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- PDB-4uzv: Structure of a triple mutant of ASV-TfTrHb -

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Basic information

Entry
Database: PDB / ID: 4uzv
TitleStructure of a triple mutant of ASV-TfTrHb
ComponentsHEMOGLOBIN
KeywordsOXIDOREDUCTASE / BACTERIAL HEMOGLOBINS / HEME LIGAND-BINDING PROPERTIES / THERMOSTABLEPROTEINS
Function / homologyGlobins / Globin-like / Orthogonal Bundle / Mainly Alpha / ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / :
Function and homology information
Biological speciesTHERMOBIFIDA FUSCA TM51 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBaiocco, P. / Bonamore, A. / Sciamanna, N. / Ilari, A. / Boechi, L. / Boffi, A. / Smulevich, G. / Feis, A.
CitationJournal: J.Phys.Chem.B / Year: 2014
Title: Role of Local Structure and Dynamics of Small Ligand Migration in Proteins: A Study of a Mutated Truncated Hemoprotein from Thermobifida Fusca by Time Resolved Mir Spectroscopy.
Authors: Patrizi, B. / Lapini, A. / Di Donato, M. / Marcelli, A. / Lima, M. / Righini, R. / Foggi, P. / Baiocco, P. / Bonamore, A. / Boffi, A.
History
DepositionSep 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Data collection
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6463
Polymers18,9701
Non-polymers6762
Water0
1
A: HEMOGLOBIN
hetero molecules

A: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2926
Polymers37,9412
Non-polymers1,3514
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/41
Buried area4450 Å2
ΔGint-59.6 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.367, 78.367, 89.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein HEMOGLOBIN /


Mass: 18970.402 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-164 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOBIFIDA FUSCA TM51 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: R9F4S3
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.7 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.893
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.893 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 4156 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 14.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 25
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BMM

2bmm


Resolution: 3.4→50 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.872 / SU B: 45.264 / SU ML: 0.683 / Cross valid method: THROUGHOUT / ESU R: 1.412 / ESU R Free: 0.642 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.34904 189 4.6 %RANDOM
Rwork0.29959 ---
obs0.30202 3954 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.051 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1070 0 47 0 1117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221153
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1752.0761575
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0425128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.95822.30865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.70815175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6941515
X-RAY DIFFRACTIONr_chiral_restr0.0780.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021940
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 3.404→3.492 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.465 14 -
Rwork0.381 262 -
obs--94.52 %

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