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- PDB-2im8: X-Ray Crystal Structure of Protein yppE from Bacillus subtilis. N... -

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Basic information

Entry
Database: PDB / ID: 2im8
TitleX-Ray Crystal Structure of Protein yppE from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR213.
ComponentsHypothetical protein yppE
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SR213 / yppE / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyYppE-like / YppE-like / YppE-like superfamily / Bacterial domain of unknown function (DUF1798) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / PHOSPHATE ION / Uncharacterized protein YppE
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKuzin, A.P. / Shastry, R. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Hang, D. / Baran, M.C. / Acton, T.B. ...Kuzin, A.P. / Shastry, R. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Hang, D. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-Ray structure of hypothetical protein yPPE. Northeast Structural Genomics Consortium target SR213.
Authors: Kuzin, A.P. / Neely, H. / Seetharaman, J. / Shastry, R. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G. / Tong, L. / Hunt, J.F.
History
DepositionOct 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein yppE
B: Hypothetical protein yppE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4853
Polymers31,3902
Non-polymers951
Water2,972165
1
A: Hypothetical protein yppE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7902
Polymers15,6951
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein yppE


Theoretical massNumber of molelcules
Total (without water)15,6951
Polymers15,6951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.735, 70.830, 76.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein yppE


Mass: 15695.204 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yppE / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: P50833
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.92 Å3/Da / Density % sol: 36.06 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8M KH2PO4, 0.8M NaH2PO4, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97934, 0.97956, 0.96806
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 2006 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.979561
30.968061
ReflectionResolution: 2→30 Å / Num. obs: 30962 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 33.6 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 29.2
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 7.5 / % possible all: 93.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→19.29 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 356865.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1401 5 %RANDOM
Rwork0.236 ---
obs0.236 28300 89.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.5853 Å2 / ksol: 0.357933 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.93 Å20 Å20 Å2
2---0.34 Å20 Å2
3---3.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2→19.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 5 165 2144
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d15.7
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 182 4.9 %
Rwork0.326 3526 -
obs--70.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.param

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