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- PDB-2d5x: Crystal structure of carbonmonoxy horse hemoglobin complexed with L35 -

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Basic information

Entry
Database: PDB / ID: 2d5x
TitleCrystal structure of carbonmonoxy horse hemoglobin complexed with L35
Components
  • Hemoglobin alpha subunit
  • Hemoglobin beta subunit
KeywordsOXYGEN STORAGE/TRANSPORT / HEMOGLOBIN / L35 / ALLOSTERIC EFFECTOR / OXYGEN STORAGE-TRANSPORT COMPLEX
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Chem-L35 / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsYokoyama, T. / Neya, S. / Tsuneshige, A. / Yonetani, T. / Park, S.Y. / Tame, J.R.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: R-state haemoglobin with low oxygen affinity: crystal structures of deoxy human and carbonmonoxy horse haemoglobin bound to the effector molecule L35
Authors: Yokoyama, T. / Neya, S. / Tsuneshige, A. / Yonetani, T. / Park, S.Y. / Tame, J.R.
History
DepositionNov 8, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 alpha subunit
B: Hemoglobin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2268
Polymers31,1712
Non-polymers2,0556
Water4,035224
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)66,45216
Polymers62,3414
Non-polymers4,11112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)62.337, 107.442, 87.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations; X, -Y, -Z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemoglobin alpha subunit / 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) / Tissue: red cell / References: UniProt: P01958
#2: Protein Hemoglobin beta subunit / 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) / Tissue: red cell / References: UniProt: P02062

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Non-polymers , 4 types, 230 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#5: Chemical ChemComp-L35 / 2-[4-({[(3,5-DICHLOROPHENYL)AMINO]CARBONYL}AMINO)PHENOXY]-2-METHYLPROPANOIC ACID


Mass: 383.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16Cl2N2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 293 K / Method: batch / pH: 6
Details: 20% PEG1000, 50mM LiCl, 50mM Mes, 0.5mM L35, pH 6.0, BATCH, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. obs: 45502 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.3
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.158 / % possible all: 56.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→19.88 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.265 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21552 2284 5 %RANDOM
Rwork0.19032 ---
obs0.19159 43215 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.455 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å20 Å2
2--0.5 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.45→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 140 224 2567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212416
X-RAY DIFFRACTIONr_angle_refined_deg1.252.0743301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5065285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1642495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86515364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.187157
X-RAY DIFFRACTIONr_chiral_restr0.0780.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021838
X-RAY DIFFRACTIONr_nbd_refined0.2280.21245
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21671
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2185
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.220
X-RAY DIFFRACTIONr_mcbond_it0.6551.51426
X-RAY DIFFRACTIONr_mcangle_it1.23822267
X-RAY DIFFRACTIONr_scbond_it2.00531004
X-RAY DIFFRACTIONr_scangle_it3.1694.51034
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 80 -
Rwork0.213 2001 -
obs--100 %

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