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- PDB-5b50: Crystal structure of heme binding protein HmuT Y240A -

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Basic information

Entry
Database: PDB / ID: 5b50
TitleCrystal structure of heme binding protein HmuT Y240A
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: 1.65 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)36,6722
Polymers36,0551
Non-polymers6161
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-17 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.010, 73.010, 145.960
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: 36055.129 Da / Num. of mol.: 1 / Fragment: UNP residues 24-359 / Mutation: Y240A
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: isolated from a natural source / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.1 M Ammonium sulfate, 0.2 M Potassium thiocyanate, 0.5 % beta-Octyl glucoside, 20 % Glycerol

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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: Apr 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.65→35.41 Å / Num. obs: 48329 / % possible obs: 100 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 16.6
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5az3

5az3


Resolution: 1.65→35.414 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 2413 5 %
Rwork0.1763 --
obs0.1778 48298 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→35.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 43 141 2527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152540
X-RAY DIFFRACTIONf_angle_d1.3913508
X-RAY DIFFRACTIONf_dihedral_angle_d12.611510
X-RAY DIFFRACTIONf_chiral_restr0.096414
X-RAY DIFFRACTIONf_plane_restr0.008461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.68370.25761340.19392672X-RAY DIFFRACTION100
1.6837-1.72030.22741190.1942690X-RAY DIFFRACTION100
1.7203-1.76030.21681330.18162636X-RAY DIFFRACTION100
1.7603-1.80430.23011510.17032619X-RAY DIFFRACTION100
1.8043-1.85310.19821410.16492674X-RAY DIFFRACTION100
1.8531-1.90760.20781450.16562665X-RAY DIFFRACTION100
1.9076-1.96920.16611300.15722668X-RAY DIFFRACTION100
1.9692-2.03960.18081260.16042684X-RAY DIFFRACTION100
2.0396-2.12120.19811480.15732664X-RAY DIFFRACTION100
2.1212-2.21780.18411390.16732676X-RAY DIFFRACTION100
2.2178-2.33470.2381230.17022709X-RAY DIFFRACTION100
2.3347-2.48090.23591590.18522678X-RAY DIFFRACTION100
2.4809-2.67240.23361670.18962676X-RAY DIFFRACTION100
2.6724-2.94120.22361250.19932747X-RAY DIFFRACTION100
2.9412-3.36650.22791500.19752728X-RAY DIFFRACTION100
3.3665-4.24030.18241650.17072771X-RAY DIFFRACTION100
4.2403-35.42230.19011580.16422928X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 27.3743 Å / Origin y: 64.2685 Å / Origin z: 159.8299 Å
111213212223313233
T0.1294 Å2-0.01 Å2-0.005 Å2-0.1117 Å20.003 Å2--0.1276 Å2
L0.6334 °2-0.5218 °2-0.4752 °2-1.1317 °20.6247 °2--1.0234 °2
S-0.0073 Å °0.0107 Å °-0.0326 Å °-0.0167 Å °0.0052 Å °0.0143 Å °0.0052 Å °0.0366 Å °0.0025 Å °
Refinement TLS groupSelection details: all

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