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- PDB-3l7n: Crystal structure of SMU.1228c -

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Basic information

Entry
Database: PDB / ID: 3l7n
TitleCrystal structure of SMU.1228c
ComponentsPutative uncharacterized protein
KeywordsTRANSFERASE / glutamine amidotransferase / Streptococcus mutans
Function / homology
Function and homology information


glutamine metabolic process
Similarity search - Function
Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamine amidotransferase type-1 domain-containing protein
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFan, X.-X. / Wang, K.-T. / Su, X.-D.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of SMU.1228c
Authors: Fan, X.-X. / Wang, K.-T. / Su, X.-D.
History
DepositionDec 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,6221
Polymers26,6221
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.083, 104.083, 195.621
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-238-

HOH

21A-283-

HOH

31A-296-

HOH

41A-316-

HOH

51A-352-

HOH

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Components

#1: Protein Putative uncharacterized protein / glutamine amidotransferase


Mass: 26622.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU_1228c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DTU5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.83 Å3/Da / Density % sol: 67.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20-22% PEG 1000, 0.2M (NH4)2SO4, 0.1M Na/K phosphate pH6.5, 0.1M Guanidine hydrochloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→66.29 Å / Num. all: 11498 / Num. obs: 11483 / % possible obs: 99 % / Observed criterion σ(F): 2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 99

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0102refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O1Y

1o1y


Resolution: 2.7→66.29 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.859 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.454 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22375 587 5.1 %RANDOM
Rwork0.20382 ---
obs0.20486 10874 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.876 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å21.11 Å20 Å2
2--2.22 Å20 Å2
3----3.33 Å2
Refinement stepCycle: LAST / Resolution: 2.7→66.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 0 120 1969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0221893
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9672563
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4585233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14925.22788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.68315325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.023155
X-RAY DIFFRACTIONr_chiral_restr0.140.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211441
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3411.51165
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.56521870
X-RAY DIFFRACTIONr_scbond_it3.8153728
X-RAY DIFFRACTIONr_scangle_it5.8644.5693
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 43 -
Rwork0.332 804 -
obs--99.88 %

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