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- PDB-2zlx: Horse methemoglobin high salt, pH 7.0 (66% relative humidity) -

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Basic information

Entry
Database: PDB / ID: 2zlx
TitleHorse methemoglobin high salt, pH 7.0 (66% relative humidity)
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 / oxygen carrier activity / hydrogen peroxide catabolic process / 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: 2.8 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 1.2Jun 13, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.3Nov 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_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_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
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8078
Polymers62,3414
Non-polymers2,4664
Water00
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4044
Polymers31,1712
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-47 kcal/mol
Surface area13120 Å2
MethodPISA
2
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4044
Polymers31,1712
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-46 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.445, 63.398, 102.590
Angle α, β, γ (deg.)90.00, 120.98, 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.: 2 / 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.: 2 / 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.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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: 2.42 Å3/Da / Density % sol: 49.28 %
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 25, 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: 2.8→20 Å / Num. obs: 11560 / % possible obs: 77.7 % / Redundancy: 1.5 % / Biso Wilson estimate: 44.9 Å2 / Rmerge(I) obs: 0.173 / Net I/σ(I): 3.2
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1227 / % possible all: 82.2

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Processing

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

2mhb


Resolution: 2.8→19.54 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.85 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.578 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29349 563 4.9 %RANDOM
Rwork0.25995 ---
obs0.26157 10996 77.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.351 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.04 Å2
2---0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4272 0 172 0 4444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214582
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4482.066292
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.665567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14924.011177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.18515652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9781511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023507
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2790.22285
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.23100
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2187
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.340.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.811.52828
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.5224481
X-RAY DIFFRACTIONr_scbond_it1.43331754
X-RAY DIFFRACTIONr_scangle_it2.2824.51811
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 43 -
Rwork0.336 872 -
obs--83.03 %

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