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- PDB-4qy7: Crystal structure of a yobA protein (BSU18810) from Bacillus subt... -

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Basic information

Entry
Database: PDB / ID: 4qy7
TitleCrystal structure of a yobA protein (BSU18810) from Bacillus subtilis subsp. subtilis str. 168 at 1.55 A resolution
ComponentsUncharacterized protein YobA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF11518 family protein / DUF3221 / OB-fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF3221 / Protein of unknown function (DUF3221) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta / Uncharacterized protein YobA
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (yobA) from Bacillus subtilis subsp. subtilis str. 168 at 1.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YobA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1052
Polymers10,6911
Non-polymers4141
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.556, 37.988, 81.245
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein YobA


Mass: 10690.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: yobA, BSU18810 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: O31835
#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 29-120 OF 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: 1.99 Å3/Da / Density % sol: 38.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 5.00% polyethylene glycol 3000, 40.00% polyethylene glycol 400, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.95369,0.97937,0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 11, 2014
Details: Vertical focusing mirror; 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
10.953691
20.979371
30.979221
ReflectionResolution: 1.55→27.746 Å / Num. obs: 12907 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.025 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 14.83
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.55-1.610.5211.645362442194.5
1.61-1.670.4092.240932183199
1.67-1.750.2883.247392492199.2
1.75-1.840.1794.943972309199.1
1.84-1.950.1078.143182275199.3
1.95-2.10.06712.645322372199
2.1-2.310.04218.445592376199.4
2.31-2.650.03221.945802401198.7
2.65-3.330.0232.345602359198.6
3.33-27.7460.01642.845122346196.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJanuary 10, 2014 BUILT=20140307data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.55→27.746 Å / Cor.coef. Fo:Fc: 0.9571 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM ...Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. 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. 5. MAD PHASE RESTRAINTS WERE USED DURING REFINEMENT. 6. NONAETHYLENE GLYCOL (2PE) MOLECULE FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 627 4.88 %RANDOM
Rwork0.1903 ---
obs0.1918 12850 99.24 %-
Displacement parametersBiso max: 97.54 Å2 / Biso mean: 28.8288 Å2 / Biso min: 11.53 Å2
Baniso -1Baniso -2Baniso -3
1--1.7543 Å20 Å20 Å2
2---0.8936 Å20 Å2
3---2.6479 Å2
Refine analyzeLuzzati coordinate error obs: 0.232 Å
Refinement stepCycle: LAST / Resolution: 1.55→27.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms730 0 7 89 826
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d486SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes26HARMONIC2
X-RAY DIFFRACTIONt_gen_planes243HARMONIC5
X-RAY DIFFRACTIONt_it1645HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion110SEMIHARMONIC5
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_contact1872SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1645HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3011HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.87
X-RAY DIFFRACTIONt_other_torsion2.96
LS refinement shellResolution: 1.55→1.7 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2232 158 5.32 %
Rwork0.2077 2811 -
all0.2085 2969 -
obs--99.24 %
Refinement TLS params.Method: refined / Origin x: 7.7967 Å / Origin y: 7.1928 Å / Origin z: 8.7526 Å
111213212223313233
T-0.0511 Å2-0.0216 Å2-0.0052 Å2--0.0311 Å20.0031 Å2---0.0591 Å2
L1.3475 °2-0.6103 °20.1497 °2-1.4624 °20.49 °2--2.5841 °2
S0.062 Å °0.0001 Å °0.0116 Å °-0.0663 Å °0.0031 Å °0.0131 Å °0.035 Å °-0.1071 Å °-0.0651 Å °

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