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- PDB-1sj5: Crystal structure of a duf151 family protein (tm0160) from thermo... -

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Basic information

Entry
Database: PDB / ID: 1sj5
TitleCrystal structure of a duf151 family protein (tm0160) from thermotoga maritima at 2.8 A resolution
Componentsconserved hypothetical protein TM0160
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


Bifunctional nuclease domain / Bifunctional nuclease domain / Bifunctional nuclease domain / Bifunctional nuclease superfamily / Bifunctional nuclease domain / Bifunctional nuclease (BFN) domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
BFN domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsSpraggon, G. / Panatazatos, D. / Klock, H.E. / Wilson, I.A. / Woods Jr., V.L. / Lesley, S.A. / Joint Center for Structural Genomics (JCSG)
CitationJournal: Protein Sci. / Year: 2004
Title: On the use of DXMS to produce more crystallizable proteins: structures of the T. maritima proteins TM0160 and TM1171.
Authors: Spraggon, G. / Pantazatos, D. / Klock, H.E. / Wilson, I.A. / Woods Jr., V.L. / Lesley, S.A.
History
DepositionMar 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE BOTH CHAINS WERE TRUNCATIONS OF THE ORIGINAL SEQUENCE TRUNCATED AT RESIDUE 145, THEN ...SEQUENCE BOTH CHAINS WERE TRUNCATIONS OF THE ORIGINAL SEQUENCE TRUNCATED AT RESIDUE 145, THEN HAVING THE ADDITIONAL RDLINSR, A C-TERMINAL EPITOPE TAG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: conserved hypothetical protein TM0160
B: conserved hypothetical protein TM0160


Theoretical massNumber of molelcules
Total (without water)36,9022
Polymers36,9022
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-20 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.001, 52.136, 73.330
Angle α, β, γ (deg.)90.00, 97.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein conserved hypothetical protein TM0160


Mass: 18451.121 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0160 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WY07

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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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growpH: 6.9 / Details: pH 6.90

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→72.55 Å / Num. obs: 8172 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Rsym value: 0.079 / Net I/σ(I): 12
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.652 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CCP4PACKAGEmodel building
REFMAC5.1.24refinement
HKL-2000data reduction
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1O5Y

1o5y
PDB Unreleased entry


Resolution: 2.8→72.55 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.891 / SU B: 18.855 / SU ML: 0.357 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27555 349 5 %RANDOM
Rwork0.21571 ---
obs0.21858 7762 98.2 %-
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 mean: 22.388 Å2
Baniso -1Baniso -2Baniso -3
1--3.52 Å20 Å2-1.26 Å2
2--1.55 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.8→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 0 0 2173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212208
X-RAY DIFFRACTIONr_bond_other_d0.0030.022152
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.973005
X-RAY DIFFRACTIONr_angle_other_deg0.87834972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8535276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022377
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02406
X-RAY DIFFRACTIONr_nbd_refined0.2320.2458
X-RAY DIFFRACTIONr_nbd_other0.2310.22403
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.21417
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3230.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.44111398
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06132272
X-RAY DIFFRACTIONr_scbond_it3.3098810
X-RAY DIFFRACTIONr_scangle_it4.84711733
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
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)
16.4306-2.95680.53416.8733-0.13993.54590.09080.0866-0.092-0.2539-0.12070.6163-0.1496-0.37790.02990.1042-0.02070.07420.22410.02930.1344-7.9667.26318.346
25.8667-1.7368-1.42374.48711.47754.0167-0.1541-0.2407-0.5512-0.05340.2802-0.14810.40350.4505-0.12610.13780.0046-0.0210.22290.04170.241215.681-7.26517.133
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 15012 - 162
2X-RAY DIFFRACTION2BB0 - 14112 - 153

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