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Yorodumi- PDB-7f6o: Crystal structure of metal-citrate-binding mutant (S26A) protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f6o | ||||||
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Title | Crystal structure of metal-citrate-binding mutant (S26A) protein (MctA) of ABC transporter endogenously bound to Mn2+-citrate complex | ||||||
Components | Iron ABC transporter, periplasmic iron-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / Substrate-binding protein / metal ion / secondary transporter / symporter | ||||||
Function / homology | Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / CITRIC ACID / : / DI(HYDROXYETHYL)ETHER / SULFUR DIOXIDE / SULFITE ION / Iron ABC transporter, periplasmic iron-binding protein Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Kanaujia, S.P. / Mandal, S.K. | ||||||
Funding support | India, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Structural and thermodynamic insights into a novel Mg 2+ -citrate-binding protein from the ABC transporter superfamily. Authors: Mandal, S.K. / Kanaujia, S.P. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2021 Title: Structural and thermodynamic insights into a novel Mg2+-citrate-binding protein from the ABC transporter superfamily Authors: Mandal, S.K. / Kanaujia, S.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f6o.cif.gz | 275.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f6o.ent.gz | 222.3 KB | Display | PDB format |
PDBx/mmJSON format | 7f6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/7f6o ftp://data.pdbj.org/pub/pdb/validation_reports/f6/7f6o | HTTPS FTP |
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-Related structure data
Related structure data | 7f6eSC 7f6fC 7f6kC 7f6nC 7f6pC 7f6qC 7f6rC 7f6sC 7f6tC 7f6uC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 3 - 338 / Label seq-ID: 5 - 340
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38167.410 Da / Num. of mol.: 2 / Mutation: S26A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (bacteria) Strain: ATCC 27634 / DSM 579 / HB8 / Gene: TTHB177 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q53VZ2 |
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-Non-polymers , 10 types, 197 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-GOL / | #8: Chemical | ChemComp-PG4 / | #9: Chemical | ChemComp-SO2 / | #10: Chemical | ChemComp-PEG / | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.68 % / Description: Orthorhombic |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium fluoride, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 2, 2019 / Details: VariMax HF | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→71.65 Å / Num. obs: 23063 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.971 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.092 / Rrim(I) all: 0.248 / Net I/σ(I): 6.4 / Num. measured all: 168215 / Scaling rejects: 243 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7F6E Resolution: 2.5→58.28 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.858 / SU B: 15.55 / SU ML: 0.183 / SU R Cruickshank DPI: 0.0534 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.45 Å2 / Biso mean: 18.819 Å2 / Biso min: 2.18 Å2
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Refinement step | Cycle: final / Resolution: 2.5→58.28 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 10872 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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