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- PDB-4ygt: Crystal structure of a DUF4309 family protein (YjgB) from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 4ygt
TitleCrystal structure of a DUF4309 family protein (YjgB) from Bacillus subtilis subsp. subtilis str. 168 at 2.13 A resolution
ComponentsUncharacterized protein YjgB
KeywordsSTRUCTURAL GENOMICS UNKNOWN FUNCTION / putative secreted lipoprotein / the first structural representative of PF14172 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / UNKNOWN FUNCTION
Function / homologyProtein of unknown function DUF4309 / Domain of unknown function (DUF4309) / Uncharacterized protein YjgB
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.13 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a DUF4309 family protein (YjgB) from Bacillus subtilis subsp. subtilis str. 168 at 2.13 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein YjgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2906
Polymers17,9451
Non-polymers3445
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.830, 90.830, 41.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Uncharacterized protein YjgB / DUF4309 family protein


Mass: 17945.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yjgB, BSU12150, NP_389097.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: O34960
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 33-191) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 33-191) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium sulfate, 20% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9793,0.7514,0.9791
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2014
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.75141
30.97911
ReflectionResolution: 2.13→45.416 Å / Num. obs: 11231 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.915 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.13 / Net I/σ(I): 14.58 / Num. measured all: 120232
Reflection shell
Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.13-2.210.8111.6351.911457116111591.72699.8
2.21-2.290.8851.3732.511210100410041.438100
2.29-2.40.931.1632.813043117111711.219100
2.4-2.520.870.9433.311751106710670.989100
2.52-2.680.9560.5835.212241113111310.612100
2.68-2.890.980.328811342112211220.346100
2.89-3.180.9920.20512.912758112611260.215100
3.18-3.640.9980.09823.412493113411340.103100
3.64-4.570.9990.05236.811613112811230.05499.6
4.57-45.4160.9990.04546.512324118711810.04899.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJanuary 10, 2014 BUILT=20140307data scaling
BUSTER2.10.2refinement
RefinementMethod to determine structure: MAD / Resolution: 2.13→45.416 Å / Cor.coef. Fo:Fc: 0.9438 / Cor.coef. Fo:Fc free: 0.9333 / Occupancy max: 1 / Occupancy min: 0.75 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. SULFATE FROM THE CRYSTALLIZATION CONDITIONS (SO4) AND 1,2-ETHANEDIOL USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 534 4.77 %RANDOM
Rwork0.1913 10668 --
obs0.1933 11202 99.8 %-
Displacement parametersBiso max: 155.84 Å2 / Biso mean: 62.4779 Å2 / Biso min: 28.97 Å2
Baniso -1Baniso -2Baniso -3
1--6.9609 Å20 Å20 Å2
2---6.9609 Å20 Å2
3---13.9219 Å2
Refine analyzeLuzzati coordinate error obs: 0.398 Å
Refinement stepCycle: LAST / Resolution: 2.13→45.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 21 50 1240
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d542SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes174HARMONIC5
X-RAY DIFFRACTIONt_it1213HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion148SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1414SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1213HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1638HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.69
X-RAY DIFFRACTIONt_other_torsion2.89
LS refinement shellResolution: 2.13→2.33 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2451 117 4.42 %
Rwork0.2273 2533 -
all0.2281 2650 -
obs--99.8 %
Refinement TLS params.Method: refined / Origin x: 34.7307 Å / Origin y: 35.9897 Å / Origin z: 27.7195 Å
111213212223313233
T-0.2169 Å20.1254 Å2-0.0046 Å2--0.0107 Å20.0148 Å2---0.2413 Å2
L5.1656 °2-3.9082 °2-0.7098 °2-4.8526 °21.8697 °2--6.4912 °2
S-0.2098 Å °-0.4713 Å °0.1111 Å °0.2057 Å °0.4187 Å °-0.3952 Å °-0.0039 Å °0.6262 Å °-0.2089 Å °
Refinement TLS groupSelection details: {A|44 - 191}

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