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- PDB-3bom: Crystal structure of trout hemoglobin at 1.35 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 3bom
TitleCrystal structure of trout hemoglobin at 1.35 Angstrom resolution
Components
  • Hemoglobin subunit alpha-4
  • Hemoglobin subunit beta-4
KeywordsOXYGEN STORAGE/TRANSPORT / Fish Hemoglobin / Structural Genomics Community Request / Protein Structure Initiative / PSI-2 / Center for Eukaryotic Structural Genomics / CESG / Heme / Iron / Metal-binding / Oxygen transport / Transport / OXYGEN STORAGE-TRANSPORT complex
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
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 beta-4 / Hemoglobin subunit alpha-4
Similarity search - Component
Biological speciesOncorhynchus mykiss (rainbow trout)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsAranda IV, R. / Bingman, C.A. / Bitto, E. / Wesenberg, G.E. / Richards, M. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be Published
Title: Trout Hemoglobin Crystal Structure at 1.35 Angstroms Resolution.
Authors: Aranda IV, R. / Bingman, C.A. / Bitto, E. / Wesenberg, G.E. / Richards, M. / Phillips Jr., G.N.
History
DepositionDec 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 23, 2013Group: Database references / Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 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_conn_type / 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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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-4
B: Hemoglobin subunit beta-4
C: Hemoglobin subunit alpha-4
D: Hemoglobin subunit beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,49412
Polymers63,7804
Non-polymers2,7148
Water14,718817
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.455, 63.162, 78.702
Angle α, β, γ (deg.)90.000, 93.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemoglobin subunit alpha-4 / / Hemoglobin alpha-4 chain / Alpha-4-globin


Mass: 15851.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oncorhynchus mykiss (rainbow trout) / Tissue: Blood / References: UniProt: P14527
#2: Protein Hemoglobin subunit beta-4 / / Hemoglobin beta-4 chain / Beta-4-globin / Hemoglobin beta-IV chain


Mass: 16038.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oncorhynchus mykiss (rainbow trout) / Tissue: Blood / References: UniProt: P02141
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 817 / 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: 2.2 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: Protein solution (15 mg/mL CO-bound trout IV Hemoglobin, 0.025 M Sodium chloride, 0.010 M Tris-HCl pH 8.0) was mixed one to one with carbon monoxide flushed well solution to yield a final ...Details: Protein solution (15 mg/mL CO-bound trout IV Hemoglobin, 0.025 M Sodium chloride, 0.010 M Tris-HCl pH 8.0) was mixed one to one with carbon monoxide flushed well solution to yield a final concentration of 22.5% PEG 1500 and 0.04-0.06 M MES/Acetate at pH 5.7. The solutions were pH-ed to verify that the crystallization conditions were at pH 5.7 due to the lower buffer molarity. Crystals were cryo-protected with 22.5% PEG 1500, 22.5% Ethylene glycol, 0.04-0.06 M MES/Acetate at pH 5.7 in a single step, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97935 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 16, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.35→39.294 Å / Num. obs: 120196 / % possible obs: 97.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.118 / Χ2: 1.403 / Net I/σ(I): 10.482
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.35-1.384.20.4592.30663750.62877.8
1.38-1.425.20.44173100.63789.3
1.42-1.4560.40478090.68695.4
1.45-1.56.80.34581470.77599.6
1.5-1.557.30.30382050.929100
1.55-1.67.40.26882041.058100
1.6-1.667.50.23582221.194100
1.66-1.747.50.21681901.43100
1.74-1.837.50.18781801.579100
1.83-1.957.50.16782171.938100
1.95-2.17.50.14682182.023100
2.1-2.317.50.14282522.045100
2.31-2.647.60.12982431.769100
2.64-3.337.50.11382811.793100
3.33-39.2947.30.08883431.44699

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.472 / Cor.coef. Fo:Fc: 0.43
Highest resolutionLowest resolution
Rotation3 Å39.29 Å
Translation3 Å39.29 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3data extraction
MAR345CCDdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OUU

1ouu


Resolution: 1.35→39.294 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.178 / SU B: 2.373 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 6037 5.026 %RANDOM
Rwork0.17 ---
obs0.172 120109 97.384 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 20.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.186 Å20 Å2-0.778 Å2
2---1.58 Å20 Å2
3---1.682 Å2
Refinement stepCycle: LAST / Resolution: 1.35→39.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4496 0 188 817 5501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224973
X-RAY DIFFRACTIONr_angle_refined_deg1.1972.0656840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5615618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81124.213197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4715821
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1711520
X-RAY DIFFRACTIONr_chiral_restr0.0820.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023736
X-RAY DIFFRACTIONr_nbd_refined0.2040.22685
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23468
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2657
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.250
X-RAY DIFFRACTIONr_mcbond_it1.111.53030
X-RAY DIFFRACTIONr_mcangle_it1.45924818
X-RAY DIFFRACTIONr_scbond_it2.37632185
X-RAY DIFFRACTIONr_scangle_it3.3114.51991
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.3850.2653370.2496779908678.318
1.385-1.4230.274180.2187537883890.009
1.423-1.4640.2314180.197940863596.792
1.464-1.5090.2324280.1697922836599.821
1.509-1.5590.1953900.16377308120100
1.559-1.6130.1934000.15574347834100
1.613-1.6740.2063830.15971967579100
1.674-1.7430.2073800.16369087288100
1.743-1.820.2123020.16666806982100
1.82-1.9090.2293120.16364096721100
1.909-2.0120.2283380.1636006634599.984
2.012-2.1340.2033430.16157026045100
2.134-2.2810.2072970.16753525649100
2.281-2.4640.2322520.1750445296100
2.464-2.6990.2262410.17246164857100
2.699-3.0170.2312360.1734207444499.978
3.017-3.4830.1931730.173719389399.974
3.483-4.2630.191860.1583118330699.94
4.263-6.0210.1981350.1742453258999.961
6.021-39.2940.203680.1851320146494.809

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