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- PDB-5az3: Crystal structure of heme binding protein HmuT -

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Basic information

Entry
Database: PDB / ID: 5az3
TitleCrystal structure of heme binding protein HmuT
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: 1.423 Å
AuthorsMuraki, N. / Aono, S.
CitationJournal: Chem Lett. / Year: 2015
Title: Structural Basis for Heme Recognition by HmuT Responsible for Heme Transport to the Heme Transporter in Corynebacterium glutamicum
Authors: Muraki, N. / Aono, S.
History
DepositionSep 18, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
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)36,6332
Polymers36,0161
Non-polymers6161
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-16 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.040, 73.040, 147.320
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: 36016.031 Da / Num. of mol.: 1 / Fragment: UNP residues 24-359
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.: 184 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.1 M ammonium sulfate, 0.2 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.42→35.59 Å / Num. obs: 75260 / % possible obs: 99.7 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 19.9
Reflection shellResolution: 1.42→1.5 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 6.9 / % possible all: 99.4

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Processing

Software
NameVersionClassification
iMOSFLMdata processing
SCALAdata scaling
PHASERphasing
Cootmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MD9

3md9


Resolution: 1.423→35.447 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1815 3769 5.01 %Random selection
Rwork0.1682 ---
obs0.1689 75158 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.423→35.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 43 184 2471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072472
X-RAY DIFFRACTIONf_angle_d1.1163419
X-RAY DIFFRACTIONf_dihedral_angle_d12.281885
X-RAY DIFFRACTIONf_chiral_restr0.066398
X-RAY DIFFRACTIONf_plane_restr0.005451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.423-1.4410.21541240.18312614X-RAY DIFFRACTION99
1.441-1.460.1951660.17152565X-RAY DIFFRACTION99
1.46-1.480.19011300.16422588X-RAY DIFFRACTION100
1.48-1.50110.20541220.16022627X-RAY DIFFRACTION99
1.5011-1.52350.17491490.15642601X-RAY DIFFRACTION99
1.5235-1.54730.15581480.15092556X-RAY DIFFRACTION99
1.5473-1.57270.16571180.14882625X-RAY DIFFRACTION99
1.5727-1.59980.17141350.14692593X-RAY DIFFRACTION100
1.5998-1.62890.18041270.14622651X-RAY DIFFRACTION100
1.6289-1.66020.1521240.14712648X-RAY DIFFRACTION100
1.6602-1.69410.20511400.14992606X-RAY DIFFRACTION100
1.6941-1.7310.17751480.14872607X-RAY DIFFRACTION100
1.731-1.77120.15461360.15122620X-RAY DIFFRACTION100
1.7712-1.81550.15531510.14832638X-RAY DIFFRACTION100
1.8155-1.86460.16221330.15162640X-RAY DIFFRACTION100
1.8646-1.91950.14561450.15152629X-RAY DIFFRACTION100
1.9195-1.98140.14681330.1522665X-RAY DIFFRACTION100
1.9814-2.05220.15041130.15232640X-RAY DIFFRACTION100
2.0522-2.13440.15631560.16022642X-RAY DIFFRACTION100
2.1344-2.23150.1471360.172667X-RAY DIFFRACTION100
2.2315-2.34910.19791180.17082690X-RAY DIFFRACTION100
2.3491-2.49630.2081610.17592652X-RAY DIFFRACTION100
2.4963-2.6890.20091660.18522659X-RAY DIFFRACTION100
2.689-2.95940.20921240.19042717X-RAY DIFFRACTION100
2.9594-3.38740.19661540.19542710X-RAY DIFFRACTION100
3.3874-4.26660.17371610.17112739X-RAY DIFFRACTION100
4.2666-35.45810.20421510.1672800X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 27.0411 Å / Origin y: 64.9175 Å / Origin z: 160.9131 Å
111213212223313233
T0.1022 Å2-0.0089 Å20.0036 Å2-0.0905 Å20.0048 Å2--0.1011 Å2
L0.6085 °2-0.4918 °2-0.4707 °2-0.897 °20.465 °2--0.8035 °2
S-0.0222 Å °0.0044 Å °-0.0241 Å °0.0106 Å °0.0086 Å °0.0303 Å °0.0114 Å °0.0246 Å °0.0134 Å °
Refinement TLS groupSelection details: all

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