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- PDB-3jtn: Crystal Structure of the c-terminal domain of YpbH -

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Basic information

Entry
Database: PDB / ID: 3jtn
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
IODIDE ION / Adapter protein MecA 2
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / PHASER / Resolution: 2.09 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 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,14116
Polymers20,3652
Non-polymers1,77714
Water1,08160
1
A: Adapter protein mecA 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0718
Polymers10,1821
Non-polymers8887
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adapter protein mecA 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0718
Polymers10,1821
Non-polymers8887
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.930, 71.660, 39.330
Angle α, β, γ (deg.)90.00, 95.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Adapter protein mecA 2 / YpbH


Mass: 10182.252 Da / Num. of mol.: 2 / Fragment: c-terminal domain, UNP residues 104-194
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: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350,0.3M calcium chloride, 0.1M Bis-Tris pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 22, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→34.363 Å / Num. all: 17571 / Num. obs: 17571 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 30.99 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.09
Reflection shellResolution: 2.09→2.21 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 2.6 / Num. unique all: 17571 / % possible all: 88

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: PHASER / Resolution: 2.09→34.363 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.698 / SU ML: 0.35 / σ(F): 0.03 / Phase error: 36.01 / 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
Rfree0.3035 795 4.88 %
Rwork0.2175 --
obs0.2219 16294 87.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.434 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso max: 226.24 Å2 / Biso mean: 43.401 Å2 / Biso min: 15.09 Å2
Baniso -1Baniso -2Baniso -3
1--5.31 Å20 Å2-6.223 Å2
2---4.305 Å2-0 Å2
3---9.615 Å2
Refinement stepCycle: LAST / Resolution: 2.09→34.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 14 60 1496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081452
X-RAY DIFFRACTIONf_angle_d1.0841972
X-RAY DIFFRACTIONf_dihedral_angle_d18.571492
X-RAY DIFFRACTIONf_chiral_restr0.061223
X-RAY DIFFRACTIONf_plane_restr0.004253
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.089-2.220.431640.3081972203665
2.22-2.3910.3681040.2592339244379
2.391-2.6320.3731860.2522631281790
2.632-3.0130.3361680.2542754292295
3.013-3.7950.2871490.1852853300297
3.795-34.3670.2331240.1882950307499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5898-0.3909-0.92192.53040.46691.9974-0.0401-0.0070.053-0.30850.02040.27230.06570.0214-0.01560.248-0.0063-0.01240.20060.01780.216713.919351.118525.2796
21.2043-1.47980.63321.5059-0.71381.30460.0385-0.1310.1011-0.0650.08960.01070.1451-0.1308-0.10830.161-0.0246-0.00940.18410.01650.205121.683630.538735.3546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA2 - 90
2X-RAY DIFFRACTION2CHAIN BB2 - 91

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