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- PDB-3cgg: Crystal structure of TehB-like SAM-dependent methyltransferase (N... -

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Basic information

Entry
Database: PDB / ID: 3cgg
TitleCrystal structure of TehB-like SAM-dependent methyltransferase (NP_600671.1) from Corynebacterium glutamicum ATCC 13032 Kitasato at 2.00 A resolution
ComponentsSAM-dependent methyltransferase
KeywordsTRANSFERASE / NP_600671.1 / TehB-like SAM-dependent methyltransferase / Methyltransferase domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


methyltransferase activity / methylation
Similarity search - Function
Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / : / SAM-dependent methyltransferases
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of TehB-like SAM-dependent methyltransferase (NP_600671.1) from Corynebacterium glutamicum ATCC 13032 Kitasato at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 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 1.4Feb 1, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAM-dependent methyltransferase
B: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,77413
Polymers42,6712
Non-polymers1,10311
Water4,936274
1
A: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0608
Polymers21,3351
Non-polymers7257
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7145
Polymers21,3351
Non-polymers3784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.330, 87.398, 92.429
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ASP / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 31 - 194 / Label seq-ID: 32 - 195

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsAUTHORS STATE THAT THE CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein SAM-dependent methyltransferase


Mass: 21335.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Species: Corynebacterium glutamicum / Strain: DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 / Gene: NP_600671.1, cg1645 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6M5C6, UniProt: Q8NQI0*PLUS
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: NANODROP, 1.0M Sodium citrate, 0.1M CHES pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97978
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 12, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979781
ReflectionResolution: 2→29.062 Å / Num. obs: 28773 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 28.45 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.053.70.6671.1776220950.667100
2.05-2.113.60.5921.3746020590.592100
2.11-2.173.70.4791.6725519810.479100
2.17-2.243.70.3922720119470.392100
2.24-2.313.60.3452.2676618620.345100
2.31-2.393.70.2772.8660718030.277100
2.39-2.483.70.2293.3647617710.229100
2.48-2.583.70.1834.2626517060.183100
2.58-2.73.70.1554.8598416310.155100
2.7-2.833.60.1236.1566615590.123100
2.83-2.983.60.0977.5544814930.097100
2.98-3.163.70.0838.6507813910.083100
3.16-3.383.60.0699.9485113420.069100
3.38-3.653.60.05711.6451712540.05799.8
3.65-43.60.05112.8408511340.05199.8
4-4.473.60.04613.2375010400.04699.6
4.47-5.163.60.04612.433329280.04699.5
5.16-6.323.50.05411.928107950.05499.4
6.32-8.943.50.0491221666270.04998.9
8.94-29.0623.20.04811.711363550.04894.7

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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
autoSHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.062 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.25 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.15
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID (NHE) AND CITRATE (CIT) FROM CRYSTALLIZATION AND ETHYLENE GLYCOL (EDO) FROM CRYO SOLUTION WERE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1455 5.1 %RANDOM
Rwork0.167 ---
obs0.169 28741 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.751 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--0.58 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2→29.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2820 0 71 274 3165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213086
X-RAY DIFFRACTIONr_bond_other_d0.0020.022113
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.964183
X-RAY DIFFRACTIONr_angle_other_deg0.98735101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0715398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97924.065155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03215469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1261526
X-RAY DIFFRACTIONr_chiral_restr0.1670.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023621
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02672
X-RAY DIFFRACTIONr_nbd_refined0.1990.2607
X-RAY DIFFRACTIONr_nbd_other0.2020.22278
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21513
X-RAY DIFFRACTIONr_nbtor_other0.0870.21584
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2235
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0730.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.212
X-RAY DIFFRACTIONr_mcbond_it1.87231983
X-RAY DIFFRACTIONr_mcbond_other0.5983804
X-RAY DIFFRACTIONr_mcangle_it2.79353033
X-RAY DIFFRACTIONr_scbond_it4.84281284
X-RAY DIFFRACTIONr_scangle_it6.516111150
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2035 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.550.5
MEDIUM THERMAL1.182
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 130 -
Rwork0.223 1962 -
all-2092 -
obs--100 %
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)
11.75480.06060.15311.01290.38751.29340.01110.092-0.04320.00770.0118-0.05280.0881-0.0055-0.0229-0.0527-0.0044-0.0007-0.08220.0103-0.086626.898746.645216.51
22.3259-0.2936-0.12040.50560.13351.38940.0321-0.02150.14620.00390.01730.0724-0.0215-0.1361-0.0494-0.05710.02820.003-0.02760.0172-0.05940.226251.381231.0345
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 19410 - 195
2X-RAY DIFFRACTION2BB11 - 19412 - 195

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