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- PDB-3l9d: The Crystal Structure of smu.1046c from Streptococcus mutans UA159 -

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Basic information

Entry
Database: PDB / ID: 3l9d
TitleThe Crystal Structure of smu.1046c from Streptococcus mutans UA159
ComponentsPutative GTP pyrophosphokinase
KeywordsTRANSFERASE / GTP pyrophosphokinase / Kinase
Function / homology
Function and homology information


guanosine tetraphosphate biosynthetic process / kinase activity
Similarity search - Function
Nucleotidyltransferase / : / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Helix Hairpins / 2-Layer Sandwich ...Nucleotidyltransferase / : / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GTP pyrophosphokinase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.484 Å
AuthorsSu, X.-D. / Huang, Y.H. / Liu, X.
CitationJournal: TO BE PUBLISHED
Title: The Crystal Structure of smu.1046c from Streptococcus mutans UA159
Authors: Su, X.-D. / Huang, Y.H. / Liu, X.
History
DepositionJan 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative GTP pyrophosphokinase
B: Putative GTP pyrophosphokinase


Theoretical massNumber of molelcules
Total (without water)59,7522
Polymers59,7522
Non-polymers00
Water2,306128
1
A: Putative GTP pyrophosphokinase


Theoretical massNumber of molelcules
Total (without water)29,8761
Polymers29,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative GTP pyrophosphokinase


Theoretical massNumber of molelcules
Total (without water)29,8761
Polymers29,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.006, 103.327, 64.008
Angle α, β, γ (deg.)90.00, 115.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-263-

HOH

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Components

#1: Protein Putative GTP pyrophosphokinase / smu.1046c


Mass: 29876.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: smu.1046c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DU97, GTP diphosphokinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8% PEG 1000, 0.1mM KCl, 0.1mM HEPES Na pH 7.0, 0.02mM MgCl2 , VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Apr 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.484→62.06 Å / Num. obs: 17850 / Observed criterion σ(I): 1 / Biso Wilson estimate: 31.55 Å2
Reflection shellHighest resolution: 2.484 Å

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
PHENIXrefinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BE3

2be3


Resolution: 2.484→38.81 Å / Occupancy max: 1 / Occupancy min: 0.7 / FOM work R set: 0.7851 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 28.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 1546 10.01 %
Rwork0.1885 13901 -
obs0.196 15447 86.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.538 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 102.94 Å2 / Biso mean: 37.3679 Å2 / Biso min: 11.83 Å2
Baniso -1Baniso -2Baniso -3
1--2.7855 Å2-0 Å24.1854 Å2
2---11.6783 Å2-0 Å2
3---14.4638 Å2
Refinement stepCycle: LAST / Resolution: 2.484→38.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 0 128 3344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093280
X-RAY DIFFRACTIONf_angle_d1.1274407
X-RAY DIFFRACTIONf_chiral_restr0.074485
X-RAY DIFFRACTIONf_plane_restr0.006568
X-RAY DIFFRACTIONf_dihedral_angle_d19.1651259
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4845-2.56460.3574690.242165172045
2.5646-2.65630.3427960.2268941103764
2.6563-2.76260.31041280.21541141126979
2.7626-2.88830.34771500.24371297144791
2.8883-3.04050.29821590.22451373153293
3.0405-3.23090.29941520.20071348150094
3.2309-3.48020.2711500.18071391154195
3.4802-3.83020.26861570.16851407156497
3.8302-4.38380.20171620.14721433159597
4.3838-5.52060.21441630.14971462162599
5.5206-38.8150.24791600.19591457161798

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