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- PDB-2g0i: Crystal structure of SMU.848 from Streptococcus mutans -

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Basic information

Entry
Database: PDB / ID: 2g0i
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 / 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
DI(HYDROXYETHYL)ETHER / Ribosomal processing cysteine protease Prp
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 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 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: hypothetical protein SMU.848
B: hypothetical protein SMU.848
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2837
Polymers31,8852
Non-polymers3995
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-36 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.617, 60.995, 85.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains a biological dimer.

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Components

#1: Protein hypothetical protein SMU.848


Mass: 15942.327 Da / Num. of mol.: 2
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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.9 Å3/Da / Density % sol: 35.16 % / Description: the file contains Friedel pairs
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-NaOH, PH7.5, 0.6%PEG400, 0.2M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBSRF 3W1A10.9797, 0.9799, 1.0
SYNCHROTRONBSRF 3W1A21
Detector
TypeIDDetectorDate
MARRESEARCH1CCDMar 5, 2005
MARRESEARCH2CCDMar 10, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) double-crystalMADMx-ray1
2Si(111) double-crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97991
311
Reflection

D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
6.414.6708630.1180.682.31115899.9
6.224.3782220.1190.592.21268099.9
6.137.3675250.0940.922.31114599.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.9550122499.810.0761.4246.5
3.934.95114010010.0661.0017
3.443.93112310010.0760.7916.8
3.123.44111610010.1040.5966.5
2.93.12110199.910.1790.5216.3
2.732.9108599.910.2360.5166.2
2.592.73110399.910.2510.4446.1
2.482.59108710010.320.4766
2.382.48109699.810.4130.3776.1
2.32.38108399.810.4580.4096
4.7450138299.820.0551.0216.7
3.764.74130410020.0550.7257
3.293.76127510020.0730.5536.8
2.993.29127099.920.1260.4636.4
2.772.99124399.920.2080.4346
2.612.77125999.720.2520.4445.8
2.482.61122399.720.3230.4885.7
2.372.48124999.820.4260.4715.7
2.282.37124699.820.5120.5445.7
2.22.28122999.920.5930.5595.7
4.9550122499.830.0451.1346.6
3.934.95113710030.040.9657
3.443.93112410030.0570.8926.6
3.123.44111399.930.0890.9016.2
2.93.12110099.630.1560.8656
2.732.9107999.430.2090.8435.7
2.592.73110210030.2470.9185.6
2.482.59108599.930.3060.8785.6
2.382.48109799.730.4260.8975.6
2.32.38108499.930.470.8685.6
ReflectionResolution: 1.85→50 Å / Num. all: 21432 / Num. obs: 21004 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 100 / Redundancy: 5.3 % / Rmerge(I) obs: 0.069 / Χ2: 0.861 / Net I/σ(I): 7.7
Reflection shellResolution: 1.85→1.92 Å / % possible obs: 98.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.479 / Num. unique obs: 2051 / Χ2: 0.786 / % possible all: 99.9

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97974.92-7.69
13 wavelength210.52-3.38
13 wavelength30.97992.97-9.19
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se40.10.7060.0830.221.229
2Se12.6610.6040.1020.1910.907
3Se58.8720.8050.7040.1971.316
4Se10.8910.6930.180.416
5Se10.9020.740.2050.713
6Se44.4110.6030.0270.2111.118
Phasing dmFOM : 0.6 / FOM acentric: 0.6 / FOM centric: 0.65 / Reflection: 11435 / Reflection acentric: 9887 / Reflection centric: 1548
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.3-42.4010.80.820.76604394210
3.9-6.30.820.830.7816991360339
3.1-3.90.770.780.7120881779309
2.8-3.10.610.610.619721738234
2.4-2.80.490.480.5332832961322
2.2-2.40.350.350.3517891655134

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
MAR345data collection
RefinementMethod to determine structure: MAD / Resolution: 1.85→49.57 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.267 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: the file contains Friedel pairs. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2100 9.9 %RANDOM
Rwork0.208 ---
all0.213 21432 --
obs0.213 21004 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.361 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20 Å2
2--0.69 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1703 0 2 179 1884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221742
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9832349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4745228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.30926.33871
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0515313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.324154
X-RAY DIFFRACTIONr_chiral_restr0.1030.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021258
X-RAY DIFFRACTIONr_nbd_refined0.2140.2858
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21236
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2138
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.210
X-RAY DIFFRACTIONr_mcbond_it2.21131144
X-RAY DIFFRACTIONr_mcangle_it2.9131786
X-RAY DIFFRACTIONr_scbond_it2.1882661
X-RAY DIFFRACTIONr_scangle_it3.3314559
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 155 -
Rwork0.256 1364 -
obs-1519 98.7 %

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