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- PDB-1ny1: CRYSTAL STRUCTURE OF B. SUBTILIS POLYSACCHARIDE DEACETYLASE NORTH... -

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Basic information

Entry
Database: PDB / ID: 1ny1
TitleCRYSTAL STRUCTURE OF B. SUBTILIS POLYSACCHARIDE DEACETYLASE NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR127.
ComponentsProbable polysaccharide deacetylase pdaA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / POLYSACCHARIDE DEAC / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


deacetylase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / sporulation resulting in formation of a cellular spore / cell wall organization / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Peptidoglycan-N-acetylmuramic acid deacetylase PdaA / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Peptidoglycan-N-acetylmuramic acid deacetylase PdaA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsForouhar, F. / Edstrom, W. / Khan, J. / Ma, L. / Chiang, Y. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Polysaccharide Deacetylase (PDAA_BACSU) from B. Subtilis (Pdaa_Bacsu) Northeast Structural Genomics Research Consortium (Nesg) Target Sr127
Authors: Forouhar, F. / Edstrom, W. / Khan, J. / Ma, L. / Chiang, Y. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionFeb 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable polysaccharide deacetylase pdaA
B: Probable polysaccharide deacetylase pdaA


Theoretical massNumber of molelcules
Total (without water)56,0362
Polymers56,0362
Non-polymers00
Water9,548530
1
A: Probable polysaccharide deacetylase pdaA


Theoretical massNumber of molelcules
Total (without water)28,0181
Polymers28,0181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable polysaccharide deacetylase pdaA


Theoretical massNumber of molelcules
Total (without water)28,0181
Polymers28,0181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.112, 88.112, 120.645
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Probable polysaccharide deacetylase pdaA / TARGET SR127 PROTEIN


Mass: 28018.053 Da / Num. of mol.: 2 / Fragment: PDAA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: PdaA / Production host: Escherichia coli (E. coli) / References: UniProt: O34928
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3350, 200mM di-ammonium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 97034 / Num. obs: 87098 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.035 / Net I/σ(I): 14.5
Reflection shellResolution: 1.8→1.86 Å / % possible obs: 88 % / Redundancy: 2.08 % / Mean I/σ(I) obs: 2.96

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.7 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.212 8536 9.8 %RANDOM
Rwork0.182 ---
obs0.182 87098 89.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.8475 Å2 / ksol: 0.334847 e/Å3
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å22.28 Å20 Å2
2--1.66 Å20 Å2
3----3.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 0 530 4382
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.642
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.225 1170 9.9 %
Rwork0.196 10655 -
obs--73.1 %
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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