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- PDB-3bj3: met-Perch hemoglobin at pH 8.0 -

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Basic information

Entry
Database: PDB / ID: 3bj3
Titlemet-Perch hemoglobin at pH 8.0
Components
  • hemoglobin alpha
  • hemoglobin beta
KeywordsOXYGEN BINDING / hemoglobin / autooxidation / heme loss / OXYGEN STORAGE/TRANSPORT
Function / homology
Function and homology information


haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding ...haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / 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 ...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
ACETYL GROUP / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin alpha / Hemoglobin beta
Similarity search - Component
Biological speciesPerca flavescens (yellow perch)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAranda IV, R. / Cai, H. / Levin, E.J. / Richards, M.P. / Phillips Jr., G.N.
CitationJournal: Proteins / Year: 2008
Title: Structural analysis of fish versus mammalian hemoglobins: Effect of the heme pocket environment on autooxidation and hemin loss.
Authors: Aranda, R. / Cai, H. / Worley, C.E. / Levin, E.J. / Li, R. / Olson, J.S. / Phillips, G.N. / Richards, M.P.
History
DepositionDec 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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_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
B: hemoglobin beta
C: hemoglobin alpha
D: hemoglobin beta
A: ACETYL GROUP
C: ACETYL GROUP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,77310
Polymers63,2194
Non-polymers2,5546
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12450 Å2
ΔGint-108 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.730, 84.897, 121.475
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hemoglobin alpha


Mass: 15523.905 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perca flavescens (yellow perch) / References: UniProt: D0VWS3*PLUS
#2: Protein hemoglobin beta


Mass: 16085.478 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perca flavescens (yellow perch) / References: UniProt: D0VWV3*PLUS
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris at pH 8.0 and 16.5% polyethylene glycol 4K, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: MAR CCD 130 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→70 Å / Num. obs: 32953

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OUU

1ouu


Resolution: 2.1→69.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.685 / SU ML: 0.181 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25205 1738 5 %RANDOM
Rwork0.20416 ---
obs0.20666 32953 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.763 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å20 Å2
2---1.01 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.1→69.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4458 0 178 152 4788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224810
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3472.0656586
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3065588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.4224.241191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41615775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7911516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023626
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.22389
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23335
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2221
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0750.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6121.52965
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00424631
X-RAY DIFFRACTIONr_scbond_it1.77132130
X-RAY DIFFRACTIONr_scangle_it2.5994.51940
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 109 -
Rwork0.246 2137 -
obs--86.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3561.47040.74445.0388-0.07311.78370.01280.12330.0651-0.5158-0.1297-0.3510.41720.48820.11690.15970.11280.17810.15840.01540.089435.0491-5.443337.5899
24.40351.35761.19223.6116-0.77144.75610.20670.49590.2005-0.1218-0.2038-0.62070.61251.1843-0.00290.14230.23220.19180.27280.07340.175941.6328-9.42642.4639
30.8075-0.19480.24741.0802-1.18143.20540.07560.0737-0.1019-0.2771-0.0824-0.25660.43880.3130.00680.22030.0550.10030.1403-0.00640.170830.0433-6.335742.0928
45.53042.3416-1.10744.5774-1.18112.0923-0.1730.37980.0873-0.41250.15720.108-0.0813-0.21920.01580.1945-0.00810.03830.09310.0254-0.020520.35239.501336.0038
56.92131.41780.59474.16971.60153.67180.07370.3594-0.0416-0.4338-0.13350.7108-0.161-0.79460.05980.10330.0163-0.02650.2390.01120.056410.25738.10438.2058
62.9379-0.5159-1.48423.13991.20322.7284-0.1395-0.10380.098-0.09650.0492-0.0169-0.07440.05770.09030.15660.01140.00610.09990.02890.111220.978811.197243.5024
74.5608-0.46840.37843.3457-0.6863.07110.1738-0.65560.3050.4335-0.02270.15490.2933-0.5623-0.15110.1077-0.17770.08820.209-0.02310.042713.5108-6.46869.3111
82.93830.80180.38221.61960.21821.03010.2504-0.2619-0.01540.324-0.1754-0.03630.3811-0.1904-0.0750.2483-0.10040.07470.14170.05060.111716.9816-9.982865.5269
92.9372.4428-4.97619.2426-0.78414.0252-0.0344-0.3162-0.7059-0.1966-0.4381-0.2140.23390.45070.47240.2091-0.05140.03140.13290.06350.137317.5766-12.01151.5537
104.01991.52560.75985.9191.45812.44870.1486-0.3740.16520.6049-0.3099-0.00580.10740.08390.16130.0424-0.06390.01650.1007-0.00590.035630.02518.358470.8266
118.544-0.431.665725.6272-2.73983.64440.16230.0715-0.85570.1576-0.2976-1.51480.01670.67060.1353-0.0068-0.0382-0.1080.29490.04560.297744.66160.033871.0227
122.95762.4051-0.12445.58130.16581.8252-0.0933-0.02440.34530.0459-0.11060.3158-0.0791-0.04860.20390.0412-0.002-0.0510.1364-0.03610.166728.493812.464665.6245
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 451 - 45
2X-RAY DIFFRACTION2AA46 - 9046 - 90
3X-RAY DIFFRACTION3AA91 - 14291 - 142
4X-RAY DIFFRACTION4BB1 - 401 - 40
5X-RAY DIFFRACTION5BB41 - 8141 - 81
6X-RAY DIFFRACTION6BB82 - 14682 - 146
7X-RAY DIFFRACTION7CC1 - 511 - 51
8X-RAY DIFFRACTION8CC52 - 13352 - 133
9X-RAY DIFFRACTION9CC134 - 142134 - 142
10X-RAY DIFFRACTION10DD1 - 441 - 44
11X-RAY DIFFRACTION11DD45 - 6445 - 64
12X-RAY DIFFRACTION12DD65 - 14665 - 146

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