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- PDB-3jtp: crystal structure of the C-terminal domain of MecA -

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Basic information

Entry
Database: PDB / ID: 3jtp
Titlecrystal structure of the C-terminal domain of MecA
ComponentsAdapter protein mecA 1
KeywordsPROTEIN BINDING / MecA / adaptor protein / degradation tag / 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
IODIDE ION / Adapter protein MecA 1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.17 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 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adapter protein mecA 1
B: Adapter protein mecA 1
C: Adapter protein mecA 1
D: Adapter protein mecA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,70539
Polymers46,2644
Non-polymers4,44235
Water1,54986
1
A: Adapter protein mecA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,70810
Polymers11,5661
Non-polymers1,1429
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adapter protein mecA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5819
Polymers11,5661
Non-polymers1,0158
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Adapter protein mecA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5819
Polymers11,5661
Non-polymers1,0158
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Adapter protein mecA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,83511
Polymers11,5661
Non-polymers1,26910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.518, 107.270, 109.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-105-

IOD

21C-102-

IOD

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Components

#1: Protein
Adapter protein mecA 1


Mass: 11565.924 Da / Num. of mol.: 4 / Fragment: c-terminal domain, UNP residues 121-218 / Mutation: N50D, L63M, T68N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: mecA / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37958
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 14% PEG 3350, 300mM calcium chloride, 4% ethylene glycol,0.1M Bis-Tris pH6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 16, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.17→20.52 Å / Num. obs: 43892 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Biso Wilson estimate: 50.3 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 36.75
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 4.55 / Num. unique all: 21946 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.17→20.52 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.774 / SU ML: 0.38 / σ(F): 0.04 / Phase error: 29.38 / Stereochemistry target values: ML
Details: The file contains friedel pairs in the _refln.pdbx_F_plus and _refln.pdbx_F_minus columns.
RfactorNum. reflection% reflection
Rfree0.2788 2059 5.17 %
Rwork0.2218 --
obs0.2247 39823 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.589 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 122.08 Å2 / Biso mean: 51.536 Å2 / Biso min: 23.55 Å2
Baniso -1Baniso -2Baniso -3
1-13.809 Å2-0 Å2-0 Å2
2---8.261 Å20 Å2
3----5.547 Å2
Refinement stepCycle: LAST / Resolution: 2.17→20.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3063 0 35 86 3184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093119
X-RAY DIFFRACTIONf_angle_d1.2344197
X-RAY DIFFRACTIONf_dihedral_angle_d18.9551123
X-RAY DIFFRACTIONf_chiral_restr0.091467
X-RAY DIFFRACTIONf_plane_restr0.004531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1693-2.21970.34262460.26112073X-RAY DIFFRACTION83
2.2197-2.275200.25472498X-RAY DIFFRACTION89
2.2752-2.33660.32452320.25852246X-RAY DIFFRACTION90
2.3366-2.405300.23722563X-RAY DIFFRACTION91
2.4053-2.48280.31852480.23192371X-RAY DIFFRACTION94
2.4828-2.571300.25392626X-RAY DIFFRACTION94
2.5713-2.67410.31762410.24552447X-RAY DIFFRACTION95
2.6741-2.79550.33372050.25252441X-RAY DIFFRACTION96
2.7955-2.942500.24392722X-RAY DIFFRACTION97
2.9425-3.12630.25792210.23632506X-RAY DIFFRACTION99
3.1263-3.36670.28941840.22832619X-RAY DIFFRACTION99
3.3667-3.703700.19892773X-RAY DIFFRACTION100
3.7037-4.23550.22581460.18082650X-RAY DIFFRACTION100
4.2355-5.32090.22411430.18982656X-RAY DIFFRACTION100
5.3209-20.52140.29231930.23882573X-RAY DIFFRACTION99

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