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- PDB-5zjg: Gamma-glutamyltranspeptidase from Pseudomonas nitroreducens compl... -

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Basic information

Entry
Database: PDB / ID: 5zjg
TitleGamma-glutamyltranspeptidase from Pseudomonas nitroreducens complexed with Gly-Gly
Components
  • Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03 L-subunit
  • Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03 S-subunit
KeywordsTRANSFERASE / theanine synthesis / transpeptidation / enzyme / protein engineering / substrate specificity / reaction specificity
Function / homology
Function and homology information


hypoglycin A gamma-glutamyl transpeptidase activity / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process
Similarity search - Function
Gamma-glutamyltranspeptidase, small (S) subunit / Gamma-glutamyltranspeptidase, large (L) subunit, C-terminal domain / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Serum Albumin; Chain A, Domain 1 / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich ...Gamma-glutamyltranspeptidase, small (S) subunit / Gamma-glutamyltranspeptidase, large (L) subunit, C-terminal domain / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Serum Albumin; Chain A, Domain 1 / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLYCINE / Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03
Similarity search - Component
Biological speciesPseudomonas nitroreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsHibi, T. / Imaoka, M. / Itoh, T. / Wakayama, M.
CitationJournal: Biosci. Biotechnol. Biochem. / Year: 2019
Title: Crystal structure analysis and enzymatic characterization of gamma-glutamyltranspeptidase from Pseudomonas nitroreducens.
Authors: Hibi, T. / Imaoka, M. / Shimizu, Y. / Itoh, T. / Wakayama, M.
History
DepositionMar 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03 L-subunit
B: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03 S-subunit
C: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03 L-subunit
D: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03 S-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,83110
Polymers115,3464
Non-polymers4846
Water10,935607
1
A: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03 L-subunit
B: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03 S-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9916
Polymers57,6732
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11910 Å2
ΔGint-72 kcal/mol
Surface area18340 Å2
MethodPISA
2
C: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03 L-subunit
D: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03 S-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8404
Polymers57,6732
Non-polymers1672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11910 Å2
ΔGint-74 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.537, 53.942, 107.260
Angle α, β, γ (deg.)91.45, 100.19, 108.08
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03 L-subunit / gamma-glutamyltranspeptidase L-subunit


Mass: 36847.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas nitroreducens (bacteria) / Gene: SAMN05216209_3923 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta Gami B (DE3) / References: UniProt: A0A239KXH0
#2: Protein Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03 S-subunit / gamma-glutamyltranspeptidase S-subunit


Mass: 20825.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas nitroreducens (bacteria) / Gene: SAMN05216209_3923 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta Gami B (DE3) / References: UniProt: A0A239KXH0
#3: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 1.95 Å3/Da / Density % sol: 36.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 16% (w/v) PEG 8000, 15% (w/v) PEG 400, 0.1M HEPES (pH 7.0), 50mM glycylglycine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.96401 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96401 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 121960 / % possible obs: 96.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 28.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.02 / Rrim(I) all: 0.055 / Χ2: 0.998 / Net I/σ(I): 26.3
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 6 % / Rmerge(I) obs: 0.52 / Num. unique obs: 5713 / CC1/2: 0.917 / Rpim(I) all: 0.221 / Rrim(I) all: 0.567 / Χ2: 1.003 / % possible all: 90.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2dg5
Resolution: 1.702→20.067 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 19.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1892 2000 2.08 %
Rwork0.1548 --
obs0.1555 96046 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.702→20.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7909 0 31 607 8547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078145
X-RAY DIFFRACTIONf_angle_d0.92411070
X-RAY DIFFRACTIONf_dihedral_angle_d10.1124798
X-RAY DIFFRACTIONf_chiral_restr0.0551226
X-RAY DIFFRACTIONf_plane_restr0.0061459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7022-1.74480.23531260.19625935X-RAY DIFFRACTION85
1.7448-1.79190.25261390.19456509X-RAY DIFFRACTION94
1.7919-1.84460.23551420.18676681X-RAY DIFFRACTION96
1.8446-1.90410.23141440.18736765X-RAY DIFFRACTION97
1.9041-1.97210.19391440.17226762X-RAY DIFFRACTION97
1.9721-2.0510.2051420.17116732X-RAY DIFFRACTION97
2.051-2.14420.2171450.1676797X-RAY DIFFRACTION97
2.1442-2.25720.20171430.16156752X-RAY DIFFRACTION97
2.2572-2.39840.17921460.15696854X-RAY DIFFRACTION98
2.3984-2.58320.19071450.15336803X-RAY DIFFRACTION98
2.5832-2.84250.18771470.15376868X-RAY DIFFRACTION98
2.8425-3.25230.17691450.15436839X-RAY DIFFRACTION99
3.2523-4.09180.17971460.13936908X-RAY DIFFRACTION99
4.0918-20.0680.17121460.14136841X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.1773-0.10192.0143.3205-0.35963.52910.1798-0.51520.2830.1886-0.11480.0151-0.45940.1245-0.07560.18-0.07430.06330.2454-0.05520.1563-10.8932.99939.6141
21.8298-0.2869-0.2241.60350.4252.55940.1556-0.1898-0.1362-0.10570.00560.01380.340.2757-0.1230.1895-0.0159-0.05020.18870.05510.1785-8.889516.0146-1.0319
31.0571-1.1956-1.20123.49360.41461.77960.1173-0.2225-0.4725-0.1297-0.36650.98890.467-0.79360.22170.3222-0.1994-0.05120.52360.03010.5408-28.500713.78623.8267
43.9021-1.4368-0.54133.6993-0.0825.24490.0044-0.661-0.44770.51160.1387-0.08150.74240.4323-0.05350.46810.0112-0.11580.30570.10850.2511-7.77069.279211.1506
52.96211.5966-1.11383.2111-0.80962.8460.1196-0.086-0.433-0.01940.0949-0.03850.83010.3183-0.10350.47080.0507-0.10990.24030.05660.2656-5.96425.2898-1.3101
61.07681.36970.20075.9942-0.90140.34910.280.11010.2737-0.2434-0.098-0.1852-0.54730.3701-0.00570.5994-0.09660.18550.29640.01690.2497-2.13732.6462-14.5698
70.5443-0.22090.24920.0971-0.12550.29380.09420.26180.2122-0.5204-0.11040.0354-0.38710.03660.12151.05220.195-0.04790.23780.08180.1022-13.706934.0543-25.4347
80.73720.2902-0.02980.909-1.47322.68570.28730.16140.1271-0.5696-0.0873-0.1825-0.37830.39790.07320.78750.09640.15180.34720.00280.2269-1.63924.3555-25.8458
91.4499-0.00720.14630.09660.3921.61070.03970.2903-0.0144-0.1341-0.10380.0462-0.1426-0.02650.03280.9820.1961-0.05550.39-0.00740.204-12.813426.2944-36.5954
103.34911.3620.76576.92541.18741.1840.1843-0.34410.1069-0.0378-0.0654-0.1438-0.31260.2587-0.10680.2082-0.11110.03540.24110.00720.1459-7.597930.20460.7674
113.27840.8736-2.79773.12140.04222.60330.1248-0.0995-0.2976-0.1211-0.03780.52760.5747-0.3396-0.07130.3179-0.0926-0.1190.18940.06480.3116-18.573610.217-1.0736
121.6566-0.05760.29610.05790.13712.5850.33440.2623-0.2737-0.7943-0.2230.26850.4131-0.0768-0.0960.5890.0839-0.16670.2118-0.02780.3048-12.778210.6421-18.8366
131.531-0.9337-0.43981.9853-0.55030.90140.2810.03240.1472-0.4989-0.22040.0298-0.51720.2147-0.03550.4606-0.01790.01840.18290.02070.1371-10.074432.0911-11.3656
142.11570.101-0.34895.59310.15594.92180.07970.11330.3687-0.1549-0.10790.0203-0.5992-0.0349-0.02940.69660.108-0.08040.2038-0.00660.2987-18.173643.8195-10.6733
150.5951-0.50820.29371.59210.22782.14640.11710.0831-0.1219-0.4114-0.04970.26860.0867-0.1517-0.02120.69440.1544-0.2050.2339-0.0010.2773-22.176727.5328-22.8382
160.73250.21830.06690.1225-0.1511.3759-0.02170.13060.1659-0.22090.05420.2017-0.1425-0.3938-0.09330.73970.2768-0.36680.40490.00760.3686-30.567233.1354-21.6014
171.3862-0.25872.60470.2696-1.2537.56430.33870.0289-0.1731-0.6546-0.0880.45730.3119-0.6171-0.33420.55440.1051-0.20450.3163-0.04220.3575-26.796627.5161-18.2148
183.85773.83682.31915.0751.94872.55330.0496-0.02520.927-0.30020.06680.2023-0.99050.3603-0.0310.4971-0.07020.06930.2147-0.02720.2985-11.354941.4729-0.5795
198.86693.48012.07396.50971.30114.99370.2498-0.92790.47040.0262-0.39730.1441-0.6138-0.5590.16610.24770.0590.03980.2298-0.0370.2229-17.821435.53333.8892
202.53472.43671.74459.36136.77864.92880.5937-0.46042.62790.88630.00950.7414-0.4928-0.9589-0.62630.37420.11660.04810.28540.07190.3952-17.927319.1145-10.4644
211.1623-1.03020.36311.6344-0.66021.677-0.487-0.5882-0.05010.77290.5314-0.19330.2280.06540.01710.45460.2543-0.040.4221-0.04170.264-8.2422-4.223958.5319
221.20440.17880.03276-2.0032.0962-0.0642-0.0376-0.02440.0622-0.0117-0.0985-0.04830.02660.07810.08590.03980.03970.2068-0.0350.1901-16.66947.436341.4164
231.7695-0.34060.40642.161-0.41251.6607-0.275-0.44210.12010.56280.3759-0.32660.05580.0141-0.07590.31880.1777-0.03240.3097-0.07990.2534-12.23566.602555.7351
241.8405-0.905-0.20140.89660.11870.045-0.2675-0.38880.57070.38110.5162-1.0078-0.04710.2682-0.0850.29010.1382-0.15910.4552-0.28410.7147-0.90212.411654.3211
251.2122-0.0138-0.32855.02751.41.5502-0.0924-0.0131-0.14880.1863-0.07470.4210.0787-0.28680.17710.1070.02010.02950.2498-0.01360.2438-21.28811.085343.9035
263.8057-0.21760.37181.6781.17912.4095-0.16950.1818-0.55910.1154-0.14530.45690.2834-0.33040.29860.1766-0.05720.05480.2136-0.04170.2717-13.5854-18.399228.6967
274.0343-1.9937-1.32013.83011.9673.20340.08110.1624-0.0992-0.4056-0.21770.2457-0.2202-0.26610.1410.144-0.0244-0.00350.1858-0.01940.1547-12.1074-8.544924.7759
281.5755-1.2042-0.72253.09892.52682.12220.13740.3366-0.1154-0.3855-0.44880.4151-0.244-0.64910.2890.22530.0349-0.04230.3241-0.05160.2153-20.5893-5.726823.4006
292.55331.27460.17054.84390.40611.2452-0.3194-0.35230.20210.33760.3692-0.30870.10370.1689-0.02230.17680.1202-0.02250.2609-0.08690.27-8.2692.285350.6094
305.5851-1.37030.62063.52642.8263.17820.2340.37150.1758-0.5412-0.0153-0.3884-0.22420.2124-0.18230.2373-0.0010.0840.23740.00050.3051-9.32148.946531.6187
310.7304-1.0443-0.17152.06250.70511.0245-0.0928-0.0382-0.13250.17730.04750.20310.1396-0.08720.01640.1217-0.00680.05340.1898-0.0080.2226-12.6423-9.167539.7103
323.6175-0.58791.26882.6725-1.0184.4238-0.03910.2350.2363-0.1960.0695-0.2995-0.19550.4203-0.00360.1635-0.05310.05640.2007-0.04020.2448-0.2277-8.421729.0749
339.929-5.99337.00079.5473-5.7718.93440.18370.2367-0.0582-0.25310.0735-0.3619-0.11470.7217-0.21690.1565-0.03190.08080.2768-0.04430.24774.3492-16.684120.6654
341.8038-0.78860.3641.07431.40883.8101-0.2319-0.2683-0.12350.1770.2058-0.03730.05540.44090.03210.16980.04950.0350.1758-0.00260.2801-3.2176-11.574440.5506
352.5455-0.17271.10922.98540.42680.8677-0.2811-0.7202-0.27120.73120.43080.08590.19740.3042-0.13680.40650.2126-0.01360.3967-0.00090.3678-1.9077-12.311753.6968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 159 )
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 199 )
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 219 )
5X-RAY DIFFRACTION5chain 'A' and (resid 220 through 252 )
6X-RAY DIFFRACTION6chain 'A' and (resid 253 through 270 )
7X-RAY DIFFRACTION7chain 'A' and (resid 271 through 317 )
8X-RAY DIFFRACTION8chain 'A' and (resid 318 through 343 )
9X-RAY DIFFRACTION9chain 'A' and (resid 344 through 363 )
10X-RAY DIFFRACTION10chain 'B' and (resid 364 through 381 )
11X-RAY DIFFRACTION11chain 'B' and (resid 382 through 401 )
12X-RAY DIFFRACTION12chain 'B' and (resid 402 through 431 )
13X-RAY DIFFRACTION13chain 'B' and (resid 432 through 472 )
14X-RAY DIFFRACTION14chain 'B' and (resid 473 through 483 )
15X-RAY DIFFRACTION15chain 'B' and (resid 484 through 495 )
16X-RAY DIFFRACTION16chain 'B' and (resid 496 through 515 )
17X-RAY DIFFRACTION17chain 'B' and (resid 516 through 530 )
18X-RAY DIFFRACTION18chain 'B' and (resid 531 through 544 )
19X-RAY DIFFRACTION19chain 'B' and (resid 545 through 557 )
20X-RAY DIFFRACTION20chain 'B' and (resid 701 through 702 )
21X-RAY DIFFRACTION21chain 'C' and (resid 26 through 77 )
22X-RAY DIFFRACTION22chain 'C' and (resid 78 through 113 )
23X-RAY DIFFRACTION23chain 'C' and (resid 114 through 159 )
24X-RAY DIFFRACTION24chain 'C' and (resid 160 through 233 )
25X-RAY DIFFRACTION25chain 'C' and (resid 234 through 270 )
26X-RAY DIFFRACTION26chain 'C' and (resid 271 through 296 )
27X-RAY DIFFRACTION27chain 'C' and (resid 297 through 317 )
28X-RAY DIFFRACTION28chain 'C' and (resid 318 through 361 )
29X-RAY DIFFRACTION29chain 'D' and (resid 364 through 401 )
30X-RAY DIFFRACTION30chain 'D' and (resid 402 through 421 )
31X-RAY DIFFRACTION31chain 'D' and (resid 422 through 483 )
32X-RAY DIFFRACTION32chain 'D' and (resid 484 through 506 )
33X-RAY DIFFRACTION33chain 'D' and (resid 507 through 516 )
34X-RAY DIFFRACTION34chain 'D' and (resid 517 through 544 )
35X-RAY DIFFRACTION35chain 'D' and (resid 545 through 557 )

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  • 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

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