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- PDB-6cuv: Engineered Holo TrpB from Pyrococcus furiosus, PfTrpB7E6 -

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Basic information

Entry
Database: PDB / ID: 6cuv
TitleEngineered Holo TrpB from Pyrococcus furiosus, PfTrpB7E6
ComponentsTryptophan synthase beta chain 1
KeywordsLYASE / internal aldimine
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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Tryptophan synthase beta chain 1
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 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 26, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
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)170,73511
Polymers170,3584
Non-polymers3777
Water1,42379
1
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4156
Polymers85,1792
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-55 kcal/mol
Surface area26090 Å2
MethodPISA
2
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3205
Polymers85,1792
Non-polymers1413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-48 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.577, 108.567, 159.331
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
Tryptophan synthase beta chain 1


Mass: 42589.566 Da / Num. of mol.: 4
Mutation: I16V, E17G, L91P, F95L, L161A, V173E, F274L, T292S, V384A
Source method: isolated from a genetically manipulated source
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: pET22-b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8U093, tryptophan synthase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.12 Å3/Da / Density % sol: 42.02 % / Mosaicity: 0.28 °
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 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.19499 Å / Relative weight: 1
ReflectionResolution: 2.26→40 Å / Num. obs: 68611 / % possible obs: 100 % / Redundancy: 6.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.058 / Rrim(I) all: 0.146 / Net I/σ(I): 8.9
Reflection shellResolution: 2.26→2.31 Å / Redundancy: 6.2 % / Num. unique obs: 4547 / CC1/2: 0.655 / Rpim(I) all: 0.719 / % 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
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VM5

5vm5


Resolution: 2.26→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 23.849 / SU ML: 0.257 / SU R Cruickshank DPI: 0.4009 / Cross valid method: THROUGHOUT / ESU R: 0.401 / ESU R Free: 0.256
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3374 5 %RANDOM
Rwork0.21 ---
obs0.2125 63878 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 120.84 Å2 / Biso mean: 48.522 Å2 / Biso min: 24.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.36 Å2
Refinement stepCycle: final / Resolution: 2.26→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11547 0 19 79 11645
Biso mean--60.66 40.69 -
Num. residues----1539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911840
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210934
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.9716061
X-RAY DIFFRACTIONr_angle_other_deg0.767325248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73151542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.0624.113479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27151855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4281557
X-RAY DIFFRACTIONr_chiral_restr0.0630.21771
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113415
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022366
LS refinement shellResolution: 2.26→2.319 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 195 -
Rwork0.363 3504 -
all-3699 -
obs--74.37 %
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)
11.86321.5485-1.24931.988-0.65814.8302-0.1910.242-0.0093-0.39010.16330.20260.588-0.76970.02770.301-0.0485-0.09380.3128-0.0040.0665-11.0349-48.43150.7818
21.226-0.0888-0.05172.6697-0.56912.20440.0615-0.2480.00660.0916-0.04850.1381-0.1396-0.377-0.0130.21230.00890.01760.3717-0.0350.0556-8.8583-35.736721.8986
35.10152.2252-0.71639.74121.34172.831-0.0881-0.0637-0.0527-0.05970.05-0.12430.14190.22320.03820.26170.0487-0.02410.24830.05850.09870.3503-51.940412.1097
43.305-0.9493-1.22832.7794-0.08415.84480.0963-0.1845-0.0957-0.1334-0.30150.05990.24060.37180.20520.30060.0414-0.04230.24240.03310.05742.8907-50.853716.5489
52.8642-0.015-0.23363.3085-0.826.3277-0.18740.22480.1659-0.1651-0.2497-0.34860.07871.39320.43710.21330.0805-0.00060.43150.10.07239.6654-49.850511.9426
60.3650.2590.40351.76890.1542.362-0.02530.00940.0583-0.25560.01020.2258-0.2136-0.27290.01520.26590.0246-0.02610.3054-0.01750.0399-8.6177-33.06210.3448
72.88114.35981.21537.24593.5957.1451-0.11810.13-0.1349-0.35460.3698-0.4256-0.35140.8533-0.25170.344-0.02540.05510.3795-0.02130.17936.1908-33.3061-2.1346
80.6701-1.97630.3615.8342-1.06220.27610.28060.0625-0.029-0.8291-0.17350.05780.04260.3763-0.10710.479-0.31570.18221.5015-0.3490.250110.5794-33.94137.3337
91.41680.2060.48091.292-0.38214.7868-0.02770.010.2619-0.1369-0.00480.024-0.61410.32110.03250.2699-0.00670.00810.192-0.02980.09990.8315-24.563113.228
104.99890.07781.53173.6358-0.13292.58020.06480.08450.21310.023-0.0437-0.0965-0.33940.215-0.02110.2795-0.03430.0450.2935-0.06370.03642.7727-24.533521.6273
110.4358-0.67770.77743.558-0.52764.3594-0.05-0.22750.08620.30510.03130.0968-0.4631-0.53980.01870.27220.07890.05290.3869-0.06420.053-8.0599-25.617357.85
120.8684-0.49130.15464.3-0.69213.15520.0256-0.10890.0772-0.11360.01710.25810.1144-0.3363-0.04270.1545-0.01540.03270.369-0.02960.0905-9.1667-41.860535.2356
131.42771.094-1.61043.90111.11533.8842-0.00490.01260.0517-0.0654-0.02690.1399-0.3633-0.08850.03190.38390.0306-0.00730.2954-0.10170.0595-0.0195-24.84245.0463
143.8593-0.6174-0.46634.8930.65294.5447-0.14780.0549-0.34860.0456-0.0243-0.3026-0.10060.39660.17210.194-0.05640.03360.3305-0.05570.08239.9549-27.52839.3535
157.8053-2.6378-0.1622.836-0.41182.5952-0.483-0.2572-0.09421.1023-0.0865-0.3717-0.11950.53050.56940.5987-0.1049-0.13570.43930.05740.195711.9043-24.548452.6114
160.67540.0876-0.49831.52980.55483.2699-0.0483-0.12930.09690.26190.00820.10310.3308-0.49050.04010.2461-0.03630.04660.3832-0.01590.0288-7.5338-42.693648.9249
173.8098-2.78070.139512.94575.23173.0562-0.09440.01940.0402-0.32440.2111-0.4597-0.00490.2712-0.11670.29260.01860.00320.35270.010.21574.4128-41.382162.0267
181.98272.10590.56593.45-2.36018.47830.1386-0.180.31920.4801-0.32040.225-0.83671.18030.18180.3934-0.0114-0.02770.8159-0.1530.211210.5883-43.598452.1228
191.1259-0.2202-0.30521.1970.46733.72460.0178-0.2562-0.130.2424-0.00810.01130.7298-0.0028-0.00960.2845-0.0431-0.01310.27790.04150.0162-2.9972-52.20644.0634
207.9587-1.15074.380213.41341.84319.93070.12480.3079-0.10510.04910.0369-0.80940.73910.9663-0.16170.28380.02380.00080.3507-0.01330.126911.63-46.335633.2535
212.6274-0.3475-0.62241.0077-0.23895.820.0117-0.21760.2210.08050.07260.1357-0.1133-0.8079-0.08430.19820.05750.06460.19130.02040.0767-57.4278-65.667650.3137
221.1820.11310.39263.21170.69342.7375-0.0190.0192-0.0295-0.06480.08270.0647-0.03650.0954-0.06380.2270.03220.02680.19190.02760.116-45.5185-69.330540.3194
235.79260.59060.08844.1821.29699.24430.2253-0.16480.29230.0455-0.2102-0.6779-0.22610.9873-0.01510.254-0.11250.00830.22680.03110.1827-34.7717-56.969940.5008
249.7632-0.04472.75195.82130.29475.1241-0.1225-0.25460.50750.6758-0.2064-0.3414-0.26150.81050.32890.4706-0.0099-0.01720.2843-0.02320.1279-41.5-54.83655.6114
251.058-0.8707-0.33781.1610.48912.3937-0.0718-0.1488-0.07740.15010.04890.22520.5373-0.03490.02290.36620.01880.03320.16040.03570.0866-47.8449-79.437648.245
2612.3228-6.65350.83986.08140.13183.6993-0.135-0.64360.1430.09230.1204-0.63390.22630.76620.01460.33170.04430.01460.38790.03560.1456-37.8861-73.197662.7448
270.41011.02133.16852.59177.97724.637-0.09390.06940.0128-0.12690.2308-0.1084-0.51810.6808-0.13690.99280.0857-0.01320.7812-0.05620.5549-29.2264-69.855762.4245
284.04681.0841-4.00462.5253-0.99728.70690.2403-0.73730.05540.3138-0.1419-0.15140.10130.7366-0.09840.26780.086-0.01940.21810.01890.1692-39.5-75.469553.7952
293.681-0.2159-0.98971.08540.53083.33090.0369-0.0969-0.3320.28730.0949-0.11620.5440.665-0.13180.35190.1464-0.05680.1653-0.02120.0647-35.5369-83.577342.6557
302.50621.25950.0556.6647-0.79593.06740.21380.1148-0.34380.188-0.0982-0.41890.31580.344-0.11560.28570.1037-0.01670.2224-0.04720.1248-37.2211-84.421238.6505
310.6028-0.1363-0.11461.22490.21023.17570.02440.3653-0.0901-0.2434-0.0150.13250.6697-0.1319-0.00940.39970.0207-0.04510.3583-0.03890.0259-46.3999-80.82699.0874
320.89520.18950.592.4994-0.54721.4038-0.00910.05010.213-0.0350.10520.2426-0.2918-0.1213-0.09610.310.04880.01980.28520.05590.1145-50.6762-61.570523.4403
333.05811.08760.52963.11561.79274.8095-0.12130.2878-0.1371-0.2880.12920.03960.28320.4043-0.00790.33740.1156-0.01430.3001-0.03670.0113-35.2116-82.115.1597
344.979-1.90331.47834.9062-3.25825.4862-0.04790.40690.6248-0.3505-0.0804-0.5803-0.58351.06420.12830.4168-0.03750.07440.5797-0.05750.1311-24.2667-72.486319.4791
3510.55385.24970.03612.7089-0.31513.10550.1925-0.21080.29020.0462-0.3740.1359-0.59970.78990.18150.56290.12280.04870.7298-0.01780.0682-25.9901-79.2995.4332
360.6077-0.40680.42491.28520.29363.15660.13410.42030.0458-0.3476-0.0690.1026-0.0804-0.1577-0.06510.33660.0598-0.01590.46560.09910.033-48.0022-66.1848.9512
370.9981.1652.55022.04052.49186.9944-0.21780.414-0.0779-0.43230.3149-0.3465-0.63831.075-0.0970.4587-0.01590.19880.68790.12640.1539-32.4016-61.0762.5743
386.1461-0.39628.77020.078-0.600412.68340.5421.4267-0.59190.04770.0797-0.04650.47622.0364-0.62170.7580.2547-0.1670.9923-0.20140.8548-35.0203-63.3087.4743
391.42970.09470.98771.62890.11013.280.02340.34150.2713-0.16550.02840.0713-0.5097-0.1395-0.05180.31270.05510.03420.25340.13440.0859-47.9077-56.32315.6785
4012.28224.26441.6259.6397-4.01877.25150.05620.36750.8020.65780.1858-0.7193-0.70610.9095-0.2420.3167-0.00230.04060.376-0.06210.4167-32.4348-57.739626.9207
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 35
2X-RAY DIFFRACTION2A36 - 95
3X-RAY DIFFRACTION3A96 - 109
4X-RAY DIFFRACTION4A110 - 132
5X-RAY DIFFRACTION5A133 - 176
6X-RAY DIFFRACTION6A177 - 259
7X-RAY DIFFRACTION7A260 - 286
8X-RAY DIFFRACTION8A287 - 301
9X-RAY DIFFRACTION9A302 - 356
10X-RAY DIFFRACTION10A357 - 388
11X-RAY DIFFRACTION11B1 - 36
12X-RAY DIFFRACTION12B37 - 83
13X-RAY DIFFRACTION13B84 - 114
14X-RAY DIFFRACTION14B115 - 150
15X-RAY DIFFRACTION15B151 - 179
16X-RAY DIFFRACTION16B180 - 266
17X-RAY DIFFRACTION17B267 - 282
18X-RAY DIFFRACTION18B283 - 302
19X-RAY DIFFRACTION19B303 - 373
20X-RAY DIFFRACTION20B374 - 385
21X-RAY DIFFRACTION21C1 - 50
22X-RAY DIFFRACTION22C51 - 133
23X-RAY DIFFRACTION23C134 - 154
24X-RAY DIFFRACTION24C155 - 180
25X-RAY DIFFRACTION25C181 - 265
26X-RAY DIFFRACTION26C266 - 285
27X-RAY DIFFRACTION27C286 - 292
28X-RAY DIFFRACTION28C293 - 312
29X-RAY DIFFRACTION29C313 - 352
30X-RAY DIFFRACTION30C353 - 384
31X-RAY DIFFRACTION31D1 - 55
32X-RAY DIFFRACTION32D56 - 83
33X-RAY DIFFRACTION33D84 - 128
34X-RAY DIFFRACTION34D129 - 157
35X-RAY DIFFRACTION35D158 - 179
36X-RAY DIFFRACTION36D180 - 274
37X-RAY DIFFRACTION37D275 - 298
38X-RAY DIFFRACTION38D299 - 304
39X-RAY DIFFRACTION39D305 - 374
40X-RAY DIFFRACTION40D375 - 385

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  • 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

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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

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