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- PDB-2ri4: Crystal Structure determination of Goat Methemoglobin at 2.7 Angstrom -

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Basic information

Entry
Database: PDB / ID: 2ri4
TitleCrystal Structure determination of Goat Methemoglobin at 2.7 Angstrom
Components
  • Hemoglobin subunit alpha-1/2
  • Hemoglobin subunit beta-A
KeywordsOxygen storage / Oxygen transport / Methemoglobin / low oxygen affinity / Allosteric Mechanism / Heme / Iron / Metal-binding / Transport
Function / homology
Function and homology information


hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle ...hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle / 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 beta-A / Hemoglobin subunit alpha-1 / Hemoglobin subunit alpha-2
Similarity search - Component
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSathya Moorthy, P. / Neelagandan, K. / Balasubramanian, M. / Ponnuswamy, M.N.
Citation
Journal: To be Published
Title: Crystal Structure determination of Goat Methemoglobin at 2.7 Angstrom
Authors: Sathya Moorthy, P. / Neelagandan, K. / Balasubramanian, M. / 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.
History
DepositionOct 10, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2016Group: Other
Revision 1.3Jan 15, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.4Oct 25, 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-1/2
B: Hemoglobin subunit beta-A
C: Hemoglobin subunit alpha-1/2
D: Hemoglobin subunit beta-A
I: Hemoglobin subunit alpha-1/2
J: Hemoglobin subunit beta-A
K: Hemoglobin subunit alpha-1/2
L: Hemoglobin subunit beta-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,34216
Polymers124,4108
Non-polymers4,9328
Water91951
1
A: Hemoglobin subunit alpha-1/2
B: Hemoglobin subunit beta-A
C: Hemoglobin subunit alpha-1/2
D: Hemoglobin subunit beta-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6718
Polymers62,2054
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Hemoglobin subunit alpha-1/2
J: Hemoglobin subunit beta-A
K: Hemoglobin subunit alpha-1/2
L: Hemoglobin subunit beta-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6718
Polymers62,2054
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.692, 68.325, 95.597
Angle α, β, γ (deg.)110.64, 91.90, 108.94
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Hemoglobin subunit alpha-1/2 / Hemoglobin alpha-1/2 chain / Alpha-1/2-globin


Mass: 15056.157 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / Cell: RBC (Red blood cells) / References: UniProt: P68238, UniProt: P0CH25*PLUS
#2: Protein
Hemoglobin subunit beta-A / Hemoglobin beta-A chain / Beta-A-globin / Alanine beta-globin


Mass: 16046.405 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / Cell: RBC (Red blood cells) / References: UniProt: P02077
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Unbuffered low-salt concentration using 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 RU200 / Wavelength: 1.5417 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 22, 2006
RadiationMonochromator: NIL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 31524 / Num. obs: 31524 / % possible obs: 90.38 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.14
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 0.9 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
AUTOMARdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G08, Bovine carbonmonoxy hemoglobin

1g08


Resolution: 2.7→22.5 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.855 / SU B: 20.028 / SU ML: 0.41 / Cross valid method: THROUGHOUT / ESU R Free: 0.524 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30815 2863 9.9 %RANDOM
Rwork0.22544 ---
obs0.23371 26018 90.46 %-
all-31524 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.781 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20.01 Å2
2---0.02 Å2-0.01 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.7→22.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8600 0 344 51 8995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0229199
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8182.06112577
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.58351118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.37924.286364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.116151440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5131524
X-RAY DIFFRACTIONr_chiral_restr0.1110.21365
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026914
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2920.25247
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.26109
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.2536
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2240.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3690.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8061.55674
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16328881
X-RAY DIFFRACTIONr_scbond_it1.88533958
X-RAY DIFFRACTIONr_scangle_it2.7074.53680
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 229 -
Rwork0.317 1983 -
obs--93.65 %

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