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- PDB-6am9: Engineered tryptophan synthase b-subunit from Pyrococcus furiosus... -

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Basic information

Entry
Database: PDB / ID: 6am9
TitleEngineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9, with Ser-bound in a predominantly closed state.
ComponentsTryptophan synthase beta chain 1
KeywordsLYASE / PLP Type II / Tryptophan Synthase / Engineered / Allostery / BIOSYNTHETIC PROTEIN
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
Chem-0JO / Chem-PLS / Tryptophan synthase beta chain 1
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsBuller, A.R. / van Roye, P.
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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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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)174,98514
Polymers173,5624
Non-polymers1,42310
Water1,910106
1
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5037
Polymers86,7812
Non-polymers7215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-47 kcal/mol
Surface area24640 Å2
MethodPISA
2
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4837
Polymers86,7812
Non-polymers7015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-48 kcal/mol
Surface area24300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.502, 109.122, 160.491
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: 43390.602 Da / Num. of mol.: 4
Mutation: I16V, E17G, I68V, F95L, F274S, T292S, T321A, 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 / 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.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PLS / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE / PYRIDOXYL-SERINE-5-MONOPHOSPHATE


Mass: 336.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N2O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H13N2O7P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
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: Aug 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.09→40 Å / Num. obs: 91166 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rpim(I) all: 0.03 / Net I/σ(I): 13.5
Reflection shellResolution: 2.09→2.13 Å / Redundancy: 6.9 % / Num. unique obs: 30761 / CC1/2: 0.695 / Rpim(I) all: 0.739 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VM5
Resolution: 2.09→40 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 20.665 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24397 4524 5 %RANDOM
Rwork0.21449 ---
obs0.216 86509 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 60.15 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å20 Å2-0 Å2
2---2.34 Å20 Å2
3----0.57 Å2
Refinement stepCycle: 1 / Resolution: 2.09→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11369 0 91 106 11566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01911731
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211114
X-RAY DIFFRACTIONr_angle_refined_deg1.211.95815921
X-RAY DIFFRACTIONr_angle_other_deg0.8982.99625424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72251538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91623.922459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.183151815
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3831554
X-RAY DIFFRACTIONr_chiral_restr0.0620.21774
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213509
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022641
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_it0.4432.3586162
X-RAY DIFFRACTIONr_mcbond_other0.4412.3586161
X-RAY DIFFRACTIONr_mcangle_it0.7783.5327690
X-RAY DIFFRACTIONr_mcangle_other0.7783.5327691
X-RAY DIFFRACTIONr_scbond_it0.3452.415569
X-RAY DIFFRACTIONr_scbond_other0.3422.415569
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6113.6098229
X-RAY DIFFRACTIONr_long_range_B_refined4.17919.16813007
X-RAY DIFFRACTIONr_long_range_B_other4.17619.15413000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 318 -
Rwork0.414 6298 -
obs--99.07 %
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)
13.7651-1.9677-1.49664.72270.50741.497-0.3273-0.5408-0.34050.97870.0851-0.45710.41890.52230.24220.59760.0673-0.12460.66260.14980.15319.215-50.402-2.711
21.01720.03130.5295.234-0.20723.19890.0532-0.13790.0242-0.0723-0.0577-0.1682-0.41640.25780.00450.3584-0.1025-0.05710.55830.00250.17277.805-34.688-23.465
37.1879-1.82133.04789.68924.34674.37850.2678-0.1128-0.59230.61530.4014-0.58950.77310.307-0.66920.60960.0426-0.09590.47250.140.22563.793-58.755-12.358
42.5164-0.7703-0.48355.13713.09725.96530.0248-0.1954-0.18750.0889-0.33760.3080.0315-0.19050.31270.4316-0.0939-0.06180.49810.05150.169-6.086-49.114-17.258
53.27590.3846-1.83692.00462.666710.7684-0.0787-0.2147-0.0830.1945-0.39930.5492-0.275-0.91940.4780.4251-0.0686-0.00360.4962-0.01040.2445-12.335-48.207-14.884
61.04830.0056-0.00321.97260.39842.81310.1129-0.479-0.13060.4461-0.0875-0.3021-0.12830.2922-0.02530.457-0.108-0.11340.63320.03920.06927.855-37.611-10.268
74.7937-4.62090.62016.4151-4.13297.3802-0.0093-0.2897-0.12410.35780.03550.2582-0.5235-0.2734-0.02620.5997-0.0413-0.00220.6579-0.14210.1047-7.179-31.983-0.01
82.45151.5482-2.82581.2285-1.845111.03530.5289-0.3186-0.30880.4561-0.08350.10650.1938-0.6257-0.44550.6303-0.05870.06160.66250.09630.5533-12.015-34.627-3.996
90.917-0.08920.46771.37770.07694.34640.0479-0.26340.18170.0847-0.0828-0.0632-0.8881-0.09520.03490.5667-0.032-0.05010.491-0.09090.05591.127-24.717-14.854
106.1171-5.32490.595514.24922.23877.9658-0.1167-0.0727-0.0768-0.49150.00130.7682-0.5572-1.1110.11540.4770.0718-0.10840.5721-0.06030.2267-13.688-31.717-24.892
110.75910.24550.85162.0286-0.72934.3319-0.23960.17350.1193-0.2326-0.0581-0.232-1.00270.80950.29770.5206-0.24820.00040.56550.04650.05939.919-27.144-53.701
120.16950.50620.33141.74961.70743.9791-0.01830.0366-0.11720.04150.0409-0.21090.29010.2836-0.02260.3463-0.0246-0.01330.5589-0.00450.26257.497-46.843-35.37
132.136-0.1376-2.26143.01281.15995.7896-0.27940.04260.10980.1365-0.06240.1174-0.37240.05560.34180.649-0.0845-0.11190.42580.00450.0677-1.705-25.596-43.876
145.7376-5.4702-4.39495.25034.17313.3757-0.15860.4007-0.8350.3081-0.4240.86030.048-0.29540.58260.8982-0.25430.12590.64140.00320.5468-14.081-37.597-39.774
152.0032-0.6627-2.75984.8010.59447.5856-0.20210.4539-0.1551-0.4093-0.47810.5235-0.2086-1.12470.68020.5091-0.0095-0.15340.5483-0.12740.1339-10.474-26.821-47.748
160.8023-0.36620.9492.8946-0.8333.5235-0.02940.1884-0.1432-0.23980.0146-0.2359-0.22370.69050.01480.38-0.0940.04560.6254-0.00870.12319.531-40.38-47.535
170.69150.38210.10981.3068-0.43473.7738-0.13440.1075-0.0564-0.54990.0874-0.11020.18880.04380.0470.468-0.05130.02460.5207-0.08050.07931.331-47.484-55.611
182.1285-0.44040.77430.32550.58332.698-0.08270.16380.0942-0.1348-0.12660.0868-0.4828-0.23870.20930.6172-0.0555-0.08910.8890.13560.5236-11.709-43.75-61.647
191.27260.3881-0.11781.20880.31315.1348-0.02670.1767-0.1337-0.2493-0.0053-0.00340.4077-0.15460.0320.3728-0.0408-0.02690.4779-0.05550.177-1.537-50.358-46.581
201.6958-0.18840.43611.88960.04764.2604-0.03730.1377-0.19-0.0696-0.05430.02770.75450.00250.09160.4558-0.089-0.0150.4928-0.04550.185-0.103-53.518-39.418
213.8503-0.84370.14053.14420.71960.98930.0514-0.48950.19551.3288-0.11220.31360.5697-0.40590.06080.9076-0.1990.08960.70230.0560.089329.969-14.14-18.869
221.29660.16590.36711.2871-0.55872.20920.17690.00830.0099-0.06960.03770.1060.3308-0.2773-0.21460.5252-0.0731-0.04340.51740.03390.082133.22-20.117-42.195
232.64380.31390.60683.299-0.28485.51730.14860.0898-0.01610.2329-0.3348-0.43440.24120.72640.18610.4081-0.0134-0.02890.48710.07210.206545.699-8.702-37.344
242.8160.2840.48023.89130.27995.90630.0435-0.32660.11341.0046-0.2358-0.4770.09990.67930.19220.5313-0.0606-0.12480.42470.04530.134246.297-5.698-29.044
250.8520.7056-0.08154.13711.36780.95410.2472-0.3089-0.12120.2408-0.2850.07950.1706-0.26820.03780.568-0.1318-0.03470.51420.07480.089532.072-19.877-31.891
264.05250.8091-0.0492.44450.85910.79130.0259-0.1594-0.32310.3761-0.00790.29940.4069-0.0084-0.01810.749-0.059-0.10560.37270.09430.159136.236-33.763-34.297
2712.7621-6.5488-5.86634.03681.77655.3936-0.4263-0.1988-0.65090.3964-0.05660.13470.41070.26360.48290.8576-0.0626-0.25210.47520.05360.168949.62-26.054-20.125
284.6703-2.2416-0.57111.399-0.97174.90280.0987-0.54-0.0576-0.20230.10310.07310.72730.6074-0.20190.9923-0.0051-0.19230.41560.01040.03949.777-22.637-21.625
291.69160.1116-0.54832.16270.45332.16330.2524-0.0407-0.44740.2577-0.2051-0.23890.55690.2755-0.04720.77440.112-0.19310.36510.03970.160946.579-33.382-36.388
302.5058-0.59430.69983.04670.93320.92860.14740.0629-0.1701-0.0572-0.0585-0.22180.43080.1477-0.08890.67230.1261-0.08060.4920.0330.176546.69-29.486-42.771
312.7075-1.59810.56888.75271.65651.2810.19980.1533-0.2206-0.471-0.1386-0.29480.45420.3491-0.06130.67240.14020.0580.58230.03010.098746.793-20.494-86.15
323.5974-1.0458-3.63632.63570.81587.6648-0.02080.2286-0.6051-0.2453-0.11080.31081.1445-0.30740.13170.77990.0018-0.16720.3-0.04070.166137.249-33.744-70.167
331.1351-1.48170.7494.4788-0.33842.7611-0.0150.0530.18530.1970.02530.11030.1861-0.2621-0.01030.3878-0.01-0.01460.48440.00910.188433.598-11.568-55.453
340.6156-0.20831.44795.0882-1.30084.2252-0.07080.229-0.02880.05220.14990.03540.43230.4604-0.07910.7340.1886-0.04770.4234-0.05690.015748.345-28.31-65.178
353.0730.47460.97923.076-1.4184.9446-0.19380.33740.17690.1493-0.2224-0.4360.24632.09620.41620.47080.1921-0.04361.03130.13890.092458.281-22.107-65.476
360.4509-0.02561.01020.8007-0.31532.39750.21850.088-0.0857-0.3405-0.0080.08470.75980.1537-0.21050.74920.056-0.03320.4948-0.01440.027838.559-21.294-70.596
371.0407-0.040.63521.38030.50123.3203-0.05210.25960.0482-0.29290.09320.1078-0.0138-0.1071-0.04110.46610.0312-0.00560.50810.05970.1835.181-7.201-69.406
381.16380.34142.78964.28022.35457.3077-0.01550.44030.0396-0.7890.2391-0.7414-0.3991.1699-0.22360.40830.00120.18260.65040.06530.230752.12-6.809-77.346
390.89230.00940.34490.9431-0.00074.14450.04520.11750.1937-0.1949-0.04860.0038-0.1781-0.02180.00340.36870.00650.00380.4370.05670.214738.225-3.41-63.895
409.06054.0489-0.27116.5533-2.76413.6750.0809-0.16340.48430.7493-0.159-0.3434-0.6620.83740.07810.44360.0068-0.04070.5262-0.01350.253952.756-4.776-52.368
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 39
2X-RAY DIFFRACTION2A40 - 91
3X-RAY DIFFRACTION3A92 - 102
4X-RAY DIFFRACTION4A103 - 136
5X-RAY DIFFRACTION5A137 - 169
6X-RAY DIFFRACTION6A170 - 254
7X-RAY DIFFRACTION7A255 - 281
8X-RAY DIFFRACTION8A282 - 301
9X-RAY DIFFRACTION9A302 - 374
10X-RAY DIFFRACTION10A375 - 385
11X-RAY DIFFRACTION11B1 - 44
12X-RAY DIFFRACTION12B45 - 85
13X-RAY DIFFRACTION13B86 - 132
14X-RAY DIFFRACTION14B133 - 140
15X-RAY DIFFRACTION15B141 - 178
16X-RAY DIFFRACTION16B179 - 232
17X-RAY DIFFRACTION17B233 - 280
18X-RAY DIFFRACTION18B281 - 292
19X-RAY DIFFRACTION19B293 - 351
20X-RAY DIFFRACTION20B352 - 385
21X-RAY DIFFRACTION21C1 - 29
22X-RAY DIFFRACTION22C30 - 102
23X-RAY DIFFRACTION23C103 - 142
24X-RAY DIFFRACTION24C143 - 178
25X-RAY DIFFRACTION25C179 - 211
26X-RAY DIFFRACTION26C212 - 257
27X-RAY DIFFRACTION27C258 - 276
28X-RAY DIFFRACTION28C277 - 306
29X-RAY DIFFRACTION29C307 - 359
30X-RAY DIFFRACTION30C360 - 383
31X-RAY DIFFRACTION31D1 - 16
32X-RAY DIFFRACTION32D17 - 44
33X-RAY DIFFRACTION33D45 - 83
34X-RAY DIFFRACTION34D84 - 120
35X-RAY DIFFRACTION35D121 - 178
36X-RAY DIFFRACTION36D179 - 212
37X-RAY DIFFRACTION37D213 - 265
38X-RAY DIFFRACTION38D266 - 301
39X-RAY DIFFRACTION39D302 - 374
40X-RAY DIFFRACTION40D375 - 385

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