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- PDB-2qgq: Crystal structure of TM_1862 from Thermotoga maritima. Northeast ... -

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Basic information

Entry
Database: PDB / ID: 2qgq
TitleCrystal structure of TM_1862 from Thermotoga maritima. Northeast Structural Genomics Consortium target VR77
ComponentsProtein TM_1862
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


[ribosomal protein uS12] (aspartate89-C3)-methylthiotransferase / aspartic acid methylthiotransferase activity / protein methylthiotransferase activity / tRNA modification / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
tm_1862 like domain / Ribosomal protein S12 methylthiotransferase RimO / TRAM domain / Methylthiotransferase / Methylthiotransferase, N-terminal / Methylthiotransferase, N-terminal domain superfamily / Uncharacterized protein family UPF0004 / Methylthiotransferase N-terminal domain profile. / Methylthiotransferase, conserved site / Methylthiotransferase radical SAM domain signature. ...tm_1862 like domain / Ribosomal protein S12 methylthiotransferase RimO / TRAM domain / Methylthiotransferase / Methylthiotransferase, N-terminal / Methylthiotransferase, N-terminal domain superfamily / Uncharacterized protein family UPF0004 / Methylthiotransferase N-terminal domain profile. / Methylthiotransferase, conserved site / Methylthiotransferase radical SAM domain signature. / pyruvate-formate lyase- activating enzyme / TRAM domain / Radical SAM, alpha/beta horseshoe / TRAM domain profile. / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Alpha-Beta Horseshoe / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ribosomal protein uS12 methylthiotransferase RimO
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsForouhar, F. / Neely, H. / Hussain, M. / Seetharaman, J. / Fang, Y. / Chen, C.X. / Cunningham, K. / Conover, K. / Ma, L.-C. / Xiao, R. ...Forouhar, F. / Neely, H. / Hussain, M. / Seetharaman, J. / Fang, Y. / Chen, C.X. / Cunningham, K. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Post-translational Modification of Ribosomal Proteins: STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF RimO FROM THERMOTOGA MARITIMA, A RADICAL S-ADENOSYLMETHIONINE METHYLTHIOTRANSFERASE.
Authors: Arragain, S. / Garcia-Serres, R. / Blondin, G. / Douki, T. / Clemancey, M. / Latour, J.M. / Forouhar, F. / Neely, H. / Montelione, G.T. / Hunt, J.F. / Mulliez, E. / Fontecave, M. / Atta, M.
History
DepositionJun 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Remark 300BIOMOLECULE: 1, 2, 3, 4, 5, 6, 7, 8 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH ...BIOMOLECULE: 1, 2, 3, 4, 5, 6, 7, 8 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.
Remark 999SEQUENCE RESIDUES 1-134 ARE NOT VISIBLE IN THE CRYSTAL STRUCTURE. ACCORDING TO THE AUTHORS, THESE ...SEQUENCE RESIDUES 1-134 ARE NOT VISIBLE IN THE CRYSTAL STRUCTURE. ACCORDING TO THE AUTHORS, THESE RESIDUES WERE APPARENTLY CLEAVED BY SUBTILISIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein TM_1862
B: Protein TM_1862
C: Protein TM_1862
D: Protein TM_1862
E: Protein TM_1862
F: Protein TM_1862
G: Protein TM_1862
H: Protein TM_1862
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,56212
Polymers283,6778
Non-polymers8854
Water25,9781442
1
A: Protein TM_1862
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6812
Polymers35,4601
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein TM_1862
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6812
Polymers35,4601
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein TM_1862


Theoretical massNumber of molelcules
Total (without water)35,4601
Polymers35,4601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein TM_1862
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6812
Polymers35,4601
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Protein TM_1862


Theoretical massNumber of molelcules
Total (without water)35,4601
Polymers35,4601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Protein TM_1862
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6812
Polymers35,4601
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Protein TM_1862


Theoretical massNumber of molelcules
Total (without water)35,4601
Polymers35,4601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Protein TM_1862


Theoretical massNumber of molelcules
Total (without water)35,4601
Polymers35,4601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.620, 88.649, 96.039
Angle α, β, γ (deg.)89.98, 90.03, 89.91
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein TM_1862


Mass: 35459.566 Da / Num. of mol.: 8 / Fragment: Residues 135-430, see remark 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Species: Thermotoga maritima / Strain: MSB8, DSM 3109, JCM 10099 / Gene: TM_1862 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9X2H6
#2: Chemical
ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1442 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 10
Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 20 micro-g/ml Subtilisin, 5 mM DTT. Reservoir solution: 100 mM CAPS pH 10.0, 40% PEG 4000, 100 mM Sodium thiosulfate, ...Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 20 micro-g/ml Subtilisin, 5 mM DTT. Reservoir solution: 100 mM CAPS pH 10.0, 40% PEG 4000, 100 mM Sodium thiosulfate, MICROBATCH UNDER OIL, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 31, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→39.67 Å / Num. all: 384919 / Num. obs: 384919 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.054 / Net I/σ(I): 14.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.54 / Rsym value: 0.428 / % possible all: 96

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→39.67 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 106775.95 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: XtalView program has also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.251 33017 9.7 %RANDOM
Rwork0.212 ---
obs0.212 342108 86.6 %-
all-384919 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.2375 Å2 / ksol: 0.361765 e/Å3
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-1.45 Å20 Å2
2---0.78 Å20 Å2
3---0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17567 0 56 1443 19066
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.273 2749 9.7 %
Rwork0.234 25510 -
obs--71.9 %

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