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- PDB-3jto: Crystal structure of the c-terminal domain of YpbH -

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Basic information

Entry
Database: PDB / ID: 3jto
TitleCrystal structure of the c-terminal domain of YpbH
ComponentsAdapter protein mecA 2
KeywordsPROTEIN BINDING / YpbH / adaptor protein / Competence / Sporulation
Function / homology
Function and homology information


negative regulation of establishment of competence for transformation / negative regulation of sporulation resulting in formation of a cellular spore / establishment of competence for transformation / sporulation resulting in formation of a cellular spore / protein-macromolecule adaptor activity
Similarity search - Function
Alpha-Beta Plaits - #1950 / MecA, C-terminal domain superfamily / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Adapter protein MecA 2
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, F. / Mei, Z. / Qi, Y. / Yan, C. / Wang, J. / Shi, Y.
CitationJournal: To be Published
Title: Crystal Structure of the MecA Degradation Tag
Authors: Wang, F. / Mei, Z. / Qi, Y. / Yan, C. / Xiang, S. / Zhou, Z. / Hu, Q. / Wang, J. / Shi, Y.
History
DepositionSep 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: Adapter protein mecA 2
B: Adapter protein mecA 2
C: Adapter protein mecA 2
D: Adapter protein mecA 2
E: Adapter protein mecA 2
F: Adapter protein mecA 2


Theoretical massNumber of molelcules
Total (without water)63,0816
Polymers63,0816
Non-polymers00
Water2,738152
1
A: Adapter protein mecA 2


Theoretical massNumber of molelcules
Total (without water)10,5141
Polymers10,5141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adapter protein mecA 2


Theoretical massNumber of molelcules
Total (without water)10,5141
Polymers10,5141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Adapter protein mecA 2


Theoretical massNumber of molelcules
Total (without water)10,5141
Polymers10,5141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Adapter protein mecA 2


Theoretical massNumber of molelcules
Total (without water)10,5141
Polymers10,5141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Adapter protein mecA 2


Theoretical massNumber of molelcules
Total (without water)10,5141
Polymers10,5141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Adapter protein mecA 2


Theoretical massNumber of molelcules
Total (without water)10,5141
Polymers10,5141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)162.056, 162.056, 142.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein
Adapter protein mecA 2 / YpbH


Mass: 10513.531 Da / Num. of mol.: 6 / Fragment: c-terminal domain, UNP residues 101-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ypbH / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P50734
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.72 Å3/Da / Density % sol: 66.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% PEG 400, 1.85M ammonium sulfate, 0.1M Hepes pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→39 Å / Num. all: 37149 / Num. obs: 37149 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 42.17 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 25.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 3 / Num. unique all: 37149 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JTN

3jtn


Resolution: 2.4→38.197 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.813 / SU ML: 0.42 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.03 / Phase error: 25.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1831 5.17 %thin shell
Rwork0.2304 ---
obs0.2324 35383 94.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.898 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 49.923 Å2
Baniso -1Baniso -2Baniso -3
1--1.597 Å20 Å20 Å2
2---1.597 Å2-0 Å2
3---3.194 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4345 0 0 152 4497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074434
X-RAY DIFFRACTIONf_angle_d1.0896022
X-RAY DIFFRACTIONf_chiral_restr0.075682
X-RAY DIFFRACTIONf_plane_restr0.004775
X-RAY DIFFRACTIONf_dihedral_angle_d17.781503
LS refinement shellResolution: 2.4002→2.4651 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3133 272 -
Rwork0.2612 2121 -
obs--84 %

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