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- PDB-2bmm: X-ray structure of a novel thermostable hemoglobin from the actin... -

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Basic information

Entry
Database: PDB / ID: 2bmm
TitleX-ray structure of a novel thermostable hemoglobin from the actinobacterium Thermobifida fusca
ComponentsTHERMOSTABLE HEMOGLOBIN FROM THERMOBIFIDA FUSCA
KeywordsOXYGEN STORAGE/TRANSPORT / BACTERIAL HEMOGLOBIN / THERMOSTABLE PROTEIN / OXYGEN STORAGE-TRANSPORT complex
Function / homologyGlobins / Globin-like / Orthogonal Bundle / Mainly Alpha / ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / :
Function and homology information
Biological speciesTHERMOBIFIDA FUSCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsIlari, A. / Franceschini, S. / Bonamore, A. / Boffi, A.
CitationJournal: FEBS J. / Year: 2005
Title: A Novel Thermostable Hemoglobin from the Actinobacterium Thermobifida Fusca.
Authors: Bonamore, A. / Ilari, A. / Giangiacomo, L. / Bellelli, A. / Morea, V. / Boffi, A.
History
DepositionMar 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THERMOSTABLE HEMOGLOBIN FROM THERMOBIFIDA FUSCA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3183
Polymers14,6431
Non-polymers6762
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.617, 84.617, 77.921
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein THERMOSTABLE HEMOGLOBIN FROM THERMOBIFIDA FUSCA


Mass: 14642.640 Da / Num. of mol.: 1 / Fragment: RESIDUES 9-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOBIFIDA FUSCA (bacteria) / Plasmid: PET23-D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: GenBank: 48835434
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.52 Å3/Da / Density % sol: 50.73 %
Crystal growpH: 5.8 / Details: ACETATE BUFFER PH 5.8, NACL 2.5 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.47→50 Å / Num. obs: 6119 / % possible obs: 96.7 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UX8

1ux8


Resolution: 2.48→72.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.897 / SU B: 12.759 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.539 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.315 316 5.2 %RANDOM
Rwork0.218 ---
obs0.223 5783 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.45 Å20 Å2
2--0.91 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.48→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 47 63 1142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221117
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5512.0781528
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2315122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.38321.16760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.72115168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.831516
X-RAY DIFFRACTIONr_chiral_restr0.1050.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02905
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2580.2640
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.2743
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.253
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3080.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8221.5635
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3962986
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0713568
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1074.5540
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.48→2.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.393 13
Rwork0.296 324

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