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- PDB-1nig: 2.0 A Structure of Protein of Unknown Function from Thermoplasma ... -

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Basic information

Entry
Database: PDB / ID: 1nig
Title2.0 A Structure of Protein of Unknown Function from Thermoplasma acidophilum
Componentshypothetical protein TA1238
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / four helixbundle / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyProtein of unknown function DUF1940 / Domain of unknown function (DUF1940) / Hypothetical Protein Ta1238; Chain: A; / Cobalamin adenosyltransferase-like / Cobalamin adenosyltransferase-like superfamily / Up-down Bundle / Mainly Alpha / DUF1940 domain-containing protein
Function and homology information
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsSanishvili, R. / Edwards, A. / Christendat, D. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2004
Title: Crystal structure of the hypothetical protein TA1238 from Thermoplasma acidophilum: a new type of helical super-bundle.
Authors: Sanishvili, R. / Pennycooke, M. / Gu, J. / Xu, X. / Joachimiak, A. / Edwards, A.M. / Christendat, D.
History
DepositionDec 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / refine / Item: _refine.pdbx_starting_model
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE AUTHORS STATE THE MOLECULE FORMS A TRIMER CRYSTALLOGRAPHICALLY, BUT IN SOLUTION THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein TA1238


Theoretical massNumber of molelcules
Total (without water)17,9211
Polymers17,9211
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein TA1238

A: hypothetical protein TA1238

A: hypothetical protein TA1238


Theoretical massNumber of molelcules
Total (without water)53,7643
Polymers53,7643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7310 Å2
ΔGint-31 kcal/mol
Surface area17230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)101.230, 101.230, 101.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-177-

HOH

21A-179-

HOH

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Components

#1: Protein hypothetical protein TA1238


Mass: 17921.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: TA1238 / Production host: Thermoplasma acidophilum (acidophilic) / References: UniProt: Q9HIT9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116 %PEG33501reservoir
20.3 Mammonium cloride1reservoir
30.1 Msodium acetate1reservoirpH4.6
412 %glycerol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.9795, 0.9793, 0.9537
SYNCHROTRONAPS 19-ID21.0332
Detector
TypeIDDetectorDateDetails
CUSTOM-MADE1CCDFeb 11, 2002mirror
CUSTOM-MADE2CCDMar 6, 2002mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Sagittally focusing double crystal Si(111) monochromatorMADMx-ray1
2Sagittally focusing double crystal Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97931
30.95371
41.03321
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / Num. obs: 11640 / % possible obs: 98.3 % / Num. measured all: 83217 / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
% possible obs: 99.99 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→70.71 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.554 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25613 533 4.7 %RANDOM
Rwork0.21132 ---
all0.21346 11270 --
obs0.21346 10810 95.93 %-
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: 32.854 Å2
Refinement stepCycle: LAST / Resolution: 2→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 0 40 1212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211287
X-RAY DIFFRACTIONr_bond_other_d0.0020.021187
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.951739
X-RAY DIFFRACTIONr_angle_other_deg0.98632763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9565149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1270.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021393
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02268
X-RAY DIFFRACTIONr_nbd_refined0.230.2312
X-RAY DIFFRACTIONr_nbd_other0.2440.21369
X-RAY DIFFRACTIONr_nbtor_other0.0910.2743
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1121.5760
X-RAY DIFFRACTIONr_mcangle_it1.75921239
X-RAY DIFFRACTIONr_scbond_it2.7443527
X-RAY DIFFRACTIONr_scangle_it3.94.5500
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.053 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.335 36
Rwork0.254 735
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)
11.331-0.1858-0.22141.36330.02391.2981-0.0284-0.1189-0.08720.11340.00650.28310.0299-0.17990.02190.00840.00210.0110.05360.02920.027713.218417.712330.3192
20.6881-0.0606-0.50770.8021-0.33670.9278-0.0079-0.0832-0.03550.0845-0.03530.12130.0201-0.15580.04320.0455-0.003-0.01320.05770.01460.087514.741915.808728.4972
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1481 - 148
2X-RAY DIFFRACTION2AB153 - 192
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 70 Å / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_d0.0240.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.881.95
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg7.965
X-RAY DIFFRACTIONr_plane_restr0.0160.02
X-RAY DIFFRACTIONr_chiral_restr0.2
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.05 Å

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