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- PDB-6amc: Engineered tryptophan synthase b-subunit from Pyrococcus furiosus... -

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Basic information

Entry
Database: PDB / ID: 6amc
TitleEngineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB4D11
ComponentsTryptophan synthase beta chain 1
KeywordsBIOSYNTHETIC PROTEIN / PLP Type II / Tryptophan Synthase / Engineered / Allostery
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
Tryptophan synthase beta chain 1
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsBuller, A.R. / Herger, M.
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Directed Evolution Mimics Allosteric Activation by Stepwise Tuning of the Conformational Ensemble.
Authors: Buller, A.R. / van Roye, P. / Cahn, J.K.B. / Scheele, R.A. / Herger, M. / Arnold, F.H.
History
DepositionAug 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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
Revision 1.3Nov 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)174,8718
Polymers174,7794
Non-polymers924
Water4,738263
1
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4364
Polymers87,3902
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-40 kcal/mol
Surface area26280 Å2
MethodPISA
2
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4364
Polymers87,3902
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-41 kcal/mol
Surface area25670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.438, 110.729, 160.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Tryptophan synthase beta chain 1


Mass: 43694.816 Da / Num. of mol.: 4 / Mutation: T321A, T292S, F274S, I68V, E17G
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.85 / Details: 15-25% PEG3350 and 0.1 M Na HEPES pH 7.85

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.93→40 Å / Num. obs: 114421 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rpim(I) all: 0.023 / Net I/σ(I): 15.4
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5601 / CC1/2: 0.605 / Rpim(I) all: 0.547 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DVZ
Resolution: 1.93→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 12.247 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25527 5711 5 %RANDOM
Rwork0.21604 ---
obs0.218 108623 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.408 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--2.95 Å2-0 Å2
3----2.84 Å2
Refinement stepCycle: 1 / Resolution: 1.93→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11501 0 4 263 11768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01911752
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210818
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.96815953
X-RAY DIFFRACTIONr_angle_other_deg0.879324927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.90851535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82323.924474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.777151804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0241558
X-RAY DIFFRACTIONr_chiral_restr0.0670.21770
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113380
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022386
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4440.9486152
X-RAY DIFFRACTIONr_mcbond_other0.4440.9486151
X-RAY DIFFRACTIONr_mcangle_it0.7891.4177680
X-RAY DIFFRACTIONr_mcangle_other0.7881.4177681
X-RAY DIFFRACTIONr_scbond_it0.320.955600
X-RAY DIFFRACTIONr_scbond_other0.3190.955600
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5831.4258273
X-RAY DIFFRACTIONr_long_range_B_refined4.40311.67913220
X-RAY DIFFRACTIONr_long_range_B_other4.39211.61313204
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 385 -
Rwork0.358 7970 -
obs--99.42 %
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)
11.35970.69840.22632.42521.36073.1964-0.10730.2205-0.0043-0.54920.1143-0.2852-0.65460.5373-0.00690.5134-0.11630.07340.46740.07430.367695.8435271.0368159.9508
21.12820.06140.24591.88690.05741.78970.0544-0.1048-0.0250.0147-0.0623-0.1613-0.08760.23980.0080.3869-0.01430.0090.50970.02170.470694.874261.6567181.7116
32.74540.39820.57711.99430.19614.294-0.07080.0123-0.0528-0.1861-0.08260.2093-0.2071-0.45640.15350.46270.05360.00680.4594-0.02130.447177.2859271.1019175.3749
41.2941-0.01760.14932.07720.13342.2803-0.04080.10820.0449-0.25890.0745-0.0356-0.46080.1951-0.03370.4347-0.04380.050.47480.03510.44592.9095267.924169.45
51.56250.45270.27891.5832-0.01792.16180.040.0372-0.2047-0.10440.0069-0.38310.37040.3961-0.04690.43570.08060.01620.50.00350.534496.9144248.7197172.7742
61.24110.7596-0.91082.567-1.59563.774-0.04390.1516-0.1684-0.19940.15480.18250.293-0.338-0.11090.49760.0006-0.01830.50270.01010.469379.8986253.5169160.2877
73.27843.4221-0.585718.6291-18.579621.613-0.15470.1274-0.04680.44740.77170.4269-0.8357-0.934-0.61710.50480.14690.02390.68510.04170.434972.8776257.2902158.7458
81.09370.9195-1.69021.2811-0.6023.95320.06640.0940.0612-0.1287-0.0160.089-0.302-0.297-0.05040.41440.0238-0.00820.49850.0360.460883.0322256.6358167.7253
91.68660.0906-0.33850.7972-0.072.31910.02680.0124-0.4003-0.0621-0.0021-0.17730.51620.0478-0.02470.43430.0065-0.01110.42470.04540.511587.3449244.8897177.072
1010.70924.9001-2.26355.7129-1.11881.58150.0764-0.04020.03860.193-0.05910.33640.0259-0.3209-0.01730.4716-0.00270.01780.52990.02350.485472.1391253.2391186.1303
113.4113-1.3095-3.0655.36330.82882.9229-0.0112-0.11080.06391.1706-0.0086-0.53670.21470.20840.01980.7029-0.0892-0.22570.82350.21830.126192.7382248.3242220.1281
121.60840.4615-0.02093.15270.40481.77980.0509-0.2489-0.0834-0.0034-0.0166-0.2714-0.01550.107-0.03430.3796-0.0483-0.03140.56730.0310.44594.6084263.4698197.1662
133.133-0.50450.37012.5189-0.69633.1557-0.0494-0.2138-0.10040.4234-0.1793-0.14590.23970.20730.22870.4726-0.1243-0.06310.56880.15730.357385.9706246.4513204.5345
142.1104-1.1986-0.50424.18380.67234.5669-0.0551-0.10980.01740.306-0.1330.1734-0.1054-0.20980.18810.4225-0.12440.00530.52020.0450.440773.2374249.689201.4419
1510.1083-3.332.4887.6317-5.86434.9331-0.171-0.4514-0.31961.17020.05720.4182-0.713-0.41330.11380.7633-0.15270.12850.741-0.19720.509972.9466249.0528215.0449
160.67040.3618-0.0532.12840.20391.4330.26-0.5888-0.02220.6019-0.2635-0.1045-0.0770.08320.00360.4037-0.1888-0.07520.71470.04190.24291.3164263.3272211.1852
170.245-0.35451.43710.7005-1.85388.9818-0.036-0.1309-0.08330.36320.14280.295-0.2043-0.5459-0.10680.5228-0.16050.12340.77210.02570.468277.536264.4358215.7296
183.7920.08853.11974.080.81328.75970.2287-0.4553-0.03110.3062-0.25020.40660.4551-0.81660.02150.5907-0.15260.01090.7486-0.00140.339486.8519265.2614218.2473
191.75280.16811.16291.75770.05892.40340.0486-0.4640.17640.1939-0.1506-0.0469-0.3804-0.16550.10210.3975-0.06480.01640.6043-0.09080.298486.1495275.2165201.224
2010.3481-22.00786.366257.0802-9.48185.529-0.4114-0.93-0.3872-0.6541.1562-0.1336-0.7338-0.8582-0.74480.45130.20480.07420.688-0.09940.696766.8525277.4959194.0141
214.1639-2.36930.03791.4309-0.03993.1882-0.2825-0.7945-0.03130.34750.4276-0.06050.13730.7689-0.14510.43250.0474-0.10410.7091-0.06060.3696139.0814287.9461222.8689
222.76461.14453.27742.5403-0.453511.18260.1058-0.22650.22890.2333-0.1742-0.24780.02960.59790.06830.32240.03120.0310.6747-0.08640.4892150.232288.7283203.6832
231.709-0.0776-0.07670.6350.65671.31020.07190.18040.1145-0.09910.0509-0.0643-0.15070.276-0.12280.4561-0.0130.03740.4545-0.02340.487134.0234296.6348198.5908
243.9199-0.1547-0.44711.129-0.06684.10530.0560.0366-0.02920.0285-0.00970.10910.2717-0.1836-0.04630.4789-0.0144-0.01790.3534-0.04950.5072125.1717281.571203.037
253.56130.06080.07142.20580.53833.7936-0.0541-0.5857-0.5310.37010.0320.080.7569-0.1590.02220.54960.016-0.0160.35320.03650.4771127.2083277.2892212.5377
262.3507-0.97680.45541.528-0.58552.26330.1075-0.08930.37190.00060.054-0.2077-0.49060.6226-0.16150.4165-0.12930.05540.3891-0.1220.4249136.4062301.615207.5931
272.5337-0.57360.29871.0151-0.1343.2872-0.0059-0.51070.2210.00910.2095-0.0107-0.3982-0.0396-0.20370.42910.02760.01670.3451-0.0870.4189124.0201301.9321217.3837
280.923-0.0933-1.50875.986-9.247117.42580.0063-0.06070.0436-0.16520.19790.0830.5479-0.332-0.20420.5698-0.0417-0.00530.54670.02880.5176114.5896292.1293222.2415
292.45170.25760.46141.25790.20593.5270.1609-0.09430.2906-0.00340.02720.034-0.3922-0.1399-0.18820.48420.04550.06390.3213-0.01240.4777122.1165303.1554207.0299
302.5546-0.14890.30913.88890.49941.98230.01110.1720.3879-0.0145-0.03030.1942-0.3248-0.21050.01930.52920.04910.06670.40850.0520.4385120.6217305.9495199.2973
311.10980.08410.29441.0868-0.94872.1359-0.11690.51480.5572-0.129-0.1076-0.0129-0.85840.02950.22450.8926-0.08210.0440.73670.06240.3796130.2637306.3733167.141
321.92170.0632-0.662.05340.36752.8309-0.05720.4305-0.21680.11270.1518-0.25280.09110.2528-0.09460.3550.04630.05120.5976-0.08450.3751138.0602286.3531184.6731
332.9639-0.05190.28921.4434-1.3495.2466-0.01450.63180.0461-0.4762-0.11910.1235-0.1645-0.24160.13360.58130.10780.06780.64360.1290.2009119.5356303.6206175.9686
344.5511.79892.07759.13430.63915.2456-0.05510.3732-0.2744-0.17790.17760.40520.3603-0.187-0.12250.50490.09420.03710.650.03460.3654112.4629296.7142184.2396
353.7898-1.07231.55170.3208-0.40340.88130.11920.1772-0.3126-0.1264-0.18340.12020.1761-0.25840.06430.91630.0657-0.03660.9196-0.04630.497110.3405300.1029167.1256
365.9575-2.19423.05583.0188-0.97433.13730.00460.57670.2344-0.61790.1494-0.3162-0.58270.2305-0.15410.39-0.03120.17140.88020.06690.1069134.1088298.3029171.6191
371.13270.71210.70612.21520.54412.22330.10390.36960.0691-0.3032-0.130.11880.1440.19550.02610.33090.0350.04490.8522-0.16050.2557134.1265284.0422168.3775
380.0796-0.28380.12541.1551-1.32415.73620.19340.0061-0.0792-0.54950.11590.3320.0846-0.3564-0.30930.4047-0.0361-0.05741.025-0.06410.2522120.126285.2482164.0775
390.6314-0.0766-0.70781.23-0.01723.6676-0.08470.4821-0.1807-0.24550.0606-0.2740.5279-0.03420.0240.3130.02220.03940.7511-0.26710.3632133.7096279.2031175.5831
404.706-0.9843-1.6572.0766-1.2272.4781-0.03050.6522-0.32910.14090.10150.0740.1948-0.1997-0.07090.38980.0094-0.00770.6063-0.19320.3078129.2853282.6562183.7656
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 32
2X-RAY DIFFRACTION2A33 - 102
3X-RAY DIFFRACTION3A103 - 169
4X-RAY DIFFRACTION4A170 - 211
5X-RAY DIFFRACTION5A212 - 254
6X-RAY DIFFRACTION6A255 - 282
7X-RAY DIFFRACTION7A283 - 293
8X-RAY DIFFRACTION8A294 - 309
9X-RAY DIFFRACTION9A310 - 373
10X-RAY DIFFRACTION10A374 - 387
11X-RAY DIFFRACTION11B1 - 34
12X-RAY DIFFRACTION12B35 - 86
13X-RAY DIFFRACTION13B87 - 121
14X-RAY DIFFRACTION14B122 - 155
15X-RAY DIFFRACTION15B156 - 173
16X-RAY DIFFRACTION16B174 - 274
17X-RAY DIFFRACTION17B275 - 299
18X-RAY DIFFRACTION18B300 - 313
19X-RAY DIFFRACTION19B314 - 382
20X-RAY DIFFRACTION20B383 - 389
21X-RAY DIFFRACTION21C1 - 27
22X-RAY DIFFRACTION22C28 - 41
23X-RAY DIFFRACTION23C42 - 102
24X-RAY DIFFRACTION24C103 - 144
25X-RAY DIFFRACTION25C145 - 181
26X-RAY DIFFRACTION26C182 - 238
27X-RAY DIFFRACTION27C239 - 282
28X-RAY DIFFRACTION28C283 - 293
29X-RAY DIFFRACTION29C294 - 349
30X-RAY DIFFRACTION30C350 - 387
31X-RAY DIFFRACTION31D1 - 47
32X-RAY DIFFRACTION32D48 - 82
33X-RAY DIFFRACTION33D83 - 134
34X-RAY DIFFRACTION34D135 - 150
35X-RAY DIFFRACTION35D151 - 176
36X-RAY DIFFRACTION36D177 - 217
37X-RAY DIFFRACTION37D218 - 272
38X-RAY DIFFRACTION38D273 - 304
39X-RAY DIFFRACTION39D305 - 362
40X-RAY DIFFRACTION40D363 - 385

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