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- PDB-3d0w: Crystal structure of YflH protein from Bacillus subtilis. Northea... -

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Basic information

Entry
Database: PDB / ID: 3d0w
TitleCrystal structure of YflH protein from Bacillus subtilis. Northeast Structural Genomics Consortium target SR326
ComponentsYflH protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / yflH / Gram-positive bacterium / Bacillus subtilis / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyProtein of unknown function DUF3243 / Protein of unknown function DUF3243 / YmfJ/YflH superfamily / Protein of unknown function (DUF3243) / Cytochrome Bc1 Complex; Chain D, domain 2 / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein YflH
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSeetharaman, J. / Kuzin, A.P. / Neely, H. / Forouhar, F. / Min, S. / Zhao, L. / Fang, Y. / Owens, L. / Ma, L.-C. / Xiao, R. ...Seetharaman, J. / Kuzin, A.P. / Neely, H. / Forouhar, F. / Min, S. / Zhao, L. / Fang, Y. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of YflH protein from Bacillus subtilis.
Authors: Seetharaman, J. / Kuzin, A.P. / Neely, H. / Forouhar, F. / Min, S. / Zhao, L. / Fang, Y. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. ...Authors: Seetharaman, J. / Kuzin, A.P. / Neely, H. / Forouhar, F. / Min, S. / Zhao, L. / Fang, Y. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMay 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YflH protein
B: YflH protein
C: YflH protein
D: YflH protein


Theoretical massNumber of molelcules
Total (without water)48,9174
Polymers48,9174
Non-polymers00
Water5,819323
1
A: YflH protein
C: YflH protein


Theoretical massNumber of molelcules
Total (without water)24,4592
Polymers24,4592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-25 kcal/mol
Surface area10020 Å2
MethodPISA
2
B: YflH protein
D: YflH protein


Theoretical massNumber of molelcules
Total (without water)24,4592
Polymers24,4592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-21.8 kcal/mol
Surface area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.300, 45.180, 99.177
Angle α, β, γ (deg.)90.00, 98.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
YflH protein


Mass: 12229.278 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yflH, BSU07680 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O34306
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.95 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M Citric acid, 30% PEG 6000, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A10.979
SYNCHROTRONNSLS X4C20.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDMar 28, 2008
MAR scanner 345 mm plate2IMAGE PLATEApr 15, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 57564 / Num. obs: 57564 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.051 / Net I/σ(I): 15.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 14 / Num. unique all: 5714 / Rsym value: 0.304 / % possible all: 97.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→33.24 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 180236.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2524 4.9 %RANDOM
Rwork0.216 ---
obs0.216 51431 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.6424 Å2 / ksol: 0.38333 e/Å3
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å25.17 Å2
2--1.06 Å20 Å2
3----0.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→33.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 0 323 3072
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d16.6
X-RAY DIFFRACTIONc_improper_angle_d0.66
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.24 338 4.7 %
Rwork0.239 6926 -
obs--75.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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