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- PDB-2xkg: C.lacteus mini-Hb Leu86Ala mutant -

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Basic information

Entry
Database: PDB / ID: 2xkg
TitleC.lacteus mini-Hb Leu86Ala mutant
ComponentsNEURAL HEMOGLOBIN
KeywordsOXYGEN STORAGE / METAL-BINDING
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Neural hemoglobin
Similarity search - Component
Biological speciesCEREBRATULUS LACTEUS (milky ribbon-worm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPesce, A. / Nardini, M. / Dewilde, S. / Capece, L. / Marti, M.A. / Congia, S. / Salter, M.D. / Blouin, G.C. / Estrin, D.A. / Ascenzi, P. ...Pesce, A. / Nardini, M. / Dewilde, S. / Capece, L. / Marti, M.A. / Congia, S. / Salter, M.D. / Blouin, G.C. / Estrin, D.A. / Ascenzi, P. / Moens, L. / Bolognesi, M. / Olson, J.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Ligand Migration in the Apolar Tunnel of Cerebratulus Lacteus Mini-Hemoglobin.
Authors: Pesce, A. / Nardini, M. / Dewilde, S. / Capece, L. / Marti, M.A. / Congia, S. / Salter, M.D. / Blouin, G.C. / Estrin, D.A. / Ascenzi, P. / Moens, L. / Bolognesi, M. / Olson, J.S.
History
DepositionJul 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: 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: NEURAL HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5387
Polymers11,5051
Non-polymers1,0336
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.650, 43.347, 59.443
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 NEURAL HEMOGLOBIN / NRHB / MINI-HEMOGLOBIN


Mass: 11504.869 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CEREBRATULUS LACTEUS (milky ribbon-worm)
Tissue: NERVE TISSUE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O76242
#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-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 87 TO ALA

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growTemperature: 277 K / pH: 6
Details: 60 % AMMONIUM SULFATE AND 50 MM SODIUM ACETATE BUFFER, PH 6, AT 4C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→34.9 Å / Num. obs: 15045 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 24.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 12.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KR7

1kr7


Resolution: 1.6→21.25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.177 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18581 759 5.1 %RANDOM
Rwork0.15372 ---
obs0.15529 14252 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.247 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→21.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms811 0 65 140 1016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021918
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1722.0871258
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5555113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71224.61539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49315129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.183152
X-RAY DIFFRACTIONr_chiral_restr0.0850.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.02709
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_it1.6251.5546
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4652854
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6013372
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2624.5402
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: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 55 -
Rwork0.175 1029 -
obs--100 %

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