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- PDB-2dxn: Glycerophosphodiesterase from Enterobacter aerogenes -

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Basic information

Entry
Database: PDB / ID: 2dxn
TitleGlycerophosphodiesterase from Enterobacter aerogenes
ComponentsPhosphohydrolase
KeywordsHYDROLASE / domain-swapping / beta-sheet extension / metalloenzyme / disulfide / alpha/beta sandwich
Function / homology
Function and homology information


glycerophosphodiester phosphodiesterase / glycerophosphodiester phosphodiesterase activity / glycerol metabolic process / 3',5'-cyclic-AMP phosphodiesterase activity / metal ion binding
Similarity search - Function
GpdQ, beta-strand dimerisation domain / GpdQ, catalytic alpha/beta sandwich domain / GpdQ, beta-strand dimerisation domain / GpdQ, catalytic alpha/beta sandwich domain / Cyclic nucleotide phosphodiesterase GpdQ/CpdA-like / Transcription Regulator spoIIAA / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like ...GpdQ, beta-strand dimerisation domain / GpdQ, catalytic alpha/beta sandwich domain / GpdQ, beta-strand dimerisation domain / GpdQ, catalytic alpha/beta sandwich domain / Cyclic nucleotide phosphodiesterase GpdQ/CpdA-like / Transcription Regulator spoIIAA / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Glycerophosphodiester phosphodiesterase GpdQ
Similarity search - Component
Biological speciesEnterobacter aerogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.92 Å
AuthorsJackson, C.J. / Carr, P.D. / Ollis, D.L.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: The structure and function of a novel glycerophosphodiesterase from Enterobacter aerogenes
Authors: Jackson, C.J. / Carr, P.D. / Liu, J.W. / Watt, S.J. / Beck, J.L. / Ollis, D.L.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: The purification, crystallization and preliminary diffraction of a glycerophosphodiesterase from Enterobacter aerogenes
Authors: Jackson, C.J. / Carr, P.D. / Kim, H.K. / Liu, J.W. / Ollis, D.L.
History
DepositionAug 28, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Dec 11, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_Rsym_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphohydrolase
B: Phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9236
Polymers61,6612
Non-polymers2624
Water1,47782
1
A: Phosphohydrolase
B: Phosphohydrolase
hetero molecules

A: Phosphohydrolase
B: Phosphohydrolase
hetero molecules

A: Phosphohydrolase
B: Phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,76918
Polymers184,9846
Non-polymers78512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area23640 Å2
ΔGint-602 kcal/mol
Surface area52590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)164.274, 164.274, 164.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Phosphohydrolase / GpdQ


Mass: 30830.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter aerogenes (bacteria) / Gene: GpdQ / Plasmid: pCY76 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: Q6XBH1, glycerophosphodiester phosphodiesterase
#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.: 82 / 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: 5.9 Å3/Da / Density % sol: 79.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.9M Na Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.28269 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28269 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 32293 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 77.2 Å2 / Rsym value: 0.077 / Net I/σ(I): 32.2
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 11.2 % / Num. unique all: 5342 / Rsym value: 0.436 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.92→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 17.302 / SU ML: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19495 1632 5.1 %RANDOM
Rwork0.16201 ---
obs0.16365 30501 99.64 %-
all-32828 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.63 Å2
Refinement stepCycle: LAST / Resolution: 2.92→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 4 82 4354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214388
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.955989
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1365540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04323.953215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.07415671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2021527
X-RAY DIFFRACTIONr_chiral_restr0.0960.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023441
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.22040
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22979
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2191
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5291.52745
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80224371
X-RAY DIFFRACTIONr_scbond_it1.49231827
X-RAY DIFFRACTIONr_scangle_it2.3444.51618
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.922→2.997 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 110 -
Rwork0.221 2231 -
obs--100 %
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)
11.50760.6487-0.23551.0118-0.33112.401-0.1343-0.0434-0.1548-0.17280.1904-0.3317-0.47310.4066-0.0561-0.0157-0.15250.2475-0.1759-0.0523-0.008846.21733.3487.879
22.1030.9833-0.84030.9680.34362.6197-0.21830.2384-0.3373-0.2920.24-0.2204-0.51080.0105-0.02170.0934-0.08740.2768-0.2171-0.022-0.064835.17528.0241.515
35.66920.13542.52940.61021.7697.4423-0.13440.5332-0.8115-0.66940.409-0.26350.11330.8115-0.2746-0.1110.04150.1773-0.24040.06570.040824.3612.1155.528
42.66190.4727-0.17021.18220.351.7145-0.19980.4791-0.3864-0.44520.2854-0.2214-0.2486-0.0835-0.08560.1158-0.04280.2485-0.1614-0.0929-0.15723.93114.391-13.618
52.15820.7476-0.96271.9160.61981.9986-0.19610.1176-0.3861-0.21580.2452-0.3759-0.4140.2073-0.04910.0238-0.07910.2657-0.1736-0.0635-0.047331.92918.834-3.134
610.07299.15232.529414.2443.47377.3899-0.67710.40680.642-0.62420.54170.1017-0.92560.45090.13550.02340.16610.1031-0.27850.0666-0.162625.62939.32515.354
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1951 - 195
2X-RAY DIFFRACTION2AA196 - 255196 - 255
3X-RAY DIFFRACTION3AA256 - 271256 - 271
4X-RAY DIFFRACTION4BB1 - 1951 - 195
5X-RAY DIFFRACTION5BB196 - 255196 - 255
6X-RAY DIFFRACTION6BB256 - 271256 - 271

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