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- PDB-1ns9: The 1.6A Structure of Horse Methemoglobin at pH 7.1 -

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Basic information

Entry
Database: PDB / ID: 1ns9
TitleThe 1.6A Structure of Horse Methemoglobin at pH 7.1
Components
  • Hemoglobin alpha subunit
  • Hemoglobin beta subunit
KeywordsOXYGEN STORAGE/TRANSPORT / aquomet hemoglobin / globin fold / bisimidazole at low pH / OXYGEN STORAGE-TRANSPORT COMPLEX
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: 1.6 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 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Water1,62190
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)108.400, 63.200, 54.600
Angle α, β, γ (deg.)90.00, 110.90, 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 bu 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 7.1 Aquomet structure / Source: (natural) Equus caballus (horse) / References: UniProt: P01958
#2: Protein Hemoglobin beta subunit


Mass: 16032.274 Da / Num. of mol.: 1 / Fragment: beta subunit / Source method: isolated from a natural source / Details: pH 7.1 Aquomet structure / 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.: 90 / 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: 2.62 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.1
Details: 1.5M ammonium sulfate, 0.35 M ammonium phosphate, pH 7.1, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
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 20, 1997
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 42596 / % possible obs: 92.3 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.047
Reflection
*PLUS
Highest resolution: 1.59 Å / Num. obs: 42686 / Num. measured all: 186644
Reflection shell
*PLUS
Highest resolution: 1.59 Å / Lowest resolution: 1.71 Å / % possible obs: 75.5 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
REFMAC5refinement
SDMSdata reduction
CNSrefinement
SDMSdata collection
SDMSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→53.45 Å / Cor.coef. Fo:Fc: 0.968 / SU B: 3.489 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 4200 10 %random
Rwork0.17992 ---
all0.17996 ---
obs0.17992 42596 93.51 %-
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: 22.954 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20.9 Å2
2---0.08 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.6→53.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 86 90 2379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222382
X-RAY DIFFRACTIONr_bond_other_d0.0010.022095
X-RAY DIFFRACTIONr_angle_refined_deg1.1682.063225
X-RAY DIFFRACTIONr_angle_other_deg0.6934862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0963285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.48615385
X-RAY DIFFRACTIONr_chiral_restr0.0710.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022614
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02454
X-RAY DIFFRACTIONr_nbd_refined0.2270.3536
X-RAY DIFFRACTIONr_nbd_other0.1840.31870
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.567
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.333
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2870.57
X-RAY DIFFRACTIONr_symmetry_hbond_other0.3460.51
X-RAY DIFFRACTIONr_mcbond_it0.7581.51432
X-RAY DIFFRACTIONr_mcangle_it1.53822265
X-RAY DIFFRACTIONr_scbond_it2.3413950
X-RAY DIFFRACTIONr_scangle_it3.8634.5960
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.297 1960
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.59 Å / Rfactor Rfree: 0.2 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.19
LS refinement shell
*PLUS
Highest resolution: 1.59 Å / Lowest resolution: 1.71 Å

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