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- PDB-6dt3: 1.2 Angstrom Resolution Crystal Structure of Nucleoside Triphosph... -

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Basic information

Entry
Database: PDB / ID: 6dt3
Title1.2 Angstrom Resolution Crystal Structure of Nucleoside Triphosphatase NudI from Klebsiella pneumoniae in Complex with HEPES
ComponentsNucleoside triphosphatase NudI
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / putative NUDIX hydrolase / HEPES
Function / homology
Function and homology information


dCTP diphosphatase / dCTP diphosphatase activity / nucleotide diphosphatase / dUTP diphosphatase / dUTP diphosphatase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / magnesium ion binding
Similarity search - Function
Nucleoside triphosphatase NudI / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Nucleoside triphosphatase NudI / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Nucleoside triphosphatase NudI
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsMinasov, G. / Shuvalova, L. / Pshenychnyi, S. / Endres, M. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2023
Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.
Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F.
History
DepositionJun 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside triphosphatase NudI
B: Nucleoside triphosphatase NudI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5453
Polymers33,3072
Non-polymers2381
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, homologous structure 3N77 is a dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-4 kcal/mol
Surface area14070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.140, 39.346, 56.294
Angle α, β, γ (deg.)77.07, 80.74, 86.20
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Nucleoside triphosphatase NudI / Nucleotide diphosphatase NudI / Pyrimidine deoxynucleoside triphosphate diphosphatase / dCTP ...Nucleotide diphosphatase NudI / Pyrimidine deoxynucleoside triphosphate diphosphatase / dCTP diphosphatase / dTTP diphosphatase / dUTP diphosphatase


Mass: 16653.455 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria)
Gene: nudI, B1727_21840 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 Gold
References: UniProt: A0A1W1Q5B1, nucleotide diphosphatase, dCTP diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides, dUTP diphosphatase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10.0 mg/mL protein, 0.5 M sodium chloride, 0.01 M Tris, pH 8.3 against Classics II (F8) (0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 25% w/v PEG3350)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 11, 2018 / Details: C(111)
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 78810 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.052 / Rrim(I) all: 0.088 / Rsym value: 0.07 / Χ2: 1.201 / Net I/σ(I): 13.7
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3881 / CC1/2: 0.593 / Rpim(I) all: 0.563 / Rrim(I) all: 0.973 / Rsym value: 0.79 / Χ2: 1.003 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→27.14 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.771 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18662 3897 4.9 %RANDOM
Rwork0.1534 ---
obs0.15503 74887 92.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.812 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.61 Å2-0.47 Å2
2--0.66 Å20 Å2
3----0.68 Å2
Refinement stepCycle: 1 / Resolution: 1.2→27.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2312 0 15 343 2670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0142618
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172325
X-RAY DIFFRACTIONr_angle_refined_deg1.41.6873574
X-RAY DIFFRACTIONr_angle_other_deg0.5051.6895478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5625332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.15621.274157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.45815439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7241526
X-RAY DIFFRACTIONr_chiral_restr0.0770.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.040.023071
X-RAY DIFFRACTIONr_gen_planes_other0.0370.02485
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_it1.381.0511271
X-RAY DIFFRACTIONr_mcbond_other1.3741.0491270
X-RAY DIFFRACTIONr_mcangle_it1.6141.5821622
X-RAY DIFFRACTIONr_mcangle_other1.6141.5841623
X-RAY DIFFRACTIONr_scbond_it21.381347
X-RAY DIFFRACTIONr_scbond_other1.9851.381347
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2881.9691953
X-RAY DIFFRACTIONr_long_range_B_refined2.80714.6022950
X-RAY DIFFRACTIONr_long_range_B_other2.80614.6062951
X-RAY DIFFRACTIONr_rigid_bond_restr11.07434943
X-RAY DIFFRACTIONr_sphericity_free16.89610190
X-RAY DIFFRACTIONr_sphericity_bonded7.487105039
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 297 -
Rwork0.237 5395 -
obs--89.65 %
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)
10.6153-0.0258-0.10190.005-0.06381.6171-0.0167-0.0851-0.06560.00230.00640.0104-0.0068-0.01380.01030.0672-0.01640.01770.0180.00420.062430.87618.486321.7907
20.78390.00590.01290.3247-0.23950.95160.0128-0.1129-0.03550.01050.02120.00730.0442-0.0961-0.0340.0326-0.00180.00920.02660.00790.027625.71998.481721.6132
30.6949-1.84050.144511.6068-0.30650.54330.011-0.0194-0.16090.3935-0.0791-0.06160.0966-0.10970.06810.0635-0.0216-0.01210.0255-0.0070.119138.8675-5.84369.6754
40.49730.07590.04730.2737-0.20861.59730.0364-0.10570.02170.0701-0.0247-0.0211-0.07620.0538-0.01170.043-0.00820.01240.0254-0.00290.02933.361312.507725.7536
53.07492.654-1.24043.2856-1.43190.7526-0.05250.0596-0.0652-0.0845-0.0013-0.06660.0123-0.03340.05380.02140.00210.00170.012-0.00890.024322.372215.49631.6306
61.38020.42620.06782.3017-0.15721.66060.04330.08540.03180.05570.00970.04160.013-0.162-0.0530.00890.00580.00890.02750.00850.025620.336725.7872-6.6064
71.3396-0.79760.49122.1975-1.87393.6470.09920.1082-0.0796-0.1047-0.00830.05930.1329-0.0063-0.09090.01720.0065-0.00350.0108-0.0040.032132.608214.7869-5.3293
80.55390.0879-0.08270.5341-0.23240.72160.00290.04760.0517-0.0057-0.0198-0.0108-0.0527-0.0430.01690.01490.00930.00650.01170.00410.033222.970224.4334-1.6586
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 24
2X-RAY DIFFRACTION2A25 - 75
3X-RAY DIFFRACTION3A76 - 88
4X-RAY DIFFRACTION4A89 - 141
5X-RAY DIFFRACTION5B-2 - 13
6X-RAY DIFFRACTION6B14 - 39
7X-RAY DIFFRACTION7B40 - 61
8X-RAY DIFFRACTION8B62 - 141

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