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- PDB-3kog: Crystal structure of Putative pore-forming toxin (YP_001301288.1)... -

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Entry
Database: PDB / ID: 3kog
TitleCrystal structure of Putative pore-forming toxin (YP_001301288.1) from Bacteroides vulgatus ATCC 8482 at 1.85 A resolution
ComponentsPutative pore-forming toxin
KeywordsMEMBRANE PROTEIN / Putative pore-forming toxin / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyDomain of unknown function DUF3869 / Domain of unknown function (DUF3869) / Prokaryotic membrane lipoprotein lipid attachment site profile. / ACETATE ION / DUF3869 domain-containing protein
Function and homology information
Biological speciesBacteroides vulgatus ATCC 8482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative pore-forming toxin (YP_001301288.1) from Bacteroides vulgatus ATCC 8482 at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative pore-forming toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3758
Polymers27,7771
Non-polymers5987
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.796, 70.337, 104.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-7-

MRD

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Components

#1: Protein Putative pore-forming toxin


Mass: 27777.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus ATCC 8482 (bacteria)
Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_4064 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6L7K2
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE THIS CONSTRUCT (28-282) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE ...SEQUENCE THIS CONSTRUCT (28-282) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.43
Details: 31.6000% 2-methyl-2,4-pentanediol, 0.2000M sodium chloride, 0.1M sodium acetate pH 4.43, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.85503,0.97926,0.97845
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.855031
20.979261
30.978451
ReflectionResolution: 1.85→29.814 Å / Num. obs: 21313 / % possible obs: 100 % / Redundancy: 4.1 % / Biso Wilson estimate: 21.528 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.94.10.7261637715490.726100
1.9-1.954.10.5651619615070.565100
1.95-2.014.10.4391.7606814750.439100
2.01-2.074.10.342.1591414370.34100
2.07-2.144.10.2942.5567213780.294100
2.14-2.214.10.2622.8559113550.262100
2.21-2.294.10.223.3537613090.22100
2.29-2.394.10.1893.9513912460.189100
2.39-2.494.10.1674.4492812010.167100
2.49-2.624.10.1425476211630.142100
2.62-2.764.10.1156.2449510980.115100
2.76-2.934.10.0977.1423510350.097100
2.93-3.134.10.0818.140299870.081100
3.13-3.384.10.0679.537779280.067100
3.38-3.74.10.05311.834828580.053100
3.7-4.144.10.04313.830937630.043100
4.14-4.7840.04313.727626910.043100
4.78-5.8540.04612.923425910.046100
5.85-8.273.80.04314.217874670.043100
8.27-29.823.50.03915.39632750.03998

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.85→29.814 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 6.503 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.129
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ACETATE (ACT), GLYCEROL (GOL), AND (4R)-2-METHYL-2,4-PENTANEDIOL (MRD) FROM THE CRYSTALLIZATION/CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 5. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1095 5.1 %RANDOM
Rwork0.182 ---
obs0.184 21310 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.51 Å2 / Biso mean: 18.402 Å2 / Biso min: 4.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1729 0 40 169 1938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221944
X-RAY DIFFRACTIONr_bond_other_d0.0020.021260
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.9532673
X-RAY DIFFRACTIONr_angle_other_deg0.9333143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6425272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.54926.26491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07615325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.383153
X-RAY DIFFRACTIONr_chiral_restr0.1020.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02360
X-RAY DIFFRACTIONr_mcbond_it0.9591.51204
X-RAY DIFFRACTIONr_mcbond_other0.2771.5484
X-RAY DIFFRACTIONr_mcangle_it1.69721981
X-RAY DIFFRACTIONr_scbond_it2.693740
X-RAY DIFFRACTIONr_scangle_it4.34.5669
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 73 -
Rwork0.271 1468 -
all-1541 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4965-0.33920.28041.24850.3460.7718-0.0912-0.02710.0376-0.05290.1747-0.1794-0.0804-0.0569-0.08350.0384-0.00940.01370.06560.00040.052829.19126.42948.593
23.53872.36693.57123.30443.43334.7673-0.00920.4123-0.1249-0.08450.2816-0.2361-0.11650.3624-0.27250.0635-0.00470.03520.10390.01580.050126.7729.9438.447
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 145
2X-RAY DIFFRACTION2A146 - 266

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