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- PDB-5bp7: Crystal structure of SAM-dependent methyltransferase from Geobact... -

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Basic information

Entry
Database: PDB / ID: 5bp7
TitleCrystal structure of SAM-dependent methyltransferase from Geobacter sulfurreducens in complex with S-Adenosyl-L-homocysteine
ComponentsSAM-dependent methyltransferase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


methyltransferase activity / methylation
Similarity search - Function
Predicted S-adenosyl-L-methionine dependent methyltransferase, YjhP-type / Methyltransferase domain / 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
S-ADENOSYL-L-HOMOCYSTEINE / SAM-dependent methyltransferase
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKutner, J. / Shabalin, I.G. / Mason, D.V. / Handing, K.B. / Gasiorowska, O.A. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health United States
CitationJournal: to be published
Title: Crystal structure of SAM-dependent methyltransferase from Geobacter sulfurreducens in complex with S-Adenosyl-L-homocysteine
Authors: Kutner, J. / Shabalin, I.G. / Mason, D. / Handing, K.B. / Gasiorowska, O.A. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
C: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7378
Polymers90,5133
Non-polymers1,2245
Water7,530418
1
A: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5913
Polymers30,1711
Non-polymers4202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5552
Polymers30,1711
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5913
Polymers30,1711
Non-polymers4202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: SAM-dependent methyltransferase
hetero molecules

B: SAM-dependent methyltransferase
hetero molecules

C: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7378
Polymers90,5133
Non-polymers1,2245
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_547-x+1/2,y-1/2,-z+21
crystal symmetry operation3_546-x+1/2,y-1/2,-z+11
Buried area5480 Å2
ΔGint-36 kcal/mol
Surface area29030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.346, 110.189, 76.681
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUPROPROAA2 - 24824 - 270
21LEULEUPROPROBB2 - 24824 - 270
12MSEMSEARGARGAA1 - 24923 - 271
22MSEMSEARGARGCC1 - 24923 - 271
13LEULEUPROPROBB2 - 24824 - 270
23LEULEUPROPROCC2 - 24824 - 270

NCS ensembles :
ID
1
2
3

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Components

#1: Protein SAM-dependent methyltransferase


Mass: 30170.896 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA / Gene: GSU2441 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q74AD5
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 1 condition #9 (0.1M HEPES, 25%w/v PEG ...Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 1 condition #9 (0.1M HEPES, 25%w/v PEG 3350, 0.2M Magnesium Chloride, 6-Hydrate pH=7.5) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 5 mM S-adenosylmethionine chloride and 1/50 v/v of 1 mg/ml TEV solution at 289 K for 3 hours
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 45134 / Num. obs: 45102 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.054 / Rrim(I) all: 0.13 / Rsym value: 0.123 / Χ2: 1.101 / Net I/av σ(I): 16.897 / Net I/σ(I): 5.1 / Num. measured all: 276539
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.1-2.1460.9951.622230.7560.4440.699100
2.14-2.186.20.91422050.7860.4020.7111000.999
2.18-2.226.20.81922250.7830.3580.7161000.895
2.22-2.266.20.70422430.8470.3080.7251000.769
2.26-2.316.20.66622220.8490.2910.7471000.728
2.31-2.376.20.56522190.9040.2470.7511000.618
2.37-2.426.20.50222060.9140.220.7671000.549
2.42-2.496.20.44722610.9220.1950.7881000.488
2.49-2.566.20.37622440.9440.1640.8181000.411
2.56-2.656.20.32522180.9550.1410.8481000.355
2.65-2.746.20.2722640.9680.1180.8711000.295
2.74-2.856.20.23822070.9730.1040.9041000.26
2.85-2.986.20.1822630.9860.0780.9531000.196
2.98-3.146.20.14222410.990.0621.0551000.155
3.14-3.336.20.10522680.9940.0461.2051000.115
3.33-3.596.20.08622640.9950.0381.3531000.094
3.59-3.956.10.07122890.9960.0311.5651000.077
3.95-4.5260.0622800.9970.0271.73299.80.066
4.52-5.760.0623120.9970.0271.98299.70.066
5.7-505.50.06424480.9970.0292.92399.60.07

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.15data extraction
REFMAC5.8.0107refinement
HKL-3000phasing
MLPHAREphasing
SHELXphasing
HKL-3000data scaling
HKL-3000data reduction
BLU-MAXdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2016 / WRfactor Rwork: 0.1677 / FOM work R set: 0.8287 / SU B: 11.476 / SU ML: 0.152 / SU R Cruickshank DPI: 0.2319 / SU Rfree: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.181 / SU Rfree Cruickshank DPI: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 2191 4.9 %RANDOM
Rwork0.1855 ---
obs0.1873 42695 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.51 Å2 / Biso mean: 40.658 Å2 / Biso min: 9.09 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å2-0 Å2-0 Å2
2---0.58 Å20 Å2
3---2.57 Å2
Refinement stepCycle: final / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5665 0 80 419 6164
Biso mean--38.06 43.56 -
Num. residues----746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195883
X-RAY DIFFRACTIONr_bond_other_d0.0060.025562
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9898009
X-RAY DIFFRACTIONr_angle_other_deg1.196312744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9385745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69122.246236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82815855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4251556
X-RAY DIFFRACTIONr_chiral_restr0.0750.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216620
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021330
X-RAY DIFFRACTIONr_mcbond_it0.7982.2662992
X-RAY DIFFRACTIONr_mcbond_other0.7962.2652991
X-RAY DIFFRACTIONr_mcangle_it1.2853.3913730
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A287020.07
12B287020.07
21A290100.06
22C290100.06
31B283920.07
32C283920.07
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 174 -
Rwork0.276 3074 -
all-3248 -
obs--99.97 %
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)
11.25371.0131-0.2364.08162.53162.42770.1926-0.07210.0411-0.1112-0.0211-0.2865-0.2015-0.0237-0.17150.1704-0.02280.01580.25460.00160.220527.922-6.64756.161
22.1183-0.0081-0.33932.34860.7563.56530.0889-0.0758-0.01850.0703-0.0592-0.2104-0.07210.2098-0.02970.0905-0.0395-0.02490.20370.01770.148436.247-9.49752.311
31.6291-0.59280.09931.4742-0.05342.0460.0662-0.070.07060.0306-0.0046-0.2695-0.14020.1645-0.06170.0924-0.02280.03370.13810.00110.175534.761-4.2146.015
42.03250.553-0.52581.12190.57311.92230.23240.17540.2304-0.1174-0.09330.1172-0.2372-0.249-0.13920.1490.01680.00880.16890.04290.129216.333-1.61743.436
50.34-0.19760.16450.9540.75181.9552-0.0351-0.0220.11050.03380.0196-0.0477-0.1394-0.11130.01540.1154-0.0205-0.01440.1865-0.01240.146919.183-1.54761.814
62.3558-2.55020.36483.06490.07230.93160.03060.14480.0506-0.0564-0.0281-0.01810.11890.1206-0.00240.2262-0.03480.01060.24530.02380.262631.02432.02877.029
72.3713-2.28120.27933.5333-0.36571.24090.07650.1122-0.2567-0.1589-0.06240.35470.1819-0.0514-0.0140.1461-0.015-0.04680.1463-0.05430.110224.97829.16271.567
83.1499-0.1374-0.74824.5320.80531.07480.04510.31540.068-0.4341-0.15590.11270.01320.04110.11070.21110.0279-0.06630.24120.01590.051230.4340.38465.276
96.637-3.02443.06662.9605-1.09311.73470.00330.16810.3345-0.1899-0.168-0.38290.04310.17930.16460.1206-0.03390.01980.19390.05940.099842.27647.10779.712
101.0726-0.81390.17222.352-0.27990.3416-0.01970.1398-0.0227-0.1078-0.0578-0.08140.02660.12210.07750.13850.01590.0220.23060.00590.115942.5329.79583.166
1116.0559-18.26310.578620.9174-0.5364.9129-0.30750.14930.19010.5784-0.1113-0.23780.021-0.10290.41880.39440.0294-0.07740.32610.00890.115332.87619.70946.211
121.31630.0418-0.46320.9979-0.59791.04-0.01570.0392-0.05890.04560.03820.01120.051-0.1511-0.02260.0816-0.0103-0.00970.2230.00610.08633.29415.62627.465
132.6963-2.5546-1.50219.18945.71549.0065-0.3801-0.82810.4830.39330.5321-0.4782-0.25820.6454-0.15190.11450.0586-0.08460.4481-0.05510.311250.44632.25530.023
141.0713-0.3793-1.05921.07250.8742.24860.024-0.13390.08510.2347-0.0054-0.10160.0706-0.0106-0.01870.13560.0121-0.01030.23970.0190.08532.3431.32537.11
151.5208-1.5528-1.72998.00174.91095.14480.0863-0.08470.2102-0.04750.06-0.2003-0.15860.1548-0.14620.0509-0.0067-0.03590.23950.05120.131941.59231.7828.39
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 36
2X-RAY DIFFRACTION2A37 - 81
3X-RAY DIFFRACTION3A82 - 123
4X-RAY DIFFRACTION4A124 - 182
5X-RAY DIFFRACTION5A183 - 249
6X-RAY DIFFRACTION6B2 - 40
7X-RAY DIFFRACTION7B41 - 87
8X-RAY DIFFRACTION8B88 - 132
9X-RAY DIFFRACTION9B133 - 182
10X-RAY DIFFRACTION10B183 - 249
11X-RAY DIFFRACTION11C0 - 9
12X-RAY DIFFRACTION12C10 - 145
13X-RAY DIFFRACTION13C146 - 176
14X-RAY DIFFRACTION14C177 - 226
15X-RAY DIFFRACTION15C227 - 249

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