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- PDB-3k6q: CRYSTAL STRUCTURE OF An antitoxin part of a putative toxin/antito... -

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Basic information

Entry
Database: PDB / ID: 3k6q
TitleCRYSTAL STRUCTURE OF An antitoxin part of a putative toxin/antitoxin system (SWOL_0700) FROM SYNTROPHOMONAS WOLFEI SUBSP. WOLFEI AT 1.80 A RESOLUTION
ComponentsPutative ligand binding protein
Keywordsligand binding protein / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


Double Stranded RNA Binding Domain - #620 / Antitoxin of toxin-antitoxin, RelE/RelB, TA system / Antitoxin of toxin-antitoxin, RelE / RelB, TA system / YefM-like domain / YefM-like superfamily / YefM-like fold / Double Stranded RNA Binding Domain / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSyntrophomonas wolfei subsp. wolfei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative ligand binding protein (YP_753395.1) from Syntrophomonas wolfei str. Goettingen at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / 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: 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 / pdbx_struct_conn_angle ...database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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

Downloads & links

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Assembly

Deposited unit
A: Putative ligand binding protein
B: Putative ligand binding protein
C: Putative ligand binding protein
D: Putative ligand binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2248
Polymers65,0404
Non-polymers1844
Water5,945330
1
A: Putative ligand binding protein
B: Putative ligand binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5443
Polymers32,5202
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-31 kcal/mol
Surface area14790 Å2
MethodPISA
2
C: Putative ligand binding protein
D: Putative ligand binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6805
Polymers32,5202
Non-polymers1603
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-39 kcal/mol
Surface area14670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.974, 56.943, 62.561
Angle α, β, γ (deg.)107.000, 103.030, 100.210
Int Tables number1
Space group name H-MP1
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Putative ligand binding protein


Mass: 16260.010 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Syntrophomonas wolfei subsp. wolfei (bacteria)
Strain: Goettingen / Gene: Swol_0700 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q0AZ30
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A 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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.2000M MgCl2, 20.0000% PEG-3350, No Buffer pH 5.8, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97905,0.97860
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 11, 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
10.918371
20.979051
30.97861
ReflectionResolution: 1.8→29.828 Å / Num. obs: 46885 / % possible obs: 97 % / Redundancy: 2 % / Biso Wilson estimate: 24.57 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 2 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.850.3442.2688434590.34495.9
1.85-1.90.2672.9662833380.26795.9
1.9-1.950.2053.7647232540.20596.3
1.95-2.010.1614.6631131760.16196.2
2.01-2.080.1216.1608230610.12196.5
2.08-2.150.1017.4590229680.10196.5
2.15-2.230.0868.5581229260.08696.9
2.23-2.320.0719.7544027370.07197.4
2.32-2.430.06411529226640.06497.1
2.43-2.550.05911.5508525600.05997.1
2.55-2.680.05312.3487024560.05397.8
2.68-2.850.04812.8455222910.04897.3
2.85-3.040.04314.4436321960.04398.3
3.04-3.290.03616401420210.03698.2
3.29-3.60.03316.1367818490.03398.1
3.6-4.020.03218.4335516900.03298.4
4.02-4.650.03416.8297714960.03498.6
4.65-5.690.03914.9250112590.03998.4
5.69-8.050.04711.119399770.04798.9
8.05-29.830.04511.59915070.04594

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.828 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 7.637 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. MAGNESIUM ION (MG), CHLORIDE ION (CL), AND ETHYLENE GLYCOL (EDO) FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2379 5.1 %RANDOM
Rwork0.193 ---
obs0.195 46885 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 49.15 Å2 / Biso mean: 19.112 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-1.45 Å20.35 Å2
2---0.45 Å2-0.82 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4509 0 10 330 4849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224741
X-RAY DIFFRACTIONr_bond_other_d0.0010.023168
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.9766436
X-RAY DIFFRACTIONr_angle_other_deg0.93737814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4595589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44125.685241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08515896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6991518
X-RAY DIFFRACTIONr_chiral_restr0.0980.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025263
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02915
X-RAY DIFFRACTIONr_mcbond_it0.9251.52836
X-RAY DIFFRACTIONr_mcbond_other0.2551.51137
X-RAY DIFFRACTIONr_mcangle_it1.62724634
X-RAY DIFFRACTIONr_scbond_it2.45231905
X-RAY DIFFRACTIONr_scangle_it3.9014.51785
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 178 -
Rwork0.236 3278 -
all-3456 -
obs--95.87 %
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)
12.9209-1.3636-1.7131.27570.68882.1582-0.0152-0.26950.09440.01870.1078-0.0501-0.14180.1995-0.09260.06150.0035-0.03610.0712-0.00960.07248.7290.71235.457
22.58071.7233-0.06281.9179-0.09471.1440.0203-0.0496-0.0569-0.0129-0.04130.0130.080.020.0210.09940.0798-0.00050.07220.01750.07928.275-15.7329.919
32.3523-0.2633-0.9440.74430.33371.4376-0.03130.16870.0779-0.0687-0.01880.052-0.0908-0.03210.05010.10580.0167-0.05090.0510.03910.082935.09112.5098.536
42.76031.6180.74142.43860.29190.9254-0.07240.0974-0.0656-0.08880.04320.020.08380.05440.02910.06980.0513-0.01680.0718-0.00750.039736.22-3.8951.242
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 138
2X-RAY DIFFRACTION2B1 - 138
3X-RAY DIFFRACTION3C1 - 138
4X-RAY DIFFRACTION4D1 - 138

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