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- PDB-6cuz: Engineered TrpB from Pyrococcus furiosus, PfTrpB7E6 with (2S,3R)-... -

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Basic information

Entry
Database: PDB / ID: 6cuz
TitleEngineered TrpB from Pyrococcus furiosus, PfTrpB7E6 with (2S,3R)-ethylserine bound as the amino-acrylate
Components(Tryptophan synthase beta chain ...) x 2
KeywordsLYASE / amino-acrylate / (2S / 3R)-ethylserine
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / cytoplasm
Similarity search - Function
Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FEV / PHOSPHATE ION / Tryptophan synthase beta chain 1
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsScheele, R.A. / Buller, A.R. / Boville, C.E. / Arnold, F.H.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Engineered Biosynthesis of beta-Alkyl Tryptophan Analogues.
Authors: Boville, C.E. / Scheele, R.A. / Koch, P. / Brinkmann-Chen, S. / Buller, A.R. / Arnold, F.H.
History
DepositionMar 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 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 / struct_conn / struct_conn_type
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _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_label_seq_id / _struct_conn_type.id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,82313
Polymers169,9024
Non-polymers9219
Water9,908550
1
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3646
Polymers84,9512
Non-polymers4134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-47 kcal/mol
Surface area25350 Å2
MethodPISA
2
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4597
Polymers84,9512
Non-polymers5085
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-53 kcal/mol
Surface area25370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.222, 109.297, 159.928
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Tryptophan synthase beta chain ... , 2 types, 4 molecules ADBC

#1: Protein Tryptophan synthase beta chain 1


Mass: 42361.449 Da / Num. of mol.: 2
Mutation: I16V, E17G, L91P, F95L, L161A, V173E, F274L, T292S, V384A
Source method: isolated from a genetically manipulated source
Details: (2S,3R)-ethylserine bound as the amino-acrylate
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: trpB1, PF1706 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8U093, tryptophan synthase
#2: Protein Tryptophan synthase beta chain 1


Mass: 42589.566 Da / Num. of mol.: 2
Mutation: I16V, E17G, L91P, F95L, L161A, V173E, F274L, T292S, V384A
Source method: isolated from a genetically manipulated source
Details: holo
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: trpB1, PF1706 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8U093, tryptophan synthase

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Non-polymers , 4 types, 559 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-FEV / (2E)-2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]pent-2-enoic acid


Mass: 344.257 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17N2O7P
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.2 Å3/Da / Density % sol: 44.09 % / Mosaicity: 0.23 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.85 / Details: 14% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.19499 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.19499 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 148965 / % possible obs: 100 % / Redundancy: 4.1 % / CC1/2: 0.981 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.05 / Rrim(I) all: 0.1 / Net I/σ(I): 8.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.115 / Num. unique obs: 7282 / CC1/2: 0.753 / Rpim(I) all: 0.613 / Rrim(I) all: 1.277 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
REFMAC5.8.0218refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VM5

5vm5


Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.426 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.135
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 7409 5 %RANDOM
Rwork0.235 ---
obs0.2363 141404 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 118.34 Å2 / Biso mean: 36.149 Å2 / Biso min: 16.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--1.36 Å2-0 Å2
3----1.47 Å2
Refinement stepCycle: final / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11373 0 57 550 11980
Biso mean--32.85 39.01 -
Num. residues----1521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01911678
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210793
X-RAY DIFFRACTIONr_angle_refined_deg1.1151.9715834
X-RAY DIFFRACTIONr_angle_other_deg0.767324915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45251517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.39724.234470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.979151834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7031552
X-RAY DIFFRACTIONr_chiral_restr0.0590.21752
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113194
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022316
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 529 -
Rwork0.367 10354 -
all-10883 -
obs--99.9 %
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)
11.03840.04320.85411.43810.22042.8856-0.05070.00060.0811-0.07780.0477-0.0786-0.14450.17050.00310.13960.04540.01830.18190.02060.0667-33.2472-13.648614.0418
23.5004-0.095-0.37093.90871.62086.799-0.1327-0.0864-0.06420.1787-0.21220.3354-0.1092-0.02220.3450.16330.10390.0120.13910.01320.1484-44.683-5.432116.884
33.45661.05370.29980.34570.09520.02820.2109-0.3896-0.00160.123-0.19780.04120.0331-0.0469-0.01310.3892-0.05220.11780.4178-0.05730.3345-56.4711-13.083917.6733
42.894-1.0919-1.58471.81682.02345.9038-0.29340.2196-0.2338-0.2437-0.46010.2283-0.3133-0.91230.75350.21510.1153-0.04360.1954-0.09710.1231-50.0672-4.05110.6019
50.66550.10550.84131.1860.00782.72750.07940.1009-0.1005-0.12970.0232-0.0580.20440.001-0.10260.20510.05370.01330.16590.02050.0792-36.7765-23.30357.7536
61.8423-0.48452.86982.3096-1.444610.024-0.225-0.26080.5584-0.5269-0.24330.2806-0.2871-1.12560.46840.30550.0837-0.14140.5565-0.02350.3009-54.1084-21.42043.2854
74.89030.28450.1782.3464-0.00693.54790.09740.085-0.296-0.3371-0.0462-0.1630.3787-0.0862-0.05120.2510.0412-0.02290.1459-0.00250.0667-39.309-27.95452.293
86.31330.41118.58652.91-0.776312.47440.3384-0.4597-0.25610.1635-0.03220.47150.5419-0.6962-0.30630.4059-0.25750.1670.53540.00990.4972-49.9695-33.750322.0572
91.1355-1.7262-0.14612.7455-0.57945.91070.0286-0.0386-0.1025-0.06410.14940.16660.6538-0.8654-0.1780.3437-0.1849-0.0660.36880.11190.0988-44.6847-30.89321.6438
102.9765-0.6285-0.17413.08170.42493.27120.185-0.1499-0.29070.2978-0.03490.04390.6577-0.6499-0.150.2917-0.0844-0.05960.29260.06320.0622-42.5792-31.868819.9199
111.0458-0.212-0.28262.2671-0.30412.84530.0886-0.1849-0.13710.10540.0176-0.07210.8299-0.0521-0.10620.3660.0352-0.06830.24280.04450.0335-33.5479-29.86353.7085
120.4947-0.27880.39361.12220.80892.56860.01580.00080.0627-0.07810.0565-0.1068-0.146-0.1446-0.07230.18510.07620.00010.22840.03460.064-34.7456-12.107436.1831
133.41020.10383.15913.22591.09058.9555-0.23140.26360.13710.0755-0.148-0.1613-0.2159-0.350.37940.2696-0.066-0.05350.23630.05130.056-44.843-31.962343.5145
146.082-1.4388-2.748119.6684-1.42791.46580.7814-0.6320.1827-0.6484-0.60770.684-0.30130.362-0.17370.4860.1124-0.16720.5055-0.03830.3199-55.5021-20.447138.127
151.69233.24280.01436.34610.09970.0450.2002-0.05530.28690.275-0.32520.7425-0.0713-0.16890.1250.33960.1915-0.10431.1485-0.2410.3545-55.7108-27.740940.2206
166.25880.1692-1.25486.24032.20381.37260.2822-0.01550.17170.1828-0.46120.6974-0.2093-0.5790.1790.58480.13010.03190.63540.00240.1288-51.5259-31.23254.1504
170.1585-0.28990.18040.86170.14562.42620.0168-0.09050.03090.0930.0303-0.1297-0.02490.0039-0.04710.24320.0322-0.01750.27270.03310.065-32.4485-14.370348.2141
185.9943-4.36711.42616.3169-4.73154.73460.18860.0309-0.10560.07360.00350.2662-0.1678-0.1306-0.19210.31190.0550.05710.4489-0.06080.0981-49.0295-9.357258.753
190.88070.0220.06840.85020.20353.05960.066-0.14390.09750.1894-0.02280.0946-0.3636-0.5207-0.04320.2180.11990.03730.33060.00370.0537-44.5066-5.990548.2232
203.07650.39910.3852.5536-0.0273.34640.0661-0.03190.1616-0.043-0.05560.0401-0.556-0.4417-0.01050.230.16370.03560.25980.02960.045-40.6353-3.862838.0524
213.49261.2820.22640.8361.03725.4818-0.44450.7172-0.1428-0.44850.29250.19170.0715-0.22610.1520.6-0.1447-0.24280.19950.05850.2918-13.3574-44.306519.0516
222.05240.0904-0.36611.8989-0.38162.5487-0.094-0.05660.11060.0860.08910.0397-0.2467-0.15130.00490.1903-0.0055-0.03190.05940.02610.0636-9.0015-31.723344.0997
231.2997-1.54481.412.69030.12575.370.0480.1083-0.04070.0085-0.00040.02980.27010.3996-0.04760.1937-0.00990.00450.05410.03090.1386-5.4771-50.112235.4603
243.6621-1.8983-1.4226.81684.032510.03960.07050.12310.28690.07170.4467-0.61520.03832.2868-0.51710.0890.0522-0.00530.6566-0.01170.14647.3498-50.859638.5286
259.84623.6891-3.23845.4062-2.4544.61530.21870.07680.1562-0.0723-0.3069-0.2935-0.30640.89790.08820.3531-0.02090.01540.29840.00420.1844-0.4805-52.130223.4
261.1492-0.06620.20011.04990.37981.5728-0.07360.04660.0761-0.11720.00090.0192-0.20280.02770.07270.2249-0.0263-0.01990.02440.03880.0795-9.1767-30.304732.4112
278.64213.9405-1.04422.88751.81784.9885-0.06710.1329-0.1136-0.04340.2145-0.1484-0.01250.4377-0.14740.2676-0.02420.01630.35750.1190.14735.839-32.776718.668
281.3493-1.7447-3.05422.32153.714411.2583-0.1451-0.0545-0.2166-0.0492-0.02050.26881.0061.80740.16570.65060.17480.01080.7353-0.03740.17310.2898-36.12125.3638
291.3445-0.09310.37091.2983-0.13043.2093-0.07850.07530.2495-0.06690.006-0.2152-0.360.4540.07250.2417-0.09940.00720.09750.02610.13833.1156-24.313234.4973
302.0777-0.17730.26522.5412-0.14332.99030.0111-0.07780.1345-0.0885-0.0732-0.2483-0.25770.43650.06210.2148-0.1161-0.00990.13250.01590.12872.8187-25.649241.9495
311.12-0.36390.75654.3774-2.53824.0476-0.1827-0.28780.17850.47140.0822-0.023-0.6616-0.03570.10050.38290.0327-0.02210.2359-0.06260.0306-0.3998-27.272381.9195
321.22390.13950.22341.9709-0.5072.3638-0.0789-0.1640.04150.00470.03640.1082-0.2477-0.12080.04240.17580.0415-0.00340.12590.01270.0504-8.9832-36.305258.4545
331.04230.7987-1.16791.5790.78976.3775-0.0396-0.16350.0877-0.0014-0.07630.0526-0.56370.39260.11590.26-0.0534-0.04770.1798-0.02020.13846.7222-25.821363.9543
342.3549-0.6399-0.0915.13550.9690.548-0.0187-0.1959-0.3413-0.1644-0.047-0.02660.11950.33920.06570.20380.06720.02210.41710.09150.109113.7779-37.989359.6016
355.48813.60781.87712.84650.30534.9845-0.1712-0.5573-0.2690.3321-0.8321-0.504-0.41581.84921.00340.4658-0.1605-0.19191.05380.52210.362415.5178-32.165369.9279
360.1070.12290.52461.42290.55073.1971-0.0578-0.08710.03950.1292-0.00480.0331-0.4839-0.14960.06260.29910.02080.00410.2747-0.03660.101-4.5772-32.461470.3643
370.83240.1973-0.23371.28570.01942.74250.0067-0.2608-0.05540.12070.0450.05140.1402-0.185-0.05170.22690.01540.00760.20410.04810.052-7.0812-47.835471.5664
380.285-0.5847-1.16112.89561.52075.2832-0.0698-0.17910.07710.49660.2407-0.5380.20960.7512-0.17090.23070.051-0.11130.39450.02710.14279.2579-46.769677.1872
391.0653-0.02640.16151.24060.26413.59850.012-0.1893-0.19740.13740.0465-0.0310.46260.0526-0.05850.16350.0322-0.010.12060.06860.1093-3.7837-52.102465.714
404.0614-0.3264-0.01142.08880.54142.92660.0383-0.1267-0.2786-0.16180.0489-0.03940.22380.0953-0.08720.19350.0465-0.03980.10690.05640.081-3.6415-50.873158.0371
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 102
2X-RAY DIFFRACTION2A103 - 129
3X-RAY DIFFRACTION3A130 - 140
4X-RAY DIFFRACTION4A141 - 180
5X-RAY DIFFRACTION5A181 - 282
6X-RAY DIFFRACTION6A283 - 301
7X-RAY DIFFRACTION7A302 - 324
8X-RAY DIFFRACTION8A325 - 335
9X-RAY DIFFRACTION9A336 - 353
10X-RAY DIFFRACTION10A354 - 383
11X-RAY DIFFRACTION11B1 - 44
12X-RAY DIFFRACTION12B45 - 91
13X-RAY DIFFRACTION13B92 - 128
14X-RAY DIFFRACTION14B129 - 141
15X-RAY DIFFRACTION15B142 - 158
16X-RAY DIFFRACTION16B159 - 178
17X-RAY DIFFRACTION17B179 - 254
18X-RAY DIFFRACTION18B255 - 279
19X-RAY DIFFRACTION19B280 - 356
20X-RAY DIFFRACTION20B357 - 384
21X-RAY DIFFRACTION21C1 - 29
22X-RAY DIFFRACTION22C30 - 83
23X-RAY DIFFRACTION23C84 - 132
24X-RAY DIFFRACTION24C133 - 156
25X-RAY DIFFRACTION25C163 - 177
26X-RAY DIFFRACTION26C178 - 256
27X-RAY DIFFRACTION27C257 - 285
28X-RAY DIFFRACTION28C286 - 301
29X-RAY DIFFRACTION29C302 - 358
30X-RAY DIFFRACTION30C359 - 383
31X-RAY DIFFRACTION31D1 - 31
32X-RAY DIFFRACTION32D32 - 92
33X-RAY DIFFRACTION33D93 - 126
34X-RAY DIFFRACTION34D127 - 145
35X-RAY DIFFRACTION35D146 - 176
36X-RAY DIFFRACTION36D177 - 212
37X-RAY DIFFRACTION37D213 - 273
38X-RAY DIFFRACTION38D274 - 301
39X-RAY DIFFRACTION39D302 - 358
40X-RAY DIFFRACTION40D359 - 385

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