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- PDB-4mdw: Crystal structure of a DUF1541 family protein (ydhK) from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 4mdw
TitleCrystal structure of a DUF1541 family protein (ydhK) from Bacillus subtilis subsp. subtilis str. 168 at 2.00 A resolution
ComponentsUncharacterized protein YdhK
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF07563 family / DUF1541 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyDomain of unknown function DUF1541 / Domain of unknown function DUF1541 / Protein of unknown function (DUF1541) / SH3 type barrels. / Roll / Mainly Beta / Uncharacterized protein YdhK
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (ydhK) from Bacillus subtilis subsp. subtilis str. 168 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein YdhK


Theoretical massNumber of molelcules
Total (without water)18,7841
Polymers18,7841
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.692, 64.174, 80.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein YdhK


Mass: 18783.787 Da / Num. of mol.: 1 / Fragment: UNP residues 41-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: ydhK, BSU05790 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: O05503
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...1. 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 41-205 OF THE TARGET SEQUENCE. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

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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: 1.9 Å3/Da / Density % sol: 35.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 5.0% polyethylene glycol 3000, 40.0% 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: BL11-1 / Wavelength: 0.91837,0.97926,0.97885
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979261
30.978851
ReflectionResolution: 2→27.692 Å / Num. obs: 9897 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.41 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.070.6921.42382152783.9
2.07-2.150.6051.73097172795.7
2.15-2.250.4312.23375187396.9
2.25-2.370.362.73169182496
2.37-2.520.2673.63206181495.4
2.52-2.710.2384.13152176796.7
2.71-2.990.1435.93172184795.9
2.99-3.420.0710.83301181196.5
3.42-4.30.03816.93145176895.4
4.30.0321.13242179394.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2→27.692 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.9135 / Occupancy max: 1 / Occupancy min: 0.37 / 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. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. MAD PHASE RESTRAINTS WERE USED DURING REFINEMENT. 7. LYSINE 195 APPEARS TO HAVE BEEN PROTECTED FROM REDUCTIVE METHYLATION AND WAS MODELED AS LYSINE. ALL OTHER LYSINES HAVE BEEN MODELED AS MLY (N-DIMETHYL-LYSINE).
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 475 4.82 %RANDOM
Rwork0.1788 ---
obs0.1824 9863 96.43 %-
Displacement parametersBiso max: 114.28 Å2 / Biso mean: 36.6102 Å2 / Biso min: 16.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.7154 Å20 Å20 Å2
2---2.8983 Å20 Å2
3---2.1829 Å2
Refine analyzeLuzzati coordinate error obs: 0.234 Å
Refinement stepCycle: LAST / Resolution: 2→27.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 0 0 107 1243
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d605SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes32HARMONIC2
X-RAY DIFFRACTIONt_gen_planes329HARMONIC5
X-RAY DIFFRACTIONt_it2264HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion157SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance1HARMONIC1
X-RAY DIFFRACTIONt_utility_angle2HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion1SINUSOIDAL1
X-RAY DIFFRACTIONt_ideal_dist_contact2382SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2264HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4077HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion3.9
X-RAY DIFFRACTIONt_other_torsion3.19
LS refinement shellResolution: 2→2.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2452 127 4.81 %
Rwork0.2046 2516 -
all0.2064 2643 -
obs--96.43 %
Refinement TLS params.Method: refined / Origin x: 16.1254 Å / Origin y: 33.4174 Å / Origin z: 19.4916 Å
111213212223313233
T-0.1422 Å2-0.0151 Å20.0012 Å2-0.1664 Å20.0086 Å2---0.1406 Å2
L0.6622 °20.0358 °20.128 °2-0.4309 °2-0.0617 °2--2.4243 °2
S-0.0352 Å °-0.0421 Å °-0.0028 Å °0.0387 Å °-0.0133 Å °-0.0156 Å °-0.0202 Å °-0.0427 Å °0.0486 Å °
Refinement TLS groupSelection details: { A|59-205 }

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