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- PDB-2gsl: X-Ray Crystal Structure of Protein FN1578 from Fusobacterium nucl... -

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Basic information

Entry
Database: PDB / ID: 2gsl
TitleX-Ray Crystal Structure of Protein FN1578 from Fusobacterium nucleatum. Northeast Structural Genomics Consortium Target NR1.
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-helical protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


ribonuclease III activity / RNA processing
Similarity search - Function
Mini-ribonuclease 3 family / Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease III domain / Ribonuclease III domain / Ribonuclease III, endonuclease domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Mini-ribonuclease 3-like protein
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsForouhar, F. / Su, M. / Jayaraman, S. / Conover, K. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Hypothetical Protein (FN1578) from Fusobacterium nucleatum, NESG Target NR1
Authors: Forouhar, F. / Su, M. / Jayaraman, S. / Conover, K. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionApr 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 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

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Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
D: Hypothetical protein
E: Hypothetical protein
F: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,71412
Polymers97,5686
Non-polymers1466
Water3,171176
1
A: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5714
Polymers32,5232
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-31 kcal/mol
Surface area13510 Å2
MethodPISA
2
C: Hypothetical protein
D: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5714
Polymers32,5232
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-31 kcal/mol
Surface area13430 Å2
MethodPISA
3
E: Hypothetical protein
F: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5714
Polymers32,5232
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-31 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.304, 108.751, 80.495
Angle α, β, γ (deg.)90.00, 108.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hypothetical protein


Mass: 16261.394 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum (bacteria)
Species: Fusobacterium nucleatum / Strain: ATCC 25586 / Gene: FN1578 / Plasmid: pETXL-10 Gold / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: GenBank: 19712792, UniProt: Q8RIL0*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 293 K / pH: 7
Details: 100mM HEPES, 100mM Mg(NO3)2, 20% PEG8K, 5 mM DTT, Microbatch under oil, pH 7, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 2006 / Details: Mirrors.
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.6→29.45 Å / Num. all: 60679 / Num. obs: 60619 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.081 / Net I/σ(I): 13.31
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 3 / Num. unique all: 6068 / Rsym value: 0.509 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
XTALVIEWrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.45 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 162894.17 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 5313 10 %RANDOM
Rwork0.23 ---
all0.233 60679 --
obs0.23 53201 87.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.2765 Å2 / ksol: 0.328052 e/Å3
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20 Å27.21 Å2
2---7.62 Å20 Å2
3---5.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6031 0 6 176 6213
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 664 9.5 %
Rwork0.274 6305 -
obs-664 69.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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