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- PDB-3qma: Blackfin tuna myoglobin imidazole complex, atomic resolution -

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Basic information

Entry
Database: PDB / ID: 3qma
TitleBlackfin tuna myoglobin imidazole complex, atomic resolution
ComponentsMyoglobin
KeywordsTRANSPORT PROTEIN / myoglobin / oxygen storage / heme / iron
Function / homology
Function and homology information


sarcoplasm / oxygen carrier activity / oxygen binding / oxidoreductase activity / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Myoglobin
Similarity search - Component
Biological speciesThunnus atlanticus (blackfin tuna)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY refinement / Resolution: 0.94 Å
Authorsde Serrano, V.S. / Rodriguez, M.M. / Schreiter, E.R.
CitationJournal: To be Published
Title: High Resolution Structures of Blackfin Tuna Myoglobin
Authors: de Serrano, V.S. / Rodriguez, M.M. / Schreiter, E.R.
History
DepositionFeb 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_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_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_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

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4137
Polymers15,4791
Non-polymers9346
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.198, 52.381, 39.022
Angle α, β, γ (deg.)90.00, 104.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin


Mass: 15479.013 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thunnus atlanticus (blackfin tuna) / References: UniProt: H3JQV6*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AMINO ACID SEQUENCE OF BLACKFIN TUNA MYOGLOBIN IS NOT AVAILABLE IN UNIPROT SEQUENCE DATABASE. ...THE AMINO ACID SEQUENCE OF BLACKFIN TUNA MYOGLOBIN IS NOT AVAILABLE IN UNIPROT SEQUENCE DATABASE. HOWEVER, IT IS ALMOST IDENTICAL TO BLUEFIN (P68189) AND BIGEYE TUNA (Q76G09) MYOGLOBINS, EXCEPT AN H->Q SUBSTITUTION AT RESIDUE 112. THIS SUBSTITUTION ALSO PRESENTS IN OTHER TUNA SPECIES.

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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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M potassium/sodium tartrate, 0.1 M sodium citrate, 2.0 M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.92 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 0.94→16.78 Å / Num. all: 81961 / Num. obs: 79945 / % possible obs: 97.54 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 27.4
Reflection shellResolution: 0.94→0.965 Å / Redundancy: 4 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.32 / % possible all: 88.35

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: RIGID BODY refinement
Starting model: PDB entry 2NRL

2nrl


Resolution: 0.94→16.78 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.431 / SU ML: 0.01 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.005 / ESU R Free: 0.005 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16039 4204 5 %RANDOM
Rwork0.1464 ---
obs0.1471 79945 97.54 %-
all-81961 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.916 Å2
Baniso -1Baniso -2Baniso -3
1--3.98 Å20 Å2-1.87 Å2
2--4.62 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 0.94→16.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 64 197 1352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221543
X-RAY DIFFRACTIONr_bond_other_d0.0020.021068
X-RAY DIFFRACTIONr_angle_refined_deg1.6022.1772132
X-RAY DIFFRACTIONr_angle_other_deg0.96832674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5675209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57325.88251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93815295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.419152
X-RAY DIFFRACTIONr_chiral_restr0.0850.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02257
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3271.5880
X-RAY DIFFRACTIONr_mcbond_other0.4811.5354
X-RAY DIFFRACTIONr_mcangle_it2.10121436
X-RAY DIFFRACTIONr_scbond_it2.7423663
X-RAY DIFFRACTIONr_scangle_it3.9534.5668
X-RAY DIFFRACTIONr_rigid_bond_restr0.99232610
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.94→0.965 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.535 286 -
Rwork0.459 5266 -
obs--87.35 %

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