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- PDB-2qe6: CRYSTAL STRUCTURE OF A PUTATIVE METHYLTRANSFERASE (TFU_2867) FROM... -

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Entry
Database: PDB / ID: 2qe6
TitleCRYSTAL STRUCTURE OF A PUTATIVE METHYLTRANSFERASE (TFU_2867) FROM THERMOBIFIDA FUSCA YX AT 1.95 A RESOLUTION
ComponentsUncharacterized protein Tfu_2867
KeywordsTRANSFERASE / PUTATIVE METHYLTRANSFERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyVaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / S-ADENOSYLMETHIONINE / Uncharacterized protein
Function and homology information
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized protein Tfu_2867 (YP_290923.1) from Thermobifida fusca YX at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Jan 25, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE. THE STRAIN CLONED DIFFERS FROM THE SEQUENCED STRAIN IN THE DATABASE. SEQUENCING CONFIRMED THE ENGINEERED MUTATION A25V. THE ELECTRON DENSITY SUPPORTS THIS ASSIGNMENT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein Tfu_2867
B: Uncharacterized protein Tfu_2867
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,30318
Polymers61,0292
Non-polymers2,27416
Water4,900272
1
A: Uncharacterized protein Tfu_2867
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5558
Polymers30,5141
Non-polymers1,0417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Uncharacterized protein Tfu_2867
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,74810
Polymers30,5141
Non-polymers1,2339
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Uncharacterized protein Tfu_2867
hetero molecules

B: Uncharacterized protein Tfu_2867
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,49520
Polymers61,0292
Non-polymers2,46718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5230 Å2
ΔGint-210 kcal/mol
Surface area22010 Å2
MethodPISA
4
A: Uncharacterized protein Tfu_2867
hetero molecules

A: Uncharacterized protein Tfu_2867
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,11116
Polymers61,0292
Non-polymers2,08214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4480 Å2
ΔGint-162 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.627, 76.024, 81.315
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Uncharacterized protein Tfu_2867


Mass: 30514.311 Da / Num. of mol.: 2 / Mutation: A25V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: YP_290923.1, Tfu_2867 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q47KX2
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NANODROP, 70.0% MPD, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97917, 0.97894
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 4, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979171
30.978941
ReflectionResolution: 1.95→29.386 Å / Num. obs: 47006 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 23.63 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-23.50.5751.31202633960.57599.4
2-2.063.50.4421.71177033250.44299.5
2.06-2.123.60.37721154732390.37799.7
2.12-2.183.60.3172.41135531670.31799.9
2.18-2.253.60.2732.51109430650.27399.9
2.25-2.333.60.2253.41087330040.225100
2.33-2.423.70.1953.91037828430.195100
2.42-2.523.60.1684.51010327790.168100
2.52-2.633.60.1355.6971126690.135100
2.63-2.763.60.1156.5929525470.115100
2.76-2.913.60.0987.5883824330.098100
2.91-3.083.60.0818.7835622960.081100
3.08-3.33.60.0689.7787721740.068100
3.3-3.563.60.05312.5734020340.053100
3.56-3.93.60.04614.1675118740.046100
3.9-4.363.60.04115.6613617110.041100
4.36-5.033.60.04413.2543915280.044100
5.03-6.173.50.04812.2452012950.048100
6.17-8.723.40.0414349710410.04100
8.72-29.3863.20.03813.618605860.03896.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→29.386 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.195 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.135
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. S-ADENYLMETHIONINE HAS BEEN MODELED BASED ON DENSITY AND RELATED STRUCTURES. 5. MPD HAS BEEN MODELED BASED ON CRYSTALLIZATION CONSITIONS. 6. HISTIDINE 49 IN EACH CHAIN IS MODELED AS NEP, N1-PHOSPHONOHISTIDINE.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2375 5.1 %RANDOM
Rwork0.171 ---
obs0.173 46969 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.045 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å20 Å2
2--3.12 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4088 0 142 272 4502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224346
X-RAY DIFFRACTIONr_bond_other_d0.0020.022904
X-RAY DIFFRACTIONr_angle_refined_deg1.7072.0195952
X-RAY DIFFRACTIONr_angle_other_deg0.98837062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9645538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63323.404188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62515652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6461538
X-RAY DIFFRACTIONr_chiral_restr0.0880.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02848
X-RAY DIFFRACTIONr_nbd_refined0.2080.2903
X-RAY DIFFRACTIONr_nbd_other0.2030.23066
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22086
X-RAY DIFFRACTIONr_nbtor_other0.0860.22128
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3390.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.26
X-RAY DIFFRACTIONr_mcbond_it2.11632907
X-RAY DIFFRACTIONr_mcbond_other0.54431070
X-RAY DIFFRACTIONr_mcangle_it2.78454328
X-RAY DIFFRACTIONr_scbond_it5.64581822
X-RAY DIFFRACTIONr_scangle_it6.827111620
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 173 -
Rwork0.242 3210 -
obs-3383 99.12 %
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)
12.28840.138-0.22511.2410.16971.2993-0.07140.0739-0.2827-0.07190.0064-0.01680.2-0.09990.065-0.19-0.00830.0031-0.2336-0.0239-0.1408-9.048-19.47740.319
21.6009-0.03230.14471.2326-0.43892.3232-0.0390.0555-0.1380.07520.0337-0.01580.07660.36010.0053-0.23750.04080.009-0.07740.001-0.201311.72-18.1160.259
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 2739 - 274
2X-RAY DIFFRACTION2BB8 - 2739 - 274

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