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- PDB-2g0j: Crystal structure of SMU.848 from Streptococcus mutans -

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Basic information

Entry
Database: PDB / ID: 2g0j
TitleCrystal structure of SMU.848 from Streptococcus mutans
Componentshypothetical protein SMU.848
KeywordsUNKNOWN FUNCTION / 2-layer (alpha-beta)-sandwich
Function / homology
Function and homology information


cysteine-type peptidase activity / ribosome biogenesis / proteolysis / metal ion binding
Similarity search - Function
Cysteine protease Prp / Cysteine protease Prp / Cysteine protease Prp superfamily / Cysteine protease Prp / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal processing cysteine protease Prp
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHou, H.-F. / Gao, Z.-Q. / Li, L.-F. / Liang, Y.-H. / Su, X.-D. / Dong, Y.-H.
CitationJournal: To be Published
Title: Crystal structure of SMU.848 from Streptococcus mutans
Authors: Hou, H.-F. / Gao, Z.-Q. / Xu, J.-H. / Xu, R. / Li, L.-Q. / Li, L.-F. / Liang, Y.-H. / Su, X.-D. / Liu, P. / Xian, D.-C. / Dong, Y.-H.
History
DepositionFeb 13, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Mar 13, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein SMU.848
B: hypothetical protein SMU.848
C: hypothetical protein SMU.848
D: hypothetical protein SMU.848


Theoretical massNumber of molelcules
Total (without water)62,8314
Polymers62,8314
Non-polymers00
Water1,33374
1
A: hypothetical protein SMU.848
B: hypothetical protein SMU.848


Theoretical massNumber of molelcules
Total (without water)31,4162
Polymers31,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-19 kcal/mol
Surface area10690 Å2
MethodPISA
2
C: hypothetical protein SMU.848
D: hypothetical protein SMU.848


Theoretical massNumber of molelcules
Total (without water)31,4162
Polymers31,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-21 kcal/mol
Surface area11010 Å2
MethodPISA
3
A: hypothetical protein SMU.848
B: hypothetical protein SMU.848

A: hypothetical protein SMU.848
B: hypothetical protein SMU.848

C: hypothetical protein SMU.848
D: hypothetical protein SMU.848

C: hypothetical protein SMU.848
D: hypothetical protein SMU.848


Theoretical massNumber of molelcules
Total (without water)125,6638
Polymers125,6638
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
crystal symmetry operation3_454-x+y-1,-x,z-1/31
crystal symmetry operation4_455y-1,x,-z1
Buried area12170 Å2
ΔGint-111 kcal/mol
Surface area38710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.160, 78.160, 130.157
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
hypothetical protein SMU.848


Mass: 15707.851 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Plasmid: Pet28(a) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8DUQ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.83 Å3/Da / Density % sol: 32.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-NaOH, PH 7.5, 28% PEG 400, 0.2M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 20, 2005
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 6 % / Av σ(I) over netI: 7 / Number: 71233 / Rmerge(I) obs: 0.11 / Χ2: 1.06 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 11810 / % possible obs: 99.7
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsChi squaredRedundancy
6.0350127298.70.0440.9325.6
4.796.03121099.80.0631.1136.1
4.184.79119699.70.0591.1036.1
3.84.18118199.80.0881.0776
3.533.8116099.80.1181.1156.1
3.323.53117399.80.1541.0936.1
3.153.32116599.90.2361.0696.1
3.023.15114899.90.3381.0846.2
2.93.02115699.90.4631.0286.2
2.82.9114999.70.5991.0016
ReflectionResolution: 2.8→50 Å / Num. all: 11846 / Num. obs: 11810 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Rmerge(I) obs: 0.11 / Χ2: 1.062 / Net I/σ(I): 7
Reflection shellResolution: 2.8→2.9 Å / % possible obs: 99.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.599 / Num. unique obs: 1149 / Χ2: 1.001 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
MAR345data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1160 9.8 %RANDOM
Rwork0.226 ---
all0.264 11229 --
obs0.24 11196 94.8 %-
Solvent computationBsol: 41.63 Å2
Displacement parametersBiso mean: 38.197 Å2
Baniso -1Baniso -2Baniso -3
1--8.102 Å2-10.422 Å20 Å2
2---8.102 Å20 Å2
3---16.203 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 0 74 3540
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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