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- PDB-2nx2: Crystal structure of protein ypsA from Bacillus subtilis, Pfam DUF1273 -

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Basic information

Entry
Database: PDB / ID: 2nx2
TitleCrystal structure of protein ypsA from Bacillus subtilis, Pfam DUF1273
ComponentsHypothetical protein ypsA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyYspA SLOG family / YspA SLOG family / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / UPF0398 protein YpsA
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsRamagopal, U.A. / Alvarado, J. / Dickey, M. / Reyes, C. / Toro, R. / Bain, K. / Gheyi, T. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein ypsA from Bacillus subtilis.
Authors: Ramagopal, U.A. / Alvarado, J. / Dickey, M. / Reyes, C. / Toro, R. / Bain, K. / Gheyi, T. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics
History
DepositionNov 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 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 1.6Dec 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
Remark 300Author states that biological unit for the protein is not yet known

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein ypsA


Theoretical massNumber of molelcules
Total (without water)21,1511
Polymers21,1511
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.052, 51.052, 138.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Hypothetical protein ypsA


Mass: 21150.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ypsA / Plasmid: BC-pSGX4(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P50838
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 18 % PEG-4K, Na-Acetate pH 4.6, Ammonium Acetate 0.1M, 0.1M, Ethylene Glycol 10%, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X3A10.9793
SYNCHROTRONNSLS X29A21.7403
SYNCHROTRONAPS 31-ID30.979
Detector
TypeIDDetector
MAR CCD 165 mm1CCD
ADSC QUANTUM 3152CCD
MAR CCD 165 mm3CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
21.74031
30.9791
ReflectionResolution: 2→50 Å / Num. all: 13121 / Num. obs: 13121 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Rmerge(I) obs: 0.09 / Χ2: 0.732 / Net I/σ(I): 26.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.95 / Num. unique all: 1260 / Rsym value: 0.91 / Χ2: 0.396 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SIRAS / Resolution: 2→47.89 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.921 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 637 4.9 %RANDOM
Rwork0.18 ---
obs0.182 13060 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.497 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2--0.54 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 0 143 1648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221545
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.9822094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1125185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.925.06379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.715283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.558157
X-RAY DIFFRACTIONr_chiral_restr0.0830.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021191
X-RAY DIFFRACTIONr_nbd_refined0.1990.2720
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21055
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2114
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.221
X-RAY DIFFRACTIONr_mcbond_it0.8571.5944
X-RAY DIFFRACTIONr_mcangle_it1.44921470
X-RAY DIFFRACTIONr_scbond_it2.0363708
X-RAY DIFFRACTIONr_scangle_it3.2064.5623
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 44 -
Rwork0.225 891 -
obs-935 100 %

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