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- PDB-2gxf: X-Ray Crystal Structure of Protein YybH from Bacillus subtilis. N... -

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Basic information

Entry
Database: PDB / ID: 2gxf
TitleX-Ray Crystal Structure of Protein YybH from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR506.
ComponentsHypothetical protein yybH
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein. / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Uncharacterized protein YybH
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsForouhar, F. / Abashidze, M. / Jayaraman, S. / Cunningham, K. / Fang, Y. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. ...Forouhar, F. / Abashidze, M. / Jayaraman, S. / Cunningham, K. / Fang, Y. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of the Hypothetical Protein YybH from Bacillus subtilis, Northeast Structural Genomics Target SR506
Authors: Forouhar, F. / Abashidze, M. / Jayaraman, S. / Cunningham, K. / Fang, Y. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
History
DepositionMay 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 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 yybH
B: Hypothetical protein yybH
C: Hypothetical protein yybH
D: Hypothetical protein yybH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4168
Polymers65,6354
Non-polymers7814
Water59433
1
A: Hypothetical protein yybH
B: Hypothetical protein yybH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2084
Polymers32,8172
Non-polymers3902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-8 kcal/mol
Surface area12600 Å2
MethodPISA
2
C: Hypothetical protein yybH
D: Hypothetical protein yybH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2084
Polymers32,8172
Non-polymers3902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-8 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.251, 88.251, 82.836
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Hypothetical protein yybH


Mass: 16408.705 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: str. 168 / Gene: yybH / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P37496
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.46 Å3/Da / Density % sol: 49.94 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.15
Details: 100mM MES (pH 6.15), 22% PEG5kMME, 200mM ammonium sulfate, and 5mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97904, 0.97943, 0.96801
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2006 / Details: mirrors.
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979041
20.979431
30.968011
ReflectionResolution: 3.1→29.42 Å / Num. all: 22751 / Num. obs: 22660 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 46.3 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.081 / Net I/σ(I): 15.17
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 5 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2252 / Rsym value: 0.584 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.1→29.42 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 411496.57 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR phasing.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1873 9.6 %RANDOM
Rwork0.259 ---
all0.261 22751 --
obs0.259 19411 85.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.266245 e/Å3
Displacement parametersBiso mean: 52.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å20 Å2
2--2.35 Å20 Å2
3----0.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3.1→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3764 0 48 33 3845
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.6
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 243 10.5 %
Rwork0.325 2061 -
obs-2061 61.2 %

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