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- PDB-3e57: Crystal structure of Tm1382, a putative Nudix hydrolase -

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Basic information

Entry
Database: PDB / ID: 3.0E+57
TitleCrystal structure of Tm1382, a putative Nudix hydrolase
Componentsuncharacterized protein Tm1382
Keywordsstructural genomics / unknown function / Nudix hydrolase / Tm1382 / PSI-2 / Protein Structure Initiative / Integrated Center for Structure and Function Innovation / ISFI
Function / homology
Function and homology information


Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Nudix hydrolase domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89 Å
AuthorsChoi, W. / Cooper, D.R. / Derewenda, Z.S. / Integrated Center for Structure and Function Innovation (ISFI)
CitationJournal: To be Published
Title: Crystal structure of Tm1382, a putative Nudix hydrolase
Authors: Choi, W. / Cooper, D.R. / Derewenda, Z.S.
History
DepositionAug 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein Tm1382
B: uncharacterized protein Tm1382


Theoretical massNumber of molelcules
Total (without water)49,1382
Polymers49,1382
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-6 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.589, 62.879, 73.896
Angle α, β, γ (deg.)90.000, 98.370, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAuthors state that the biological unit is the same as asymmetric unit.

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Components

#1: Protein uncharacterized protein Tm1382


Mass: 24568.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1382 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9X1A2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Trisodium Citrate pH 5.5, PEG 3000, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-BM10.97933
SYNCHROTRONALS 5.0.221
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDApr 1, 2008
ADSC QUANTUM 3152CCDJul 17, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Liquid nitrogen cooled dual crystalSINGLE WAVELENGTHMx-ray1
2Liquid nitrogen cooled dual crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979331
211
ReflectionRedundancy: 3.4 % / Av σ(I) over netI: 19.2 / Number: 60740 / Rmerge(I) obs: 0.078 / Χ2: 1.75 / D res high: 2.3 Å / D res low: 40 Å / Num. obs: 17618 / % possible obs: 90.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.954099.710.0482.7323.6
3.934.9599.910.0622.8593.8
3.443.9310010.072.0293.8
3.123.4410010.0961.4743.8
2.93.1299.910.1341.2613.7
2.732.998.510.1661.2943.4
2.592.7391.910.2071.2233.2
2.482.5979.610.2361.2473
2.382.4870.310.241.1912.9
2.32.3867.310.2651.1972.6
ReflectionResolution: 1.89→50 Å / Num. obs: 34267 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.059 / Χ2: 1.136
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.973.70.38733961.2751,2100
1.97-2.053.70.26734111.1511,299.9
2.05-2.143.70.1933981.0661,2100
2.14-2.253.70.13834381.131,2100
2.25-2.393.70.11234041.1321,2100
2.39-2.583.70.09533961.1181,2100
2.58-2.843.70.08234441.2621,2100
2.84-3.253.70.06734391.2451,2100
3.25-4.093.60.04434501.0381,299.9
4.09-503.70.03834910.9421,299.1

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se23.2360.6310.5410.2270.457
2Se25.7090.9740.8140.220.444
3Se36.4760.8950.4590.2990.313
4Se600.630.0090.0540.495
5Se34.040.9550.810.260.286
6Se36.7960.5650.8020.0360.222
Phasing dmFOM : 0.82 / FOM acentric: 0.83 / FOM centric: 0.76 / Reflection: 17594 / Reflection acentric: 16712 / Reflection centric: 882
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.6-36.8670.910.920.84865743122
4.1-6.60.910.910.8326052407198
3.3-4.10.880.880.8132513068183
2.9-3.30.810.810.732753122153
2.5-2.90.760.770.6551554970185
2.3-2.50.790.790.682443240241

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.89→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.836 / SU B: 6.763 / SU ML: 0.1 / SU R Cruickshank DPI: 0.148 / SU Rfree: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1714 5 %RANDOM
Rwork0.199 ---
obs0.201 34212 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.22 Å2 / Biso mean: 32.51 Å2 / Biso min: 15.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å2-0.17 Å2
2---0.15 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.89→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 0 220 3192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223027
X-RAY DIFFRACTIONr_bond_other_d0.0010.022129
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.9654061
X-RAY DIFFRACTIONr_angle_other_deg0.79835135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9075359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95523.889162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0215558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2111524
X-RAY DIFFRACTIONr_chiral_restr0.0720.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023357
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
X-RAY DIFFRACTIONr_nbd_refined0.1870.2533
X-RAY DIFFRACTIONr_nbd_other0.1880.22157
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21449
X-RAY DIFFRACTIONr_nbtor_other0.0850.21687
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2181
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.220
X-RAY DIFFRACTIONr_mcbond_it1.2471.52356
X-RAY DIFFRACTIONr_mcbond_other0.1631.5752
X-RAY DIFFRACTIONr_mcangle_it1.34222858
X-RAY DIFFRACTIONr_scbond_it2.0831451
X-RAY DIFFRACTIONr_scangle_it2.8634.51203
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 115 -
Rwork0.227 2211 -
all-2326 -
obs--92.08 %
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)
10.85750.41070.12320.75480.28850.17740.0002-0.02590.05460.0118-0.0233-0.05240.0533-0.01870.0232-0.02590.0053-0.0114-0.05450.00830.0283-3.121321.426672.92
20.9548-0.25560.01991.1583-0.1830.54210.06310.3185-0.0481-0.05810.0075-0.0675-0.04690.0443-0.0706-0.0325-0.0033-0.00090.0797-0.0001-0.07254.56699.633345.7731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 19516 - 207
2X-RAY DIFFRACTION2BB4 - 19516 - 207

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