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- PDB-3ijm: The structure of a restriction endonuclease-like fold superfamily... -

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Basic information

Entry
Database: PDB / ID: 3ijm
TitleThe structure of a restriction endonuclease-like fold superfamily protein from Spirosoma linguale.
Componentsuncharacterized restriction endonuclease-like fold superfamily protein
Keywordsstructural genomics / unknown function / DUF820 / Cyanobacteria / PD(D/E)xK superfamily / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologytt1808, chain A - #20 / tt1808, chain A / Alpha-Beta Complex / Alpha Beta / : / Restriction endonuclease domain-containing protein
Function and homology information
Biological speciesSpirosoma linguale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsCuff, M.E. / Tesar, C. / Samano, S. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of a restriction endonuclease-like fold superfamily protein from Spirosoma linguale.
Authors: Cuff, M.E. / Tesar, C. / Samano, S. / Bearden, J. / Joachimiak, A.
History
DepositionAug 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 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
Revision 1.3Nov 27, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: uncharacterized restriction endonuclease-like fold superfamily protein
B: uncharacterized restriction endonuclease-like fold superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3016
Polymers33,9982
Non-polymers3034
Water5,459303
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-35 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.770, 65.849, 68.917
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsauthors state that the biological unit is unknown, but likely a dimer, as seen in the AU (A+B).

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Components

#1: Protein uncharacterized restriction endonuclease-like fold superfamily protein


Mass: 16998.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spirosoma linguale (bacteria) / Strain: DSM 74 / Gene: DUF820, SlinDRAFT_22400 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: C4CXR0, UniProt: D2QNN3*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M NaCl, 0.1M Bis Tris pH6.5, 1.5M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97950, 0.97992
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 31, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.979921
ReflectionRedundancy: 7.2 % / Av σ(I) over netI: 41.88 / Number: 242345 / Rmerge(I) obs: 0.058 / Χ2: 1.17 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 33607 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.615098.410.0513.5066.4
3.664.6199.910.0442.3997
3.23.6610010.0441.8427.2
2.913.210010.0481.4587.3
2.72.9110010.0531.2287.3
2.542.710010.0591.1557.3
2.412.5410010.0661.0667.3
2.312.4110010.071.0317.3
2.222.3110010.0790.957.4
2.142.2210010.0860.9267.3
2.072.1410010.0930.8977.4
2.022.0710010.1160.8937.3
1.962.0210010.1360.8387.4
1.911.9610010.1630.8237.3
1.871.9110010.1770.7947.3
1.831.8710010.2280.7637.3
1.791.8310010.2730.7787.3
1.761.7910010.3170.7537.3
1.731.7610010.3960.7277.3
1.71.7310010.4770.7076.6
ReflectionResolution: 1.7→50 Å / Num. all: 33607 / Num. obs: 33607 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.058 / Χ2: 1.172 / Net I/σ(I): 10.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.477 / Num. unique all: 1674 / Χ2: 0.707 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.7 Å / D res low: 47.62 Å / FOM : 0.177 / FOM acentric: 0.185 / FOM centric: 0.111 / Reflection: 33554 / Reflection acentric: 30000 / Reflection centric: 3554
Phasing MAD set

Highest resolution: 1.7 Å / Lowest resolution: 47.62 Å / Reflection centric: 3554

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentric
11.641000030000
20.990.964.26.40.190.1929993
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
110.88-47.621.7410.10.1007358
16.14-10.882.0210.10.100459181
14.28-6.141.4910.10.1001176288
13.28-4.281.15100002220389
12.66-3.281.62100003618501
12.24-2.662.58100005326611
11.93-2.244.05100007356710
11.7-1.931.54100009772816
210.88-47.620.960.898.58.90.610.657258
26.14-10.880.980.866.380.690.56459181
24.28-6.140.970.96.48.90.520.371176288
23.28-4.280.980.956.68.70.340.262220389
22.66-3.280.980.974.66.40.290.213617501
22.24-2.660.990.993.95.60.180.125325611
21.93-2.24113.75.60.090.067354710
21.7-1.93113.55.10.040.039770816
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se38.23246-0.750-0.1170
2Se38.56055-0.8670.259-0.1770
3Se66.26864-0.77-0.051-0.0870
4Se36.60461-0.750-0.117-0.066
5Se36.39992-0.8680.26-0.177-0.072
6Se48.825-0.769-0.051-0.087-0.012
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
10.88-47.620.3750.4350.2991317358
6.14-10.880.4730.5350.316640459181
4.28-6.140.4660.5110.28314641176288
3.28-4.280.4120.4490.20326092220389
2.66-3.280.3520.380.15141193618501
2.24-2.660.2120.2270.08359375326611
1.93-2.240.0940.10.03480667356710
1.7-1.930.0340.0360.011105889772816
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 33554
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.06-10068.80.762509
5.57-7.0663.90.854520
4.77-5.5756.80.888593
4.23-4.7756.80.897684
3.85-4.2358.10.911737
3.55-3.8558.50.901817
3.31-3.5561.20.895853
3.12-3.3159.90.877927
2.95-3.1262.60.854982
2.81-2.9562.10.8421015
2.69-2.81620.851069
2.58-2.69660.8491083
2.49-2.58690.8391188
2.4-2.4971.40.8321177
2.32-2.471.60.8471223
2.25-2.3275.50.8271284
2.19-2.25750.8381282
2.13-2.1975.10.8491340
2.07-2.1377.60.8461380
2.02-2.0779.20.8441410
1.98-2.0281.30.8371443
1.93-1.9881.20.8261464
1.89-1.9381.30.8031517
1.85-1.8980.10.791547
1.82-1.8584.30.7911547
1.78-1.8283.80.8081606
1.75-1.78840.7711612
1.7-1.7586.80.7222745

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.42 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.193 / WRfactor Rwork: 0.162 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.89 / SU B: 4.245 / SU ML: 0.063 / SU R Cruickshank DPI: 0.102 / SU Rfree: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1701 5.1 %RANDOM
Rwork0.166 ---
all0.168 33552 --
obs0.168 33552 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.4 Å2 / Biso mean: 22.025 Å2 / Biso min: 10.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å20 Å2
2---2.24 Å20 Å2
3---3.47 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 18 303 2619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222422
X-RAY DIFFRACTIONr_bond_other_d0.0010.021585
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9753309
X-RAY DIFFRACTIONr_angle_other_deg0.89833920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46925.505109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92515407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.964156
X-RAY DIFFRACTIONr_chiral_restr0.0870.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212683
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02449
X-RAY DIFFRACTIONr_mcbond_it0.8621.51483
X-RAY DIFFRACTIONr_mcbond_other0.2611.5592
X-RAY DIFFRACTIONr_mcangle_it1.45422431
X-RAY DIFFRACTIONr_scbond_it2.0883939
X-RAY DIFFRACTIONr_scangle_it3.4044.5874
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 130 -
Rwork0.252 2282 -
all-2412 -
obs--99.55 %
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)
11.6741-0.05-0.41571.24410.30530.64140.02020.0407-0.02050.0272-0.06030.17550.0495-0.04840.04010.0395-0.0127-0.00790.0377-0.00530.02857.287456.074515.2241
21.8134-0.0686-0.09571.8034-0.04590.31560.0150.03380.0377-0.0163-0.0238-0.07490.0097-0.01220.00880.0698-0.00390.00280.0511-0.00030.004128.934362.705511.7968
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 148
2X-RAY DIFFRACTION2B-2 - 148

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