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- PDB-4tkq: Native-SAD phasing for YetJ from Bacillus Subtilis -

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Basic information

Entry
Database: PDB / ID: 4tkq
TitleNative-SAD phasing for YetJ from Bacillus Subtilis
ComponentsUncharacterized protein YetJ
KeywordsMEMBRANE PROTEIN / native-SAD phasing / multiple crystals / low energy / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS
Function / homologyBax inhibitor 1-related / Inhibitor of apoptosis-promoting Bax1 / calcium channel activity / calcium ion transport / negative regulation of apoptotic process / membrane / plasma membrane / Uncharacterized protein YetJ
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8025 Å
AuthorsLiu, Q. / Chang, Y. / Hendrickson, W.A. / New York Consortium on Membrane Protein Structure (NYCOMPS)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095315 United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Multi-crystal native SAD analysis at 6 keV.
Authors: Liu, Q. / Guo, Y. / Chang, Y. / Cai, Z. / Assur, Z. / Mancia, F. / Greene, M.I. / Hendrickson, W.A.
History
DepositionMay 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YetJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2635
Polymers24,1171
Non-polymers1464
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.869, 61.869, 288.401
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Uncharacterized protein YetJ


Mass: 24116.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yetJ, BSU07200 / Production host: Escherichia coli (E. coli) / References: UniProt: O31539
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl

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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: 3.3 Å3/Da / Density % sol: 62.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 30% PEG 600, 100 mM CaCl2, 100 mM Tris-HCl, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 2.07 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.07 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 8784 / % possible obs: 98.9 % / Redundancy: 535.8 % / Net I/σ(I): 56.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.8025→39.257 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.79 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2598 757 5.04 %
Rwork0.2205 --
obs0.2225 15009 98.94 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8025→39.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 4 0 1636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021673
X-RAY DIFFRACTIONf_angle_d0.6042274
X-RAY DIFFRACTIONf_dihedral_angle_d11.186571
X-RAY DIFFRACTIONf_chiral_restr0.044279
X-RAY DIFFRACTIONf_plane_restr0.003269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8025-3.01880.31491600.27162713X-RAY DIFFRACTION95
3.0188-3.32250.32751510.2592868X-RAY DIFFRACTION100
3.3225-3.80290.28461540.23032888X-RAY DIFFRACTION100
3.8029-4.78990.23041670.20082874X-RAY DIFFRACTION100
4.7899-39.26040.2221250.20172909X-RAY DIFFRACTION100
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)
13.65781.2228-1.05451.02290.88842.7833-0.01490.13150.2758-0.78680.0827-0.4345-0.22710.078900.3403-0.0235-0.00640.59380.01870.359317.247234.2727-5.2686
20.2615-0.1241-0.22440.1527-0.01180.302-0.2132-0.0475-0.3442-0.14150.07840.10090.28590.2632-00.5289-0.03090.0430.60790.06370.557118.397217.988311.13
30.6055-0.328-0.41580.48450.3070.30650.9018-0.80341.61990.66180.1243-0.9986-1.07420.36270.01740.689-0.04440.08070.7854-0.01380.708319.137138.868111.3972
41.1967-0.73970.19790.4509-0.09860.2495-0.16790.3078-0.1834-0.02410.27750.1320.25430.0463-00.42650.0213-0.03320.720.03160.481613.36520.88351.3555
50.09480.074-0.01420.12570.08110.2159-0.1898-0.52940.7314-0.47580.71530.4346-0.5954-0.05580.00850.49630.08780.03330.76820.14310.66420.9441.2959-1.1573
61.53520.05550.42330.2128-0.58891.8375-0.2254-0.1117-0.19490.42320.30320.2877-0.1581-0.1994-00.43340.02490.00650.5784-0.00560.45086.082728.865118.1152
71.4990.3268-0.50860.7810.98051.78870.06030.32950.16350.17730.1262-0.1784-0.183-0.2089-00.33650.0391-0.06270.61210.05810.52476.693836.8556.6006
81.2952-0.6705-0.05870.3592-0.04431.6466-0.38390.30990.1368-0.14650.58330.18470.135-0.106-00.3620.03980.01030.60140.02820.51178.81525.78794.7913
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:35)
2X-RAY DIFFRACTION2(chain A and resid 36:56)
3X-RAY DIFFRACTION3(chain A and resid 57:66)
4X-RAY DIFFRACTION4(chain A and resid 67:107)
5X-RAY DIFFRACTION5(chain A and resid 108:121)
6X-RAY DIFFRACTION6(chain A and resid 122:151)
7X-RAY DIFFRACTION7(chain A and resid 152:184)
8X-RAY DIFFRACTION8(chain A and resid 185:212)

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