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- PDB-5b4z: Crystal structure of heme binding protein HmuT H141A mutant -

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Basic information

Entry
Database: PDB / ID: 5b4z
TitleCrystal structure of heme binding protein HmuT H141A mutant
ComponentsABC-type transporter, periplasmic component
KeywordsTRANSPORT PROTEIN / Heme / ABC transporter
Function / homology: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / ABC-type transporter, periplasmic component
Function and homology information
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 / Category: diffrn_source / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)36,6972
Polymers36,0801
Non-polymers6161
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-14 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.380, 73.380, 147.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 36080.156 Da / Num. of mol.: 1 / Fragment: UNP residues 24-359 / Mutation: H141A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / Gene: Cgl0389 / Plasmid: pET22b / 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.: 230 / 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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.25 M Ammonium sulfate, 0.20 M Potassium thiocyanate, 0.20 M Ammonium tartrate, 5%(v/v) Polypropylene glycol, 0.025%(w/v) beta-Octyl glucoside

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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→48.94 Å / Num. obs: 97636 / % possible obs: 98.8 % / Redundancy: 9.58 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.98
Reflection shellResolution: 1.3→1.34 Å / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 3.73 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
PHENIX1.8.4refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5az3

5az3


Resolution: 1.3→48.94 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.056 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.038 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16894 4800 4.9 %RANDOM
Rwork0.15106 ---
obs0.15195 92836 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.139 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.3→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 43 230 2512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192403
X-RAY DIFFRACTIONr_bond_other_d0.0020.022300
X-RAY DIFFRACTIONr_angle_refined_deg1.3182.0153307
X-RAY DIFFRACTIONr_angle_other_deg0.93135299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8195331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71125.39389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.39115374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7891514
X-RAY DIFFRACTIONr_chiral_restr0.0890.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212819
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02479
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_it0.7281.2741288
X-RAY DIFFRACTIONr_mcbond_other0.7251.2731287
X-RAY DIFFRACTIONr_mcangle_it1.0131.9191625
X-RAY DIFFRACTIONr_mcangle_other1.0131.9211626
X-RAY DIFFRACTIONr_scbond_it0.9851.4781115
X-RAY DIFFRACTIONr_scbond_other0.981.4751113
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2282.1541680
X-RAY DIFFRACTIONr_long_range_B_refined1.89411.4262862
X-RAY DIFFRACTIONr_long_range_B_other1.66210.932738
X-RAY DIFFRACTIONr_rigid_bond_restr0.69734703
X-RAY DIFFRACTIONr_sphericity_free17.901557
X-RAY DIFFRACTIONr_sphericity_bonded5.20254830
LS refinement shellResolution: 1.303→1.337 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 303 -
Rwork0.174 6648 -
obs--96.46 %

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