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- PDB-1ns6: The 2.1A Structure of Horse (alpha hemichrome/beta met) Hemoglobi... -

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Basic information

Entry
Database: PDB / ID: 1ns6
TitleThe 2.1A Structure of Horse (alpha hemichrome/beta met) Hemoglobin at pH 5.4
Components
  • Hemoglobin alpha subunit
  • Hemoglobin beta subunitHemoglobin subunit beta
KeywordsOXYGEN STORAGE/TRANSPORT / hemichrome / bisimidazole alpha heme / aquomet beta heme / globin fold / OXYGEN STORAGE-TRANSPORT COMPLEX
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
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsRobinson, V.L. / Smith, B.B. / Arnone, A.
Citation
Journal: Biochemistry / Year: 2003
Title: A pH-Dependent Aquomet-to-Hemichrome Transition in Crystalline Horse Methemoglobin
Authors: Robinson, V.L. / Smith, B.B. / Arnone, A.
#1: Journal: Proc.R.Soc.London,Ser.B / Year: 1947
Title: An X-Ray Study of Horse Methaemoglobin. I
Authors: Boyes-Watson, J. / Davidson, E. / Perutz, M.F.
#2: Journal: Proc.R.Soc.London,Ser.B / Year: 1954
Title: The Structure of Haemoglobin. III. Direct Determination of the Molecular Transform
Authors: Perutz, M.F.
History
DepositionJan 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Aug 16, 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 alpha subunit
B: Hemoglobin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4044
Polymers31,1712
Non-polymers1,2332
Water1,51384
1
A: Hemoglobin alpha subunit
B: Hemoglobin beta subunit
hetero molecules

A: Hemoglobin alpha subunit
B: Hemoglobin beta subunit
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
Unit cell
Length a, b, c (Å)108.110, 63.330, 53.850
Angle α, β, γ (deg.)90.00, 84.72, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
DetailsThe biological assembly (tetramer) is generated from the dimer in the asymetric unit by the operation: -x, y, -z.

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Components

#1: Protein Hemoglobin alpha subunit


Mass: 15138.280 Da / Num. of mol.: 1 / Fragment: alpha subunit / Source method: isolated from a natural source / Details: pH 5.4 Hemichrome Structure / Source: (natural) Equus caballus (horse) / References: UniProt: P01958
#2: Protein Hemoglobin beta subunit / Hemoglobin subunit beta


Mass: 16032.274 Da / Num. of mol.: 1 / Fragment: beta subunit / Source method: isolated from a natural source / Details: pH 5.4 Hemichrome Structure / Source: (natural) Equus caballus (horse) / References: UniProt: P02062
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.76 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.4
Details: 1.5M ammonium sulfate, 0.35M ammonium phosphate then soaked to pH 5.4 in solutions of 3.35 M ammonium sulfate buffered with 0.2M ammonium phosphate, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
pH: 7.1 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 %horse methemoglobin11
21.5 Mammonium sulfate11
30.35 Mammonium phosphate11pH7.1

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: UCSD MARK II / Detector: AREA DETECTOR / Date: Sep 15, 1997
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.04→30 Å / Num. obs: 21884 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.053
Reflection
*PLUS
Highest resolution: 2.07 Å / Num. obs: 21680 / Num. measured all: 125115
Reflection shell
*PLUS
Highest resolution: 2.07 Å / Lowest resolution: 2.23 Å / % possible obs: 87.7 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
SDMSdata reduction
CNSrefinement
SDMSdata collection
SDMSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G0B

1g0b


Resolution: 2.05→54.23 Å / Cor.coef. Fo:Fc: 0.953 / SU B: 4.946 / SU ML: 0.136 / σ(F): 2 / ESU R: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.188 2160 9.9 %random
Rwork0.16262 ---
all0.189 ---
obs0.16262 21824 95.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.383 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.04 Å2
2--0.08 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.05→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 86 84 2373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222384
X-RAY DIFFRACTIONr_bond_other_d0.0010.022095
X-RAY DIFFRACTIONr_angle_refined_deg1.2442.063225
X-RAY DIFFRACTIONr_angle_other_deg0.73234862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2823285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.06915386
X-RAY DIFFRACTIONr_chiral_restr0.0760.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022608
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02454
X-RAY DIFFRACTIONr_nbd_refined0.2280.3521
X-RAY DIFFRACTIONr_nbd_other0.1870.31817
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.562
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1350.329
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.510
X-RAY DIFFRACTIONr_mcbond_it0.7781.51427
X-RAY DIFFRACTIONr_mcangle_it1.59922265
X-RAY DIFFRACTIONr_scbond_it2.6133957
X-RAY DIFFRACTIONr_scangle_it4.4994.5960
LS refinement shellResolution: 2.05→2.103 Å / Num. reflection Rfree: 0 / Num. reflection Rwork: 838 / Total num. of bins used: 20
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.07 Å / Rfactor Rfree: 0.194 / Rfactor Rwork: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.25
LS refinement shell
*PLUS
Highest resolution: 2.07 Å / Lowest resolution: 2.23 Å

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