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- PDB-4zfk: Ergothioneine-biosynthetic Ntn hydrolase EgtC with glutamine -

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Basic information

Entry
Database: PDB / ID: 4zfk
TitleErgothioneine-biosynthetic Ntn hydrolase EgtC with glutamine
ComponentsAmidohydrolase EgtC
KeywordsHYDROLASE / Ntn hydrolase / ergothioneine biosynthesis / sulfur chemistry / Mycobacteria
Function / homology
Function and homology information


gamma-glutamyl hercynylcysteine S-oxide hydrolase / ergothioneine biosynthesis from histidine via gamma-glutamyl-hercynylcysteine sulfoxide / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / glutamine metabolic process
Similarity search - Function
Ergothioneine biosynthesis protein EgtC / Gamma-glutamyl-hercynylcysteine sulfoxide hydrolase, Actinobacteria / Gamma-glutamyl-hercynylcysteine sulfoxide hydrolase EgtC-like / Glutamine amidotransferases class-II / Glutamine amidotransferase domain / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal ...Ergothioneine biosynthesis protein EgtC / Gamma-glutamyl-hercynylcysteine sulfoxide hydrolase, Actinobacteria / Gamma-glutamyl-hercynylcysteine sulfoxide hydrolase EgtC-like / Glutamine amidotransferases class-II / Glutamine amidotransferase domain / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMINE / Gamma-glutamyl-hercynylcysteine sulfoxide hydrolase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 Å
AuthorsVit, A. / Seebeck, F.P. / Blankenfeldt, W.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation147005 Switzerland
CitationJournal: Chembiochem / Year: 2015
Title: Structure of the Ergothioneine-Biosynthesis Amidohydrolase EgtC.
Authors: Vit, A. / Mashabela, G.T. / Blankenfeldt, W. / Seebeck, F.P.
History
DepositionApr 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amidohydrolase EgtC
B: Amidohydrolase EgtC
C: Amidohydrolase EgtC
D: Amidohydrolase EgtC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,22235
Polymers100,9624
Non-polymers2,26031
Water20,7711153
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint51 kcal/mol
Surface area32570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.796, 109.993, 139.327
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Amidohydrolase EgtC


Mass: 25240.451 Da / Num. of mol.: 4 / Mutation: E53D, V137L, H188R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: egtC, MSMEG_6248, MSMEI_6087 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0R5M9, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10N2O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1153 / 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate pH 4.7, 50% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.82→46.44 Å / Num. obs: 85790 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 13.49 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.069 / Net I/σ(I): 11.5 / Num. measured all: 355388
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.82-1.854.20.79821863744720.6090.44599.9
9.63-46.443.50.02534.122996600.9990.01696.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation19.7 Å1.99 Å

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Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
MOLREP11.0.05phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZFJ

4zfj


Resolution: 1.82→35.457 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1765 4256 4.97 %
Rwork0.1458 81442 -
obs0.1474 85698 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.74 Å2 / Biso mean: 18.6238 Å2 / Biso min: 3.12 Å2
Refinement stepCycle: final / Resolution: 1.82→35.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6806 0 270 1153 8229
Biso mean--43.42 32.51 -
Num. residues----920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067137
X-RAY DIFFRACTIONf_angle_d1.0579730
X-RAY DIFFRACTIONf_chiral_restr0.041103
X-RAY DIFFRACTIONf_plane_restr0.0051282
X-RAY DIFFRACTIONf_dihedral_angle_d10.7782517
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 (%)
1.82-1.84070.26881370.243526592796100
1.8407-1.86230.26881190.220427182837100
1.8623-1.8850.22321390.208426962835100
1.885-1.90890.25341400.197326452785100
1.9089-1.9340.20571420.186827202862100
1.934-1.96050.23081480.177326592807100
1.9605-1.98850.19811460.177126772823100
1.9885-2.01820.20431280.170526912819100
2.0182-2.04970.20491310.158827082839100
2.0497-2.08330.1731320.146926832815100
2.0833-2.11930.16441440.139527282872100
2.1193-2.15780.20651410.146626642805100
2.1578-2.19930.21311080.146927362844100
2.1993-2.24420.1881470.140226892836100
2.2442-2.2930.19141590.130526952854100
2.293-2.34630.17751400.135726832823100
2.3463-2.4050.16441290.127127082837100
2.405-2.470.16551580.132327082866100
2.47-2.54260.17141340.133227152849100
2.5426-2.62470.18211340.133827202854100
2.6247-2.71840.16161280.128127002828100
2.7184-2.82720.17141570.129527182875100
2.8272-2.95590.16511590.136827162875100
2.9559-3.11160.16951410.1427222863100
3.1116-3.30640.14451220.12827562878100
3.3064-3.56150.1491430.130927522895100
3.5615-3.91950.14681540.129427462900100
3.9195-4.48570.15461580.122727662924100
4.4857-5.64780.14591430.139827982941100
5.6478-35.46390.1961950.18262866306199
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)
10.35970.13440.12030.6216-0.11520.22380.01950.06510.06320.0282-0.00650.03810.03150.01150.02020.017-0.0008-0.00130.05970.00410.028632.398-1.57764.8375
21.84670.08830.28481.9596-0.55411.66840.0612-0.0229-0.28210.05640.01480.03140.2492-0.0045-0.04940.1147-0.0024-0.01290.07180.00310.140632.6373-19.479210.2589
32.5165-0.26560.05081.9365-0.14641.58010.0690.238-0.1735-0.1804-0.01970.15830.1957-0.1806-0.03470.0877-0.0178-0.03590.1562-0.01910.122820.4613-10.8316-1.2149
41.37290.1041-0.15221.5854-0.14770.8930.00340.0669-0.0268-0.0131-0.0293-0.0494-0.0170.00180.0190.05760.00320.0060.09450.02430.078555.5214.50291.9714
51.45260.1687-0.05861.87160.62641.66580.0384-0.05620.19090.121-0.0528-0.0308-0.13050.05270.01030.0928-0.00820.00040.09220.02810.13357.697920.93110.9605
61.1537-0.1858-0.18951.77680.41241.27950.05530.22220.2072-0.19970.0012-0.2057-0.19990.1909-0.03320.1034-0.01320.03690.18580.07820.157666.178216.3723-4.3361
71.2542-0.2546-0.05312.33170.36011.0121-0.0776-0.0495-0.07420.26510.01790.07330.1142-0.05150.04590.1859-0.02240.02220.0729-0.00590.085237.85234.130134.4385
81.62550.3137-0.11992.61510.07311.87440.01320.02470.187-0.0369-0.0172-0.0657-0.1117-0.0586-0.00840.1223-0.00950.00210.06630.01050.105640.582821.738928.731
92.1028-0.1360.19681.23740.38112.282-0.0622-0.15910.07360.57310.02140.1638-0.0097-0.20430.02240.2764-0.01240.06590.1079-0.03240.146230.946316.516343.573
101.7724-0.44490.02671.6389-0.22430.5797-0.08510.00720.09710.1923-0.0024-0.0839-0.02470.06070.08190.1571-0.0056-0.04940.07630.0190.099758.6246-7.240430.3265
112.00940.04070.73542.38150.02141.18070.08510.1784-0.2556-0.0638-0.04430.11260.17010.0724-0.02630.13950.0179-0.02250.0946-0.02220.125153.8484-23.429222.2743
122.2191-0.30180.23641.2003-0.19420.98050.0152-0.1212-0.04550.3137-0.0588-0.2150.04820.14060.07530.21130.0112-0.07230.12670.0350.131667.4869-20.227235.3387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 89 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 170 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 171 through 228 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 89 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 90 through 170 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 171 through 232 )B0
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 89 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 90 through 170 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 171 through 230 )C0
10X-RAY DIFFRACTION10chain 'D' and (resid 2 through 89 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 90 through 170 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 171 through 228 )D0

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