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- PDB-2gsn: Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase -

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Basic information

Entry
Database: PDB / ID: 2gsn
TitleStructure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase
Componentsphosphodiesterase-nucleotide pyrophosphatase
KeywordsHYDROLASE / Alpha Beta / NPP
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
Gyrase A; domain 2 - #180 / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / Gyrase A; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphodiesterase-nucleotide pyrophosphatase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri str. 306 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsZalatan, J.G. / Fenn, T.D. / Brunger, A.T. / Herschlag, D.
CitationJournal: Biochemistry / Year: 2006
Title: Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: implications for mechanism and evolution
Authors: Zalatan, J.G. / Fenn, T.D. / Brunger, A.T. / Herschlag, D.
History
DepositionApr 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: phosphodiesterase-nucleotide pyrophosphatase
B: phosphodiesterase-nucleotide pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7446
Polymers85,4822
Non-polymers2624
Water13,313739
1
A: phosphodiesterase-nucleotide pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8723
Polymers42,7411
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: phosphodiesterase-nucleotide pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8723
Polymers42,7411
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.683, 78.692, 129.527
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: THR / End label comp-ID: MET / Refine code: 4 / Auth seq-ID: 44 - 425 / Label seq-ID: 5 - 386

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsDimer in asymmetric unit, likely functional as a monomer

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Components

#1: Protein phosphodiesterase-nucleotide pyrophosphatase


Mass: 42741.086 Da / Num. of mol.: 2 / Fragment: Residues (44-425)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri str. 306 (bacteria)
Species: Xanthomonas axonopodis / Strain: pv. citri str. 306 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PIS1, nucleotide diphosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 739 / 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 Å3/Da / Density % sol: 38.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris HCl, 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.2826,1.2831,1.2782
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 30, 2005
RadiationMonochromator: Double crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28261
21.28311
31.27821
ReflectionResolution: 1.75→50 Å / Num. all: 67365 / Num. obs: 67365 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.097
Reflection shellResolution: 1.75→1.81 Å / % possible all: 81.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
BOSdata collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.137 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.118 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2027 3398 5.1 %RANDOM
Rwork0.17056 ---
all0.17221 67365 --
obs0.17221 63794 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.358 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5882 0 4 739 6625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0216195
X-RAY DIFFRACTIONr_bond_other_d0.0020.025535
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.9368483
X-RAY DIFFRACTIONr_angle_other_deg0.802312808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9385796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99622.517286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68615912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9011561
X-RAY DIFFRACTIONr_chiral_restr0.0720.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027171
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021318
X-RAY DIFFRACTIONr_nbd_refined0.20.21360
X-RAY DIFFRACTIONr_nbd_other0.1890.25828
X-RAY DIFFRACTIONr_nbtor_refined0.170.22986
X-RAY DIFFRACTIONr_nbtor_other0.0810.23510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2576
X-RAY DIFFRACTIONr_metal_ion_refined0.0420.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.2162
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.262
X-RAY DIFFRACTIONr_mcbond_it0.6181.54990
X-RAY DIFFRACTIONr_mcbond_other0.1261.51586
X-RAY DIFFRACTIONr_mcangle_it0.71626263
X-RAY DIFFRACTIONr_scbond_it1.26532667
X-RAY DIFFRACTIONr_scangle_it1.8334.52220
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5649 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.260.5
medium thermal0.442
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 209 -
Rwork0.365 3809 -
obs--80.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.41030.17280.11370.6830.12930.614-0.0420.12130.0865-0.07660.02710.0486-0.0392-0.01930.0149-0.10690.0046-0.0129-0.10790.0087-0.125623.984639.771327.0702
21.1868-0.1356-0.03930.56320.0220.3169-0.0298-0.0763-0.00510.08560.0173-0.02890.02610.0050.0125-0.07360.0003-0.0056-0.11440.0023-0.132141.099339.086260.4249
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA44 - 4255 - 386
3X-RAY DIFFRACTION2BB44 - 4255 - 386

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