[English] 日本語
Yorodumi- PDB-7f6e: Crystal structure of metal-citrate-binding protein (MctA) of ABC ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f6e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of metal-citrate-binding protein (MctA) of ABC transporter endogenously bound to Mg2+-citrate complex (Form I) | ||||||
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 / outer membrane-bounded periplasmic space / metal ion binding / (2S)-2-HYDROXYPROPANOIC ACID / CITRIC ACID / CARBON DIOXIDE / S-1,2-PROPANEDIOL / 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: 1.77 Å | ||||||
Authors | Kanaujia, S.P. / Mandal, S.K. / Gogoi, P. | ||||||
Funding support | India, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7f6e.cif.gz | 420.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7f6e.ent.gz | 342.9 KB | Display | PDB format |
PDBx/mmJSON format | 7f6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f6e_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7f6e_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 7f6e_validation.xml.gz | 46.6 KB | Display | |
Data in CIF | 7f6e_validation.cif.gz | 68.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/7f6e ftp://data.pdbj.org/pub/pdb/validation_reports/f6/7f6e | HTTPS FTP |
-Related structure data
Related structure data | 7f6fC 7f6kC 7f6nC 7f6oC 7f6pC 7f6qC 7f6rC 7f6sC 7f6tC 7f6uC 3c9hS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: End auth comp-ID: VAL / End label comp-ID: VAL
NCS ensembles :
|
-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 38183.410 Da / Num. of mol.: 3 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 |
---|
-Non-polymers , 9 types, 759 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-CO2 / #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-EDO / #8: Chemical | #9: Chemical | ChemComp-PGO / | #10: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.98 % / Description: Monoclinic |
---|---|
Crystal grow | Temperature: 293 K / Method: microbatch / pH: 5.5 Details: 0.1 M sodium citrate tribasic dihydrate pH 5.5, 16% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 21, 2017 / Details: VariMax HF | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.77→52.98 Å / Num. obs: 92348 / % possible obs: 95.8 % / Redundancy: 5.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.03 / Rrim(I) all: 0.072 / Net I/σ(I): 15.2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C9H Resolution: 1.77→52.98 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.831 / SU ML: 0.061 / SU R Cruickshank DPI: 0.1042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 78.75 Å2 / Biso mean: 23.425 Å2 / Biso min: 8.81 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.77→52.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.77→1.819 Å / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|