[English] 日本語
Yorodumi
- PDB-4pip: Engineered EgtD variant EgtD-M252V,E282A in complex with tryptoph... -

+
Open data


ID or keywords:

Loading...

-
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


N-alpha,N-alpha,N-alpha-trimethyl-L-histidine biosynthesis from histidine / L-histidine Nalpha-methyltransferase / dimethylhistidine N-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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 5 types, 1380 molecules

#2: Chemical
ChemComp-TRP / TRYPTOPHAN / 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 / 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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 1369 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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: 0

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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more