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- PDB-2nn4: Crystal structure of Bacillus subtilis yqgQ, Pfam DUF910 -

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Basic information

Entry
Database: PDB / ID: 2nn4
TitleCrystal structure of Bacillus subtilis yqgQ, Pfam DUF910
ComponentsHypothetical protein yqgQ
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Novel fold / pfam:DUF910 / 10278a / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyYqgQ-like / YqgQ-like / YqgQ-like superfamily / YqgQ-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein YqgQ
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsDamodharan, L. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of YqgQ protein from Bacillus subtilis, a conserved hypothetical protein.
Authors: Lakshminarasimhan, D. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionOct 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Database references
Revision 1.4Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein yqgQ
B: Hypothetical protein yqgQ
C: Hypothetical protein yqgQ


Theoretical massNumber of molelcules
Total (without water)26,1063
Polymers26,1063
Non-polymers00
Water84747
1
A: Hypothetical protein yqgQ


Theoretical massNumber of molelcules
Total (without water)8,7021
Polymers8,7021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein yqgQ


Theoretical massNumber of molelcules
Total (without water)8,7021
Polymers8,7021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical protein yqgQ


Theoretical massNumber of molelcules
Total (without water)8,7021
Polymers8,7021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.85, 41.25, 55.18
Angle α, β, γ (deg.)90.00, 113.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hypothetical protein yqgQ


Mass: 8701.916 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yqgQ / Plasmid: pSGX4 (BS) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL / References: UniProt: P54494
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.066M sodium di-hydrogen phophate, 3.385M di-potassium hydrogen phosphate, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9801
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2006 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 12344 / Num. obs: 12344 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1075 / % possible all: 84.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→47.59 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 127065.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: the missing residues listed in Remark 465 are due to lack of electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 959 8.1 %RANDOM
Rwork0.247 ---
obs0.247 11871 93.6 %-
all-11871 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.1294 Å2 / ksol: 0.390188 e/Å3
Displacement parametersBiso mean: 38.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.42 Å20 Å26.15 Å2
2---6.56 Å20 Å2
3---3.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.1→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1590 0 0 47 1637
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d17.6
X-RAY DIFFRACTIONc_improper_angle_d1.93
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it2.442
X-RAY DIFFRACTIONc_scangle_it3.852.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 128 8.1 %
Rwork0.314 1447 -
obs--75.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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