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- PDB-4hx9: Designed Phosphodeoxyribosyltransferase -

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Basic information

Entry
Database: PDB / ID: 4hx9
TitleDesigned Phosphodeoxyribosyltransferase
ComponentsNucleoside deoxyribosyltransferase
KeywordsTRANSFERASE / Non natural and design enzyme / Rossmann Fold / Phosphodeoxyribosyltransferase
Function / homology
Function and homology information


nucleoside deoxyribosyltransferase / nucleotide salvage / nucleoside deoxyribosyltransferase activity
Similarity search - Function
Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside deoxyribosyltransferase
Similarity search - Component
Biological speciesLactobacillus leichmannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsKaminski, P.A. / Labesse, G.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Phosphodeoxyribosyltransferases, designed enzymes for deoxyribonucleotides synthesis.
Authors: Kaminski, P.A. / Labesse, G.
History
DepositionNov 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Mar 20, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside deoxyribosyltransferase
B: Nucleoside deoxyribosyltransferase
E: Nucleoside deoxyribosyltransferase
F: Nucleoside deoxyribosyltransferase
C: Nucleoside deoxyribosyltransferase
D: Nucleoside deoxyribosyltransferase
G: Nucleoside deoxyribosyltransferase
H: Nucleoside deoxyribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,70528
Polymers144,1948
Non-polymers2,51020
Water3,765209
1
A: Nucleoside deoxyribosyltransferase
B: Nucleoside deoxyribosyltransferase
hetero molecules

A: Nucleoside deoxyribosyltransferase
B: Nucleoside deoxyribosyltransferase
hetero molecules

A: Nucleoside deoxyribosyltransferase
B: Nucleoside deoxyribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,17621
Polymers108,1466
Non-polymers2,03015
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area15950 Å2
ΔGint-111 kcal/mol
Surface area35620 Å2
MethodPISA
2
E: Nucleoside deoxyribosyltransferase
F: Nucleoside deoxyribosyltransferase
C: Nucleoside deoxyribosyltransferase
D: Nucleoside deoxyribosyltransferase
G: Nucleoside deoxyribosyltransferase
H: Nucleoside deoxyribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,97921
Polymers108,1466
Non-polymers1,83415
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17050 Å2
ΔGint-108 kcal/mol
Surface area34920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.454, 218.454, 218.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein
Nucleoside deoxyribosyltransferase / N-deoxyribosyltransferase


Mass: 18024.301 Da / Num. of mol.: 8 / Mutation: F13R,E91Q,D92G,V93T,N123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus leichmannii (bacteria) / Gene: ntd / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Bli5
References: UniProt: Q9R5V5, nucleoside deoxyribosyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: NH4SO4 1.2 M, 0.1 M HEPES at pH 7.7, PEG400 2%, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.68→39.9 Å / Num. all: 48494 / Num. obs: 47987 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.68→2.82 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
AMoREphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F8Y

1f8y


Resolution: 2.68→38.62 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.904 / SU B: 27.626 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.839 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24953 2436 5 %RANDOM
Rwork0.19523 ---
obs0.19801 46023 99.81 %-
all-48576 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.587 Å2
Refinement stepCycle: LAST / Resolution: 2.68→38.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10060 0 148 209 10417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210473
X-RAY DIFFRACTIONr_bond_other_d0.0010.027106
X-RAY DIFFRACTIONr_angle_refined_deg1.171.96914160
X-RAY DIFFRACTIONr_angle_other_deg0.83317358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74951235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.55925.449523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.302151773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6131531
X-RAY DIFFRACTIONr_chiral_restr0.0680.21453
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111504
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022039
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3681.56183
X-RAY DIFFRACTIONr_mcbond_other0.061.52545
X-RAY DIFFRACTIONr_mcangle_it0.69329961
X-RAY DIFFRACTIONr_scbond_it1.04734290
X-RAY DIFFRACTIONr_scangle_it1.6724.54199
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.68→2.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 188 -
Rwork0.308 3351 -
obs--99.89 %
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)
11.6566-0.14990.46172.0658-1.14843.2936-0.05620.0277-0.11910.040.22540.5502-0.105-0.7953-0.16920.0941-0.0113-0.03330.2955-0.00360.23314.387938.071336.1612
20.5243-0.1818-0.6681.5577-0.96323.65820.0489-0.05780.0860.150.1820.0971-0.4404-0.494-0.23080.11250.06370.00350.1325-0.00110.072128.553252.360149.8205
33.66210.518-1.70271.929-1.61842.3307-0.15240.1732-0.05120.08980.21550.61170.0883-0.6103-0.06320.3614-0.02610.05290.4659-0.11540.56785.057729.801190.1392
41.594-0.0638-0.25952.3198-0.74153.06390.07940.0955-0.27850.03290.09530.30310.6454-0.4545-0.17470.2755-0.0671-0.08510.20470.04540.183320.428814.20680.3456
51.46120.08282.02142.89541.06444.1752-0.3173-0.01970.64320.41330.0727-0.2487-0.64220.35810.24460.6977-0.0343-0.15520.2887-0.11580.719729.2649.44998.2735
62.8436-1.35191.95472.0099-0.74333.4609-0.36670.36240.72640.3827-0.1478-0.9715-0.37330.56910.51450.2371-0.0835-0.22570.23980.15450.524844.596834.336886.8711
73.86980.442-0.29032.460.09872.0593-0.0674-1.00080.15760.92130.03050.0792-0.1148-0.23270.03690.91170.14120.02070.55070.00070.264820.401725.8432118.3363
82.7531-0.58980.48193.0633-1.41242.4534-0.1243-0.5313-0.09040.59030.1562-0.1412-0.0033-0.167-0.03180.43520.044-0.11910.23610.05960.170236.421711.4623107.8023
90.08710.0388-0.2520.4042-0.29080.8516-0.00930.0107-0.00550.15260.0138-0.064-0.0124-0.1383-0.00450.2783-0.0077-0.06360.30460.07150.308127.953833.921875.7145
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 201
2X-RAY DIFFRACTION2B2 - 201
3X-RAY DIFFRACTION3E2 - 202
4X-RAY DIFFRACTION4F2 - 202
5X-RAY DIFFRACTION5C2 - 201
6X-RAY DIFFRACTION6D2 - 202
7X-RAY DIFFRACTION7G2 - 202
8X-RAY DIFFRACTION8H2 - 202
9X-RAY DIFFRACTION9A203 - 336
10X-RAY DIFFRACTION9B202 - 345
11X-RAY DIFFRACTION9F203 - 330
12X-RAY DIFFRACTION9D203 - 330
13X-RAY DIFFRACTION9E301 - 323
14X-RAY DIFFRACTION9C301 - 308
15X-RAY DIFFRACTION9G301 - 313
16X-RAY DIFFRACTION9H301 - 324

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