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- PDB-5b51: Crystal structure of heme binding protein HmuT R242A mutant -

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Basic information

Entry
Database: PDB / ID: 5b51
TitleCrystal structure of heme binding protein HmuT R242A mutant
ComponentsABC-type transporter, periplasmic component
KeywordsTRANSPORT PROTEIN / Heme / ABC transporter
Function / homology
Function and homology information


: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / ABC-type transporter, periplasmic component
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMuraki, N. / Aono, S.
CitationJournal: Int J Mol Sci / Year: 2016
Title: Structural Characterization of Heme Environmental Mutants of CgHmuT that Shuttles Heme Molecules to Heme Transporters
Authors: Muraki, N. / Kitatsuji, C. / Ogura, M. / Uchida, T. / Ishimori, K. / Aono, S.
History
DepositionApr 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_special_symmetry / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC-type transporter, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6782
Polymers36,0611
Non-polymers6161
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-16 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.060, 73.060, 147.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-675-

HOH

21A-698-

HOH

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Components

#1: Protein ABC-type transporter, periplasmic component / HmuT


Mass: 36061.109 Da / Num. of mol.: 1 / Fragment: UNP residues 24-359 / Mutation: R242A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / Gene: Cgl0389 / Plasmid: pET22 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NTB8
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.90 M Ammonium sulfate, 0.19 M Ammonium tartrate, 0.16 M Potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.3→48.68 Å / Num. obs: 96893 / % possible obs: 98.3 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 17.52
Reflection shellResolution: 1.3→1.34 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4.58 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5az3

5az3


Resolution: 1.3→42.27 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.217 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18066 4770 4.9 %RANDOM
Rwork0.16252 ---
obs0.16343 92123 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.755 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.3→42.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 43 225 2606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192507
X-RAY DIFFRACTIONr_bond_other_d0.0020.022409
X-RAY DIFFRACTIONr_angle_refined_deg1.3512.0123457
X-RAY DIFFRACTIONr_angle_other_deg0.9435556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7515353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91325.31994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.48515396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9831515
X-RAY DIFFRACTIONr_chiral_restr0.0810.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212923
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02502
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_it0.8811.4231331
X-RAY DIFFRACTIONr_mcbond_other0.8791.4221330
X-RAY DIFFRACTIONr_mcangle_it1.1682.1441672
X-RAY DIFFRACTIONr_mcangle_other1.1682.1451673
X-RAY DIFFRACTIONr_scbond_it1.4371.6681176
X-RAY DIFFRACTIONr_scbond_other1.4311.6641174
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7672.4181772
X-RAY DIFFRACTIONr_long_range_B_refined2.06512.6382998
X-RAY DIFFRACTIONr_long_range_B_other1.96112.252889
X-RAY DIFFRACTIONr_rigid_bond_restr0.94834916
X-RAY DIFFRACTIONr_sphericity_free16.75557
X-RAY DIFFRACTIONr_sphericity_bonded7.02155033
LS refinement shellResolution: 1.299→1.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 313 -
Rwork0.189 6733 -
obs--98.2 %

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