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- PDB-4pip: Engineered EgtD variant EgtD-M252V,E282A in complex with tryptoph... -

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Basic information

Entry
Database: PDB / ID: 4pip
TitleEngineered EgtD variant EgtD-M252V,E282A in complex with tryptophan and SAH
ComponentsHistidine-specific methyltransferase EgtD
KeywordsTRANSFERASE / methyltransferase / ergothioneine / histidine betaine
Function / homology
Function and homology information


L-histidine Nalpha-methyltransferase / L-histidine N(alpha)-methyltransferase activity / ergothioneine biosynthesis from histidine via gamma-glutamyl-hercynylcysteine sulfoxide / protein methyltransferase activity / methylation
Similarity search - Function
Methyltransferase EgtD-like / Histidine-specific methyltransferase, SAM-dependent / Histidine N-alpha-methyltransferase, Actinobacteria-type / Histidine N-alpha-methyltransferase / : / Histidine-specific methyltransferase, SAM-dependent / 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 / TRYPTOPHAN / Histidine N-alpha-methyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsVit, A. / Seebeck, F.P. / Blankenfeldt, W.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Foundation147005 Switzerland
Citation
Journal: Chembiochem / Year: 2015
Title: Ergothioneine Biosynthetic Methyltransferase EgtD Reveals the Structural Basis of Aromatic Amino Acid Betaine Biosynthesis.
Authors: Vit, A. / Misson, L. / Blankenfeldt, W. / Seebeck, F.P.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Crystallization and preliminary X-ray analysis of the ergothioneine-biosynthetic methyltransferase EgtD.
Authors: Vit, A. / Misson, L. / Blankenfeldt, W. / Seebeck, F.P.
History
DepositionMay 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine-specific methyltransferase EgtD
B: Histidine-specific methyltransferase EgtD
C: Histidine-specific methyltransferase EgtD
D: Histidine-specific methyltransferase EgtD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,20915
Polymers140,7704
Non-polymers2,43911
Water24,6631369
1
A: Histidine-specific methyltransferase EgtD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7813
Polymers35,1931
Non-polymers5892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine-specific methyltransferase EgtD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8064
Polymers35,1931
Non-polymers6133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histidine-specific methyltransferase EgtD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8415
Polymers35,1931
Non-polymers6484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histidine-specific methyltransferase EgtD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7813
Polymers35,1931
Non-polymers5892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.045, 67.634, 112.125
Angle α, β, γ (deg.)90.000, 109.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Histidine-specific methyltransferase EgtD / Histidine-alpha-N-methyltransferase


Mass: 35192.594 Da / Num. of mol.: 4 / Mutation: T2A, A29T, P30Q, A75S, M252V, E282A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 607 / Gene: egtD, MSMEG_6247, MSMEI_6086 / Plasmid: pET19m / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0R5M8, L-histidine Nalpha-methyltransferase

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Non-polymers , 5 types, 1380 molecules

#2: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1369 / 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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% w/v PEG3350, 0.2 M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→41.856 Å / Num. all: 103604 / Num. obs: 103604 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.22 Å2 / Rpim(I) all: 0.065 / Rrim(I) all: 0.128 / Rsym value: 0.11 / Net I/av σ(I): 5.286 / Net I/σ(I): 7.4 / Num. measured all: 391092
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.93.70.5871.356192150450.3510.5872.199.9
1.9-2.013.70.3991.952614142410.240.3993100
2.01-2.153.90.2852.751896133910.1660.2854.399.9
2.15-2.323.70.2033.746196125080.1220.2035.6100
2.32-2.553.80.1524.943871114940.0890.1527.1100
2.55-2.853.90.1166.240356104220.0680.1168.9100
2.85-3.293.70.0857.73427591870.050.08511.799.9
3.29-4.023.90.06493064178250.0360.06415.9100
4.02-5.693.70.0559.12257360870.0320.05517.2100
5.69-41.8563.70.0439.61247834040.0250.04315.699.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.21data scaling
XDSdata scaling
PDB_EXTRACT3.14data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4PIO

4pio


Resolution: 1.8→41.856 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 5270 5.09 %
Rwork0.194 98267 -
obs0.1964 103537 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.36 Å2 / Biso mean: 24.4662 Å2 / Biso min: 5.36 Å2
Refinement stepCycle: final / Resolution: 1.8→41.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9602 0 282 1369 11253
Biso mean--19.27 29.66 -
Num. residues----1258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710046
X-RAY DIFFRACTIONf_angle_d1.10413708
X-RAY DIFFRACTIONf_chiral_restr0.0461583
X-RAY DIFFRACTIONf_plane_restr0.0051794
X-RAY DIFFRACTIONf_dihedral_angle_d13.3493631
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82050.36361510.277632793430100
1.8205-1.84190.30021880.272532683456100
1.8419-1.86430.3561530.264232243377100
1.8643-1.88790.29911610.251133093470100
1.8879-1.91280.271690.240132153384100
1.9128-1.9390.29021570.233833113468100
1.939-1.96670.2791820.228732483430100
1.9667-1.9960.27571630.218432863449100
1.996-2.02720.28112090.217431893398100
2.0272-2.06050.25711700.208532763446100
2.0605-2.0960.25661600.195432753435100
2.096-2.13410.23721860.193732623448100
2.1341-2.17520.22631860.187832643450100
2.1752-2.21960.24241720.187232663438100
2.2196-2.26780.25571790.182332773456100
2.2678-2.32060.27161580.177732663424100
2.3206-2.37860.21751660.179232693435100
2.3786-2.44290.26211810.173232683449100
2.4429-2.51480.23271680.173532873455100
2.5148-2.59590.24311810.176432803461100
2.5959-2.68870.25061880.177532433431100
2.6887-2.79630.23671780.176232923470100
2.7963-2.92360.23051900.17943254344499
2.9236-3.07770.26191870.178932793466100
3.0777-3.27040.19771680.169932903458100
3.2704-3.52280.21411660.164733013467100
3.5228-3.87710.16861950.164632823477100
3.8771-4.43760.19741860.17133053491100
4.4376-5.58880.241830.193733363519100
5.5888-41.86720.25441890.26583366355599
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)
11.3317-0.4503-0.48570.52390.17880.9335-0.01410.11810.09920.00830.01190.051-0.11720.03430.02090.1251-0.0198-0.01620.0713-0.01020.10587.5149-1.0193-38.2534
21.11-0.1287-0.95211.2015-0.26730.8240.07680.15640.14780.1096-0.1066-0.1096-0.14350.11590.04810.1551-0.0135-0.0210.18320.05750.101515.50184.7935-48.2407
33.031-0.9404-0.38981.45410.1810.9587-0.12040.1931-0.26910.0931-0.02510.2250.0907-0.05360.02170.0621-0.0112-0.00960.0018-0.02530.08511.1354-8.139-37.6401
41.68060.0727-0.10121.7018-0.52311.2408-0.0454-0.0536-0.01240.12730.002-0.4746-0.08940.00130.03390.14190.0225-0.03830.06960.0080.1808-22.344733.593-20.0815
50.8630.1574-0.70371.17930.78932.4924-0.0454-0.251-0.0248-0.0989-0.00740.19670.0512-0.27850.04980.16060.00120.00150.25060.05580.1162-40.20126.4036-5.4755
61.1819-0.1635-0.32641.40240.18360.4732-0.0382-0.41030.24780.0642-0.0193-0.0045-0.0115-0.070.03310.10640.0103-0.01340.1895-0.04150.0898-36.866537.5917-4.0041
71.56320.68780.10431.6415-0.64111.2284-0.1033-0.0836-0.2409-0.16920.0142-0.26880.2147-0.02850.02670.05860.04460.02060.05190.01690.1526-22.301725.2359-15.395
84.30941.2238-1.28071.5734-0.61591.321-0.00280.16990.4604-0.08570.04210.3769-0.4984-0.1265-0.06730.364-0.0016-0.05630.4111-0.01580.38485.401444.0345-13.7279
94.0671-0.9086-0.48662.2746-0.05881.6883-0.0278-0.1630.069-0.1054-0.09080.2029-0.0485-0.17170.07170.17170.00440.01770.1586-0.03780.133513.139230.5034-6.4695
101.66350.4761-1.52050.41480.21892.2809-0.16410.1335-0.42020.0799-0.1884-0.08950.20.01220.310.19530.02880.02940.12710.00320.222726.59525.8595-22.3827
111.125-0.098-0.12080.65670.20030.9767-0.0123-0.02090.05130.0561-0.09660.1444-0.041-0.16610.09590.1926-0.0059-0.00140.1498-0.0210.184714.248231.0022-15.0906
121.550.2712-0.36781.0084-1.02672.38170.0411-0.04810.32240.1731-0.08280.20150.0308-0.70190.11170.1778-0.02150.04750.3505-0.05950.30430.009827.9426-5.3004
133.01740.41330.54460.94570.8992.9076-0.04750.2491-0.2707-0.25020.0726-0.10880.11190.1167-0.04260.2215-0.01060.04840.1481-0.02040.233616.923817.4041-27.1656
142.40040.7463-0.27880.96750.36281.1496-0.12880.06910.1792-0.04740.1581-0.1317-0.15120.1715-0.03370.18030.0012-0.01630.09860.00280.1557-35.087-3.6941-40.0804
152.53990.069-0.43961.08980.44771.07330.0727-0.00690.6142-0.05050.0051-0.0612-0.2326-0.0001-0.05780.18630.01230.00030.11010.00420.2023-40.877-1.5097-28.3928
161.11670.73960.51161.75841.10291.8636-0.21350.3057-0.0269-0.29840.3654-0.2681-0.09780.3321-0.01550.0881-0.0520.04410.1852-0.01870.127-31.1169-11.1826-43.4582
170.2913-0.2382-0.44310.30940.00530.47490.0355-0.06470.174-0.16440.3001-0.0096-0.3308-0.02430.33110.03010.0022-0.138-0.0635-0.1268-0.0079-10.74698.7485-26.6494
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 77 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 162 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 320 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 13 through 57 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 90 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 91 through 162 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 163 through 321 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 27 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 28 through 57 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 58 through 91 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 92 through 267 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 268 through 288 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 289 through 321 )C0
14X-RAY DIFFRACTION14chain 'D' and (resid 4 through 77 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 78 through 182 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 183 through 321 )D0
17X-RAY DIFFRACTION17chain 'A' and (resid 401 through 401 ) or chain 'B' and (resid 401 through 401 ) or chain 'C' and (resid 402 through 402 ) or chain 'D' and (resid 401 through 401 )A401
18X-RAY DIFFRACTION17chain 'A' and (resid 401 through 401 ) or chain 'B' and (resid 401 through 401 ) or chain 'C' and (resid 402 through 402 ) or chain 'D' and (resid 401 through 401 )B401
19X-RAY DIFFRACTION17chain 'A' and (resid 401 through 401 ) or chain 'B' and (resid 401 through 401 ) or chain 'C' and (resid 402 through 402 ) or chain 'D' and (resid 401 through 401 )C402
20X-RAY DIFFRACTION17chain 'A' and (resid 401 through 401 ) or chain 'B' and (resid 401 through 401 ) or chain 'C' and (resid 402 through 402 ) or chain 'D' and (resid 401 through 401 )D401

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