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

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Basic information

Entry
Database: PDB / ID: 1vjl
TitleCrystal structure of a duf151 family protein (tm0160) from thermotoga maritima at 1.90 A resolution
Componentshypothetical protein TM0160Hypothesis
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
Unknown ligand / BFN domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics / 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, V.L. / Lesley, S.A.
History
DepositionMar 10, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionMar 16, 2004ID: 1O5Y
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN CONTINUOUS, UNINTERPRETABLE ELECTRON DENSITY NEAR RESIDUES (5,121,126) IN BOTH SUBUNITS ...HETEROGEN CONTINUOUS, UNINTERPRETABLE ELECTRON DENSITY NEAR RESIDUES (5,121,126) IN BOTH SUBUNITS IS LISTED AS UNL, AN UNKNOWN LIGAND CONTAINING OXYGENS.
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: hypothetical protein TM0160
B: hypothetical protein TM0160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3196
Polymers37,2482
Non-polymers714
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-44 kcal/mol
Surface area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.509, 51.061, 72.974
Angle α, β, γ (deg.)90.00, 97.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein hypothetical protein TM0160 / Hypothesis


Mass: 18623.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: predicted protein related to wound inducive proteins in plants
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0160 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WY07
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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 (%)
12.4549.3
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop, nanodrop7.510 % isopropanol, 20 % PEG 4000; 0.1 M HEPES pH7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
2772vapor diffusion, sitting drop, nanodrop7.510 % isopropanol, 20 % PEG 4000; 0.1 M HEPES pH7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONALS 5.0.311
SYNCHROTRONALS 5.0.220.9793
Detector
TypeIDDetectorDate
ADSC1CCDJun 15, 2003
ADSC2CCDJun 15, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single crystal, cylindrically bent, Si(220)SINGLE WAVELENGTHMx-ray1
2Double-crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97931
ReflectionResolution: 1.9→50 Å / Num. obs: 24182 / % possible obs: 100 % / Redundancy: 2.18 % / Biso Wilson estimate: 42.13 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 19.58
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.31 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 1.44 / % possible all: 92.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.1.9999refinement
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→32.96 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.199 / SU ML: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. CHLORINE WAS MODELED SINCE IT OCCURS IN THE CRYSTALLIZATION BUFFER AND RESULTED IN NO RESIDUAL DIFFERENCE DENSITY AT THE SITES. 3. ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. CHLORINE WAS MODELED SINCE IT OCCURS IN THE CRYSTALLIZATION BUFFER AND RESULTED IN NO RESIDUAL DIFFERENCE DENSITY AT THE SITES. 3. CONTINUOUS, UNINTERPRETABLE ELECTRON DENSITY NEAR RESIDUES (5,121,126) IN BOTH SUBUNITS IS LISTED AS UNL, AN UNKNOWN LIGAND CONTAINING OXYGENS.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1214 5 %RANDOM
Rwork0.198 ---
obs0.201 23110 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.3 Å20 Å20.25 Å2
2--1.36 Å20 Å2
3---2.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2175 0 8 164 2347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222210
X-RAY DIFFRACTIONr_bond_other_d0.0020.022143
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.9643008
X-RAY DIFFRACTIONr_angle_other_deg0.81334955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2075276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.58924.13887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65515392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2071514
X-RAY DIFFRACTIONr_chiral_restr0.1030.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022380
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02402
X-RAY DIFFRACTIONr_nbd_refined0.2040.2452
X-RAY DIFFRACTIONr_nbd_other0.1870.22195
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.21497
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0330.21
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0791.51494
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4722274
X-RAY DIFFRACTIONr_scbond_it2.2593865
X-RAY DIFFRACTIONr_scangle_it3.2984.5734
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.397 81
Rwork0.352 1652
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)
16.3987-2.2082-0.44672.45540.1661.0827-0.0223-0.3151-0.26330.03410.15060.12090.02670.0198-0.1283-0.1363-0.0309-0.0073-0.20570.0475-0.26223.87560.38618.3276
211.97978.537412.136159.846743.489361.8614-1.03890.27950.1675-0.71780.59121.9923-0.0686-0.23890.44770.0821-0.0387-0.01550.15030.08850.0426-23.11114.155.3214
313.4063-5.38936.430217.71635.246712.75340.52590.723-0.952-1.43350.0189-0.04480.09040.4076-0.54480.07710.1042-0.0355-0.1385-0.09920.12423.1897-19.22919.0967
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 140
2X-RAY DIFFRACTION1B0 - 130
3X-RAY DIFFRACTION1A301
4X-RAY DIFFRACTION1A401 - 406
5X-RAY DIFFRACTION2A141 - 150
6X-RAY DIFFRACTION3B131 - 141

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