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

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Basic information

Entry
Database: PDB / ID: 3gys
TitleCrystal structure determination of cat (Felis silvestris catus) hemoglobin at 2.9 angstrom resolution
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta-A/B
KeywordsOxygen storage / Oxygen transport / METHEMOGLOBIN / LOW-OXYGEN AFFINITY / ORTHORHOMBIC / chromatography / Heme / Iron / Transport / Polymorphism
Function / homology
Function and homology information


hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / 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 family profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / 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: 2.9 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 2.9 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
DepositionApr 5, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jun 20, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
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
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta-A/B
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta-A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,81416
Polymers124,8828
Non-polymers4,9328
Water1629
1
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
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-119 kcal/mol
Surface area24890 Å2
MethodPISA
2
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta-A/B
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta-A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9078
Polymers62,4414
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint-116 kcal/mol
Surface area24860 Å2
MethodPISA
3
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta-A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4544
Polymers31,2212
Non-polymers1,2332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-54 kcal/mol
Surface area13290 Å2
MethodPISA
4
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta-A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4544
Polymers31,2212
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-53 kcal/mol
Surface area13490 Å2
MethodPISA
5
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta-A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4544
Polymers31,2212
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-53 kcal/mol
Surface area13350 Å2
MethodPISA
6
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta-A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4544
Polymers31,2212
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-54 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.022, 96.465, 146.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15328.458 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Felis silvestris catus (domestic cat) / 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.: 4 / Source method: isolated from a natural source / Source: (natural) Felis silvestris catus (domestic cat) / References: UniProt: P07412
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 40% PEG 3350, 50mM phosphate buffer at pH 6.7, 1M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5417 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 12, 2007
RadiationMonochromator: MIRROS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 26800 / Num. obs: 23886 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.65 % / Rsym value: 0.098 / Net I/σ(I): 4.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.14 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 2304 / Rsym value: 0.2648 / % possible all: 98.5

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Processing

Software
NameVersionClassification
MAR345345data collection
PHASERphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D4X

3d4x


Resolution: 2.9→24.13 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.889 / SU B: 20.016 / SU ML: 0.378 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.508 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27106 2656 10 %RANDOM
Rwork0.18712 ---
obs0.19562 23762 95.99 %-
all-26800 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.397 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2--1.16 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.9→24.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8685 0 344 9 9038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.014
X-RAY DIFFRACTIONr_angle_refined_deg1.583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.766
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.027
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.081
X-RAY DIFFRACTIONr_chiral_restr0.102
X-RAY DIFFRACTIONr_gen_planes_refined0.005
X-RAY DIFFRACTIONr_nbd_refined0.248
X-RAY DIFFRACTIONr_nbtor_refined0.308
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.151
X-RAY DIFFRACTIONr_metal_ion_refined0.022
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.291
X-RAY DIFFRACTIONr_mcbond_it0.818
X-RAY DIFFRACTIONr_mcangle_it
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 186 -
Rwork0.28 1791 -
obs--98.55 %

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