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- PDB-2zlt: Horse methemoglobin high salt, pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 2zlt
TitleHorse methemoglobin high salt, pH 7.0
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOxygen storage / Oxygen transport / protein hydration / allosteric transitions / variability in quaternary structure / solvent content and crystal structure / water-mediated transformation / Heme / Iron / Metal-binding / Polymorphism / 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
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKaushal, P.S. / Sankaranarayanan, R. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Water-mediated variability in the structure of relaxed-state haemoglobin
Authors: Kaushal, P.S. / Sankaranarayanan, R. / Vijayan, M.
#1: Journal: Proteins / Year: 2005
Title: A new relaxed state in horse methemoglobin characterized by crystallographic studies
Authors: Sankaranarayanan, R. / Biswal, B.K. / Vijayan, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structures of human oxy- and deoxyhaemoglobin at different levels of humidity: variability in the T state
Authors: Biswal, B.K. / Vijayan, M.
#3: Journal: Curr.Sci. / Year: 2001
Title: Structure of human methaemoglobin: The variation of a theme
Authors: Biswal, B.K. / Vijayan, M.
#4: Journal: PROC.R.SOC.LOND A MATH.PHYS.SCI. / Year: 1954
Title: The structure of hemoglobin III: Direct determination of the molecular transform
Authors: Perutz, M.F.
#5: Journal: Acta Crystallogr. / Year: 1953
Title: Discontinuous lattice changes in hemoglobin crystal
Authors: Huxley, H.E. / Kendrew, J.C.
History
DepositionApr 10, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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_ref_seq_dif / 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_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 subunit alpha
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4044
Polymers31,1712
Non-polymers1,2332
Water3,891216
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)64,8078
Polymers62,3414
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-50.9 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.650, 63.336, 54.957
Angle α, β, γ (deg.)90.00, 110.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 15138.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P01958
#2: Protein Hemoglobin subunit beta / Hemoglobin beta chain / Beta-globin


Mass: 16032.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02062
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 7
Details: 2.6M ammonium sulfate, 0.01M ammonium phosphate, pH 7.0, LIQUID DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 12, 2003 / Details: OSMIC MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→18.32 Å / Num. obs: 26933 / % possible obs: 97.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 8.7
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MHB

2mhb


Resolution: 1.9→18.32 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22592 1350 5 %RANDOM
Rwork0.19013 ---
obs0.19197 25579 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.588 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→18.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2169 0 86 216 2471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212323
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2422.0633183
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6275284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78224.1392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38915347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.771156
X-RAY DIFFRACTIONr_chiral_restr0.090.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021769
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.2954
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21582
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2112
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8581.51416
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.62422250
X-RAY DIFFRACTIONr_scbond_it2.6123907
X-RAY DIFFRACTIONr_scangle_it4.0384.5933
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 94 -
Rwork0.289 1908 -
obs--99.8 %

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