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- PDB-3k32: The crystal structure of predicted subunit of tRNA methyltransfer... -

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Basic information

Entry
Database: PDB / ID: 3k32
TitleThe crystal structure of predicted subunit of tRNA methyltransferase from Methanocaldococcus jannaschii DSM
ComponentsUncharacterized protein MJ0690
KeywordsTRANSFERASE / Predicted subunit of tRNA methyltransferase / Methanocaldococcus jannaschii DSM / PSI-2 / Protein Structure Initiative / Structural Genomics / Midwest Center for Structural Genomics (MCSG)
Function / homologyHUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein MJ0690
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsWu, R. / Zhang, R. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of predicted subunit of tRNA methyltransferase from Methanocaldococcus jannaschii DSM
Authors: Wu, R. / Zhang, R. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein MJ0690
B: Uncharacterized protein MJ0690
C: Uncharacterized protein MJ0690
D: Uncharacterized protein MJ0690
E: Uncharacterized protein MJ0690
F: Uncharacterized protein MJ0690
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,07110
Polymers140,7036
Non-polymers3684
Water4,540252
1
A: Uncharacterized protein MJ0690
B: Uncharacterized protein MJ0690
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9933
Polymers46,9012
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-7 kcal/mol
Surface area17730 Å2
MethodPISA
2
C: Uncharacterized protein MJ0690
D: Uncharacterized protein MJ0690
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9933
Polymers46,9012
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-9 kcal/mol
Surface area17590 Å2
MethodPISA
3
E: Uncharacterized protein MJ0690
F: Uncharacterized protein MJ0690
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0854
Polymers46,9012
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-8 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.669, 121.951, 81.224
Angle α, β, γ (deg.)90.00, 116.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein MJ0690 / Predicted subunit of tRNA methyltransferase


Mass: 23450.488 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: MJ0690 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q58102
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bistris Propane 7.0, 0.6M K/Na tartrate tetrahydrated, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929, 0.97948
DetectorType: SBC-2 / Detector: CCD / Date: May 20, 2008 / Details: mirrors
RadiationMonochromator: Si 111, channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.979481
ReflectionResolution: 2.34→50 Å / Num. all: 54039 / Num. obs: 51681 / % possible obs: 97.8 % / Redundancy: 4.3 % / Biso Wilson estimate: 37.28 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.35
Reflection shellResolution: 2.34→2.48 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 1.94 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX1.5_2refinement
MLPHAREphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000data collection
RefinementMethod to determine structure: MAD / Resolution: 2.5→34.775 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.881 / SU ML: 0.44 / σ(F): 1.36 / Phase error: 25.08 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2631 2197 5.18 %
Rwork0.1769 --
obs0.1813 42416 98.29 %
all-40225 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.42 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso mean: 27.149 Å2
Baniso -1Baniso -2Baniso -3
1-1.0606 Å2-0 Å2-0.0144 Å2
2---2.0874 Å2-0 Å2
3---1.0269 Å2
Refinement stepCycle: LAST / Resolution: 2.5→34.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9360 0 24 252 9636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089563
X-RAY DIFFRACTIONf_angle_d1.10212848
X-RAY DIFFRACTIONf_dihedral_angle_d20.273624
X-RAY DIFFRACTIONf_chiral_restr0.0731445
X-RAY DIFFRACTIONf_plane_restr0.0051597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.58940.30212100.19893954X-RAY DIFFRACTION97
2.5894-2.6930.27062370.16833933X-RAY DIFFRACTION97
2.693-2.81550.29552050.1783966X-RAY DIFFRACTION97
2.8155-2.96390.29232320.19153954X-RAY DIFFRACTION98
2.9639-3.14950.31632200.19273970X-RAY DIFFRACTION97
3.1495-3.39250.26942300.17784049X-RAY DIFFRACTION99
3.3925-3.73350.24372200.15824071X-RAY DIFFRACTION100
3.7335-4.27290.23922160.15084106X-RAY DIFFRACTION100
4.2729-5.38020.22262250.14434099X-RAY DIFFRACTION100
5.3802-34.77860.21832020.18014117X-RAY DIFFRACTION99
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)
10.51720.44570.19730.92241.03511.46280.00080.0402-0.0679-0.05530.0432-0.12360.10430.1166-0.07090.1305-0.0282-0.01740.117-0.02230.097130.875227.231266.5347
21.63110.29330.05280.2983-0.26991.5978-0.03030.1110.0829-0.0381-0.05670.097-0.1215-0.0680.05050.1256-0.0016-0.01250.0445-0.02570.09992.546525.471552.8342
30.7210.1243-0.13450.4583-0.17751.1755-0.0390.00280.0041-0.05480.018-0.0397-0.01070.120.03560.057-0.0158-0.00620.0862-0.00790.083529.8013-13.424352.1971
40.25750.3201-0.35730.4034-0.38191.34050.0129-0.06830.04850.0617-0.03220.2123-0.1543-0.0853-0.00280.0866-0.00940.00890.0919-0.00210.21192.762-14.554867.4818
51.8399-0.99870.34311.0965-0.77240.7784-0.03430.0560.00770.08590.04570.18450.1442-0.0372-0.00160.1990.01570.03610.04450.0150.1143.450811.896691.6805
61.7267-1.4019-0.61851.15270.64661.3917-0.0956-0.04910.02330.29050.063-0.09020.08530.01890.03260.17260.01850.00540.0431-0.01590.071832.83060.720291.5427
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3 - 200
2X-RAY DIFFRACTION2chain BB3 - 200
3X-RAY DIFFRACTION3chain CC3 - 200
4X-RAY DIFFRACTION4chain DD4 - 200
5X-RAY DIFFRACTION5chain EE4 - 200
6X-RAY DIFFRACTION6chain FF3 - 200

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