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- PDB-7rnq: Holo structure of engineered TrpB, 2B9-H275E, from Pyrococcus fur... -

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Basic information

Entry
Database: PDB / ID: 7rnq
TitleHolo structure of engineered TrpB, 2B9-H275E, from Pyrococcus furiosus in the extended-open conformation
ComponentsTryptophan synthase beta chain 1
KeywordsBIOSYNTHETIC PROTEIN / PLP / tryptophan synthase / directed evolution
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. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme
Similarity search - Domain/homology
PHOSPHATE ION / Tryptophan synthase beta chain 1
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsHiggins, P.M. / Buller, A.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2-GM137417 United States
CitationJournal: Nat Commun / Year: 2022
Title: Substrate multiplexed protein engineering facilitates promiscuous biocatalytic synthesis.
Authors: McDonald, A.D. / Higgins, P.M. / Buller, A.R.
History
DepositionJul 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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)174,91112
Polymers174,4394
Non-polymers4728
Water4,900272
1
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4556
Polymers87,2192
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-57 kcal/mol
Surface area26400 Å2
MethodPISA
2
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4556
Polymers87,2192
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-58 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.013, 82.683, 322.558
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: 43609.688 Da / Num. of mol.: 4 / Mutation: H275E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: trpB1, PF1706 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8U093, tryptophan synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.85 / Details: 13-21% PEG3350, 0.1 M HEPES pH 7.85

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97618 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 10, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97618 Å / Relative weight: 1
ReflectionResolution: 2.1→41 Å / Num. obs: 89740 / % possible obs: 99.5 % / Redundancy: 13.4 % / CC1/2: 0.995 / Rpim(I) all: 0.065 / Net I/σ(I): 11.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 54391 / CC1/2: 0.818 / Rpim(I) all: 0.684 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AM7
Resolution: 2.102→40.003 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 14.515 / SU ML: 0.179 / Cross valid method: FREE R-VALUE / ESU R: 0.254 / ESU R Free: 0.197
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2478 4501 5.021 %
Rwork0.2139 85150 -
all0.216 --
obs-89651 99.469 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.609 Å2
Baniso -1Baniso -2Baniso -3
1-1.379 Å20 Å20 Å2
2--0.651 Å2-0 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 2.102→40.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11387 0 24 272 11683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01311695
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710717
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.63215909
X-RAY DIFFRACTIONr_angle_other_deg1.1371.57124681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89751548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3322.66515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.332151760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6241553
X-RAY DIFFRACTIONr_chiral_restr0.0380.21513
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022405
X-RAY DIFFRACTIONr_nbd_refined0.1660.22143
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.210057
X-RAY DIFFRACTIONr_nbtor_refined0.1470.25643
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.24835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2428
X-RAY DIFFRACTIONr_metal_ion_refined0.1380.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.213
X-RAY DIFFRACTIONr_nbd_other0.2180.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.27
X-RAY DIFFRACTIONr_mcbond_it0.1971.8666165
X-RAY DIFFRACTIONr_mcbond_other0.1971.8666163
X-RAY DIFFRACTIONr_mcangle_it0.3492.7977701
X-RAY DIFFRACTIONr_mcangle_other0.3492.7977701
X-RAY DIFFRACTIONr_scbond_it0.1931.8965530
X-RAY DIFFRACTIONr_scbond_other0.1871.885515
X-RAY DIFFRACTIONr_scangle_it0.3292.8368201
X-RAY DIFFRACTIONr_scangle_other0.3232.8128178
X-RAY DIFFRACTIONr_lrange_it3.82822.39312588
X-RAY DIFFRACTIONr_lrange_other3.79722.22812537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.102-2.1560.3623190.3259060.32365200.7540.7795.47550.301
2.156-2.2150.313510.30260440.30364030.8110.81899.87510.279
2.215-2.2790.2893080.26959590.2762730.8590.86499.90440.241
2.279-2.3490.3072910.25557030.25859940.8570.8721000.225
2.349-2.4260.2712660.24756130.24858860.8810.88699.88110.221
2.426-2.5110.2752670.24653820.24756970.8810.89399.15750.22
2.511-2.6050.2922670.23752320.2455030.8790.9199.92730.212
2.605-2.7110.2912730.23350320.23653050.8830.9171000.21
2.711-2.8310.2622410.23448060.23650520.910.9299.9010.212
2.831-2.9680.2932460.24346320.24648830.8950.91399.89760.224
2.968-3.1280.2642440.24443900.24546370.9070.90899.93530.228
3.128-3.3160.2672390.23341590.23544020.9110.92399.90910.222
3.316-3.5430.251950.21439560.21541510.9210.9351000.207
3.543-3.8250.2352060.19836830.238920.9330.94899.92290.196
3.825-4.1860.2031520.17334430.17435990.9530.96299.88890.175
4.186-4.6740.21770.15730630.15932590.9610.9799.4170.165
4.674-5.3850.1931480.1727230.17229060.9630.96598.79560.179
5.385-6.5650.2741440.19923690.20325140.9280.94299.96020.205
6.565-9.1620.206930.17819120.1820050.9580.9621000.191
9.162-40.0030.188740.20211430.20112250.9650.96299.34690.222
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)
11.3232-0.14040.33651.2397-0.70033.93730.0747-0.37460.01780.517-0.0096-0.189-0.3730.3367-0.06510.4282-0.0029-0.0370.218-0.05870.14350.36446.3239-44.1328
23.7517-1.5781.56493.1423-0.68982.9106-0.0601-0.27520.10190.34580.07390.1664-0.2316-0.3359-0.01370.30030.04740.07190.224-0.01480.03-11.01547.4103-54.4797
33.45720.1643-0.10324.15290.99016.2780.061-0.2874-0.17160.6201-0.12480.39180.5203-0.55990.06380.4219-0.0179-0.02020.24380.0410.1397-5.3199-11.111-51.4046
46.4243-0.4789-2.93413.65680.7331.7353-0.5645-0.4418-0.70760.76360.05460.48150.6236-0.20470.50990.9837-0.15320.08610.77360.0170.3012-5.442-15.1387-38.6119
52.3518-0.79291.04782.0281-0.19372.8890.0045-0.26310.11280.4997-0.00670.0196-0.3438-0.2660.00220.49850.08110.04690.2868-0.050.0195-7.87899.6482-45.7984
66.07481.6851-0.90664.4655-2.58222.991-0.0978-0.48610.33380.77390.0058-0.0196-0.4174-0.61750.09190.58520.14670.12680.4967-0.07290.0994-17.399615.1761-42.9532
79.99481.83713.81720.45770.72251.55730.1707-0.5174-0.06560.2037-0.11340.16770.1558-0.4339-0.05720.6425-0.02230.13190.68020.0830.3368-22.53621.3053-33.0002
84.73711.2371-3.06590.3318-0.79352.1244-0.0773-0.39-0.2290.0446-0.0915-0.01220.1877-0.09350.16881.0792-0.06480.1820.98180.09360.3253-20.2885-2.4645-34.397
90.9341-0.05571.29241.06090.85885.14150.0427-0.39240.12650.4265-0.04640.3541-0.0636-0.8960.00380.43980.09240.21090.58270.01130.2533-23.03737.7246-46.9285
104.2708-0.58530.41473.57860.01432.24150.0722-0.2568-0.10840.19810.01280.4355-0.166-0.6418-0.0850.34170.10420.12680.50480.02090.1143-23.72937.6456-55.1175
111.5547-0.54060.2541.96740.39053.8075-0.00520.16830.2282-0.3892-0.10250.3058-0.671-0.31880.10770.24730.1189-0.02190.19340.02250.1812-17.749611.697-86.1209
124.822-1.36490.46642.518-0.02182.2411-0.0069-0.1203-0.04860.20450.0272-0.166-0.0959-0.0336-0.02030.1280.02680.02080.0190.00260.0407-2.50981.5489-70.5866
134.653-1.1180.33118.65170.10554.59160.01330.1526-0.056-0.17590.12540.5144-0.0949-0.7628-0.13870.18710.0952-0.03220.4108-0.01160.2657-26.75827.2571-80.6678
143.7419-5.24452.980611.63011.741310.5819-0.0768-0.1299-0.0150.23410.1-0.00910.122-0.1419-0.02320.1493-0.02760.04640.28890.05460.2653-21.58011.1784-73.4293
152.796-1.06611.21424.05111.50315.39480.0768-0.1417-0.3505-0.07150.39090.40730.6237-0.7503-0.46770.2153-0.0891-0.02930.45740.03130.3734-26.9394-3.6973-72.4582
164.12240.23830.78851.289-2.08444.41120.08130.0181-0.4224-0.50620.37390.50020.9388-1.2053-0.45520.3965-0.1274-0.1270.7391-0.15430.7053-30.4582-2.9664-82.6493
171.27090.03170.03722.45910.2611.82230.08060.1346-0.0039-0.2455-0.0529-0.1555-0.1223-0.0504-0.02770.13750.06850.03190.06360.01250.0124-3.89271.5766-83.3542
180.7194-0.85990.41818.9095-1.36822.21420.00580.1113-0.4714-0.5953-0.01610.44790.454-0.43250.01030.38780.0069-0.01140.3664-0.12140.3869-12.6883-11.3007-96.2251
191.65030.05080.34662.43660.02793.22940.09940.0268-0.1996-0.0545-0.0582-0.15950.20750.0478-0.04120.1220.05130.00230.0331-0.01190.0847-1.5695-7.7567-77.6301
203.0668-4.98461.07569.0188-2.88041.8602-0.0899-0.0729-0.2203-0.01020.06460.13860.24330.06920.02530.3664-0.00220.0030.35830.00050.4654-8.9387-23.0943-66.8476
211.14510.0128-0.03581.09680.06793.6309-0.10830.3570.1593-0.29050.1354-0.4055-0.06020.7697-0.02710.3358-0.08530.00990.42750.0080.223828.903342.1527-39.9037
222.3381.68-0.78314.1165-0.5962.9402-0.14560.08470.07070.04470.16120.08760.0732-0.1384-0.01560.24920.0031-0.02670.26010.02390.055517.736138.2647-27.4796
236.9029-1.4063.04244.2092-1.67585.7714-0.0294-0.0417-0.0180.01130.00610.3423-0.4209-0.18290.02330.4303-0.016-0.04660.22330.0180.235718.001255.5441-28.4382
243.4054-1.31740.18781.5618-1.16794.23270.02920.2950.0728-0.1204-0.1120.3057-0.2991-0.40830.08280.55110.0111-0.10480.3045-0.00140.288714.778958.7072-32.4615
252.16491.1999-0.48351.70.25512.7827-0.12390.17230.2225-0.05330.1168-0.1249-0.13990.19650.00710.2774-0.0507-0.02380.32870.01860.096623.477942.1436-38.2768
262.7037-0.0632-0.58783.6594-0.15564.59-0.15990.3483-0.2584-0.08350.14510.10380.6998-0.21850.01470.3592-0.12320.00590.3331-0.02460.061613.245526.8279-36.3406
2710.0397-0.225-6.66570.39340.24454.7194-0.09630.46020.3253-0.10180.15140.4156-0.0869-0.631-0.05510.44030.0271-0.12960.60470.11080.4834.517942.2063-46.871
281.6939-0.75953.82742.4575-3.15529.7615-0.2440.20870.1518-0.1755-0.01550.0229-0.4970.14760.25940.50420.110.01080.62920.08890.48952.322946.9436-41.3075
291.51740.2709-1.13271.2102-0.1284.869-0.06490.2083-0.151-0.04540.05540.41150.4249-0.7320.00950.318-0.1129-0.01970.43940.03790.19745.684931.0946-32.5274
3012.92221.48922.51565.07961.20061.03560.3129-0.03440.8304-0.0959-0.34410.33-0.0484-0.50550.03120.40080.03790.05310.56480.08790.50390.942945.4089-21.1122
311.61292.60570.01964.2722-0.09241.36340.6287-0.30630.10981.097-0.29850.2090.6954-0.7249-0.33020.9842-0.1349-0.01520.81860.15060.256313.450927.745314.1598
323.19451.03730.49432.7123-0.15591.95970.1224-0.0952-0.08180.253-0.1323-0.24770.0890.11910.00980.37320.0187-0.05230.28110.02340.036323.407634.507-10.2777
333.1684-0.39961.08353.5557-1.00495.49720.183-0.27360.1850.3576-0.33420.1033-0.024-0.28580.15130.4892-0.10330.10070.41010.010.18144.484730.865-3.0047
345.3233-3.5317-1.25074.69364.09955.4402-0.3112-0.25530.65910.13670.02040.1647-0.5817-0.35130.29080.750.06920.24480.60270.01940.5299-0.921743.3421-6.4319
350.21440.10390.43290.07220.26191.0113-0.02550.01480.15010.0065-0.06320.0043-0.0001-0.06510.08870.531-0.01220.02360.4918-0.00510.50720.202542.10998.0997
360.0185-0.01360.06140.14210.33261.5548-0.0695-0.0821-0.03350.2214-0.10510.14160.2344-0.45680.17460.9475-0.18850.14610.69040.01890.19359.913130.5036.8242
371.28791.08870.12542.493-0.54444.44810.1397-0.2013-0.16610.3994-0.1973-0.41620.18050.65750.05750.4690.0125-0.14080.37590.05050.129631.115737.3485-1.3395
380.1591-0.77370.61426.4391-2.28244.6576-0.0745-0.15150.13310.7001-0.1268-0.2018-0.4989-0.64180.20130.7910.03850.04980.7027-0.15710.362517.165249.804610.64
391.0910.11770.48780.9388-1.25145.18310.0345-0.19140.28590.4732-0.1072-0.1264-0.50740.24160.07270.5373-0.0336-0.07510.312-0.02120.157725.67648.6104-0.8148
406.1603-0.16340.12092.7227-0.63653.1066-0.0462-0.23520.71970.31130.0351-0.1838-0.41660.28450.01110.4979-0.0295-0.07670.3237-0.02050.167627.067850.4364-7.9279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 55
2X-RAY DIFFRACTION2ALLA56 - 99
3X-RAY DIFFRACTION3ALLA100 - 150
4X-RAY DIFFRACTION4ALLA151 - 174
5X-RAY DIFFRACTION5ALLA175 - 236
6X-RAY DIFFRACTION6ALLA237 - 256
7X-RAY DIFFRACTION7ALLA257 - 275
8X-RAY DIFFRACTION8ALLA276 - 299
9X-RAY DIFFRACTION9ALLA300 - 357
10X-RAY DIFFRACTION10ALLA358 - 385
11X-RAY DIFFRACTION11ALLB1 - 49
12X-RAY DIFFRACTION12ALLB50 - 91
13X-RAY DIFFRACTION13ALLB92 - 108
14X-RAY DIFFRACTION14ALLB109 - 118
15X-RAY DIFFRACTION15ALLB119 - 145
16X-RAY DIFFRACTION16ALLB146 - 180
17X-RAY DIFFRACTION17ALLB181 - 266
18X-RAY DIFFRACTION18ALLB267 - 290
19X-RAY DIFFRACTION19ALLB291 - 380
20X-RAY DIFFRACTION20ALLB381 - 389
21X-RAY DIFFRACTION21ALLC1 - 50
22X-RAY DIFFRACTION22ALLC51 - 115
23X-RAY DIFFRACTION23ALLC116 - 140
24X-RAY DIFFRACTION24ALLC141 - 169
25X-RAY DIFFRACTION25ALLC170 - 212
26X-RAY DIFFRACTION26ALLC213 - 254
27X-RAY DIFFRACTION27ALLC255 - 282
28X-RAY DIFFRACTION28ALLC283 - 301
29X-RAY DIFFRACTION29ALLC302 - 374
30X-RAY DIFFRACTION30ALLC375 - 385
31X-RAY DIFFRACTION31ALLD1 - 28
32X-RAY DIFFRACTION32ALLD29 - 91
33X-RAY DIFFRACTION33ALLD92 - 128
34X-RAY DIFFRACTION34ALLD129 - 155
35X-RAY DIFFRACTION35ALLD156 - 171
36X-RAY DIFFRACTION36ALLD172 - 198
37X-RAY DIFFRACTION37ALLD199 - 254
38X-RAY DIFFRACTION38ALLD255 - 301
39X-RAY DIFFRACTION39ALLD302 - 352
40X-RAY DIFFRACTION40ALLD353 - 386

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