta-A/B-globin


Mass: 15892.134 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Felis silvestris catus (domestic cat) / Cell: RED BLOOD CELLS / Tissue: blood / References: UniProt: P07412
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 26, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 28427 / % possible obs: 95.2 % / Redundancy: 2.46 % / Rmerge(I) obs: 0.0685 / Net I/σ(I): 6.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.3036 / Mean I/σ(I) obs: 1.2 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
AUTOMARdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HDA

1hda


Resolution: 2.2→29.52 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.223 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.379 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25812 2838 10.1 %RANDOM
Rwork0.18817 ---
obs0.19525 25202 95.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.963 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å2-0.4 Å2
2---0.01 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4404 0 172 157 4733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224716
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3192.0486448
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4665568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71324.082196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48115720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9681512
X-RAY DIFFRACTIONr_chiral_restr0.090.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023602
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.22110
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.23187
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2168
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2940.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9481.52896
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23924526
X-RAY DIFFRACTIONr_scbond_it2.15432026
X-RAY DIFFRACTIONr_scangle_it3.1554.51914
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 207 -
Rwork0.233 1805 -
obs--93.23 %

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