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- PDB-3re9: Crystal structure of sortaseC1 from Streptococcus suis -

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Basic information

Entry
Database: PDB / ID: 3re9
TitleCrystal structure of sortaseC1 from Streptococcus suis
ComponentsSortase-like protein
KeywordsTRANSFERASE / Class C sortase / sortaseC-specific lid / helix / open-form / substrate-binding site / transpeptidase
Function / homology
Function and homology information


membrane => GO:0016020 / hydrolase activity
Similarity search - Function
Sortase C / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Sortase-like protein
Similarity search - Component
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsLu, G. / Qi, J. / Gao, F. / Yan, J. / Tang, J. / Gao, G.F.
CitationJournal: Proteins / Year: 2011
Title: A novel "open-form" structure of sortaseC from Streptococcus suis.
Authors: Lu, G. / Qi, J. / Gao, F. / Yan, J. / Tang, J. / Gao, G.F.
History
DepositionApr 4, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Sortase-like protein


Theoretical massNumber of molelcules
Total (without water)21,1661
Polymers21,1661
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.343, 101.021, 36.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Sortase-like protein


Mass: 21166.049 Da / Num. of mol.: 1 / Fragment: UNP residues 67-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Strain: 05ZYH33 / Gene: SSU05_2098 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A4VY75, EC: 2.3.2.12
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2244.56
2
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCL, 0.54M sodium citrate, 8% V/V iso-propanol, 8% V/V tert-butanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
22
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-00711.5418
SYNCHROTRONBSRF 3W1A20.97893, 0.98050, 0.90000
Detector
TypeIDDetectorDate
RIGAKU RAXIS VII1IMAGE PLATEMay 13, 2007
MAR scanner 345 mm plate2IMAGE PLATEJul 30, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 channelSINGLE WAVELENGTHMx-ray1
2MADx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.978931
30.98051
40.91
ReflectionResolution: 2.4→36.94 Å / Num. all: 7851 / Num. obs: 7831 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 11.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.77 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 6.6 / Num. unique all: 759 / Rsym value: 0.221 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→36.94 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.862 / SU B: 8.75 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26104 361 4.6 %RANDOM
Rwork0.20628 ---
all0.20873 7831 --
obs0.20873 7469 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.091 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1414 0 0 93 1507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221453
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9691978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7945180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61223.84665
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15515250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.498159
X-RAY DIFFRACTIONr_chiral_restr0.0970.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021087
X-RAY DIFFRACTIONr_nbd_refined0.1960.2642
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3030.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0740.24
X-RAY DIFFRACTIONr_mcbond_it0.7111.5928
X-RAY DIFFRACTIONr_mcangle_it1.15421460
X-RAY DIFFRACTIONr_scbond_it1.7133592
X-RAY DIFFRACTIONr_scangle_it2.6394.5517
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 33 -
Rwork0.237 528 -
obs-528 100 %

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