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- PDB-3e5z: X-Ray structure of the putative gluconolactonase in protein famil... -

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Basic information

Entry
Database: PDB / ID: 3e5z
TitleX-Ray structure of the putative gluconolactonase in protein family PF08450. Northeast Structural Genomics Consortium target DrR130.
Componentsputative Gluconolactonase
Keywordsstructural genomics / unknown function / X-Ray NESG Q9RXN3 gluconolactonase / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
Senescence marker protein-30 (SMP-30) / : / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Gluconolactonase, putative
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsKuzin, A.P. / Abashidze, M. / Seetharaman, J. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Kuzin, A.P. / Abashidze, M. / Seetharaman, J. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Tong, S.N. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-Ray structure of the putative gluconolactonase in protein family PF08450. Northeast Structural Genomics Consortium target DrR130.
Authors: Kuzin, A.P. / Abashidze, M. / Seetharaman, J. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Tong, S.N. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionAug 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative Gluconolactonase
B: putative Gluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7904
Polymers65,7422
Non-polymers492
Water4,306239
1
A: putative Gluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8952
Polymers32,8711
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: putative Gluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8952
Polymers32,8711
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.420, 93.400, 76.990
Angle α, β, γ (deg.)90.00, 98.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein putative Gluconolactonase


Mass: 32870.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR_0277 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9RXN3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M NaCl 0.1M TOPS 18% PEG 3350, MgL2 as additive, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2008 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 81184 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.4
Reflection shellResolution: 2.01→2.08 Å / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 4.8 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→19.92 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 10.885 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22908 1867 5 %RANDOM
Rwork0.19282 ---
obs0.19466 35195 100 %-
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: 26.406 Å2
Baniso -1Baniso -2Baniso -3
1-3.69 Å20 Å20.76 Å2
2---2.5 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.01→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4490 0 2 239 4731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214616
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9466284
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2385578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52823.246228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88115690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4571542
X-RAY DIFFRACTIONr_chiral_restr0.0860.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023684
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21978
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23076
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7541.52942
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11824598
X-RAY DIFFRACTIONr_scbond_it1.69231916
X-RAY DIFFRACTIONr_scangle_it2.6424.51686
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.006→2.058 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 112 -
Rwork0.225 2029 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 33.9275 Å / Origin y: 50.1732 Å / Origin z: 56.7859 Å
111213212223313233
T-0.125 Å2-0.0064 Å2-0.0103 Å2--0.0158 Å20.0251 Å2---0.0795 Å2
L0.1144 °2-0.1485 °2-0.0788 °2-2.0537 °21.0589 °2--0.7122 °2
S0.0165 Å °-0.0001 Å °-0.0028 Å °-0.0034 Å °-0.0343 Å °0.0306 Å °-0.0578 Å °-0.0281 Å °0.0178 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B298 - 429
2X-RAY DIFFRACTION1A298 - 404
3X-RAY DIFFRACTION1B297
4X-RAY DIFFRACTION1A297
5X-RAY DIFFRACTION1B2 - 291
6X-RAY DIFFRACTION1A2 - 291

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