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- PDB-7rnp: Engineered tryptophan synthase b-subunit from Pyrococcus furiosus... -

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Basic information

Entry
Database: PDB / ID: 7rnp
TitleEngineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9_H275E with 4-Cl-Trp non-covalently bound
ComponentsTryptophan synthase beta chain 1
KeywordsBIOSYNTHETIC PROTEIN / tryptophan synthase
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
4-chloro-L-tryptophan / Tryptophan synthase beta chain 1
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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)175,00810
Polymers174,4394
Non-polymers5696
Water36020
1
A: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5045
Polymers87,2192
Non-polymers2853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-36 kcal/mol
Surface area25100 Å2
MethodPISA
2
B: Tryptophan synthase beta chain 1
C: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5045
Polymers87,2192
Non-polymers2853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-38 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.162, 81.198, 321.014
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) / 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-6G5 / 4-chloro-L-tryptophan


Mass: 238.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11ClN2O2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 20 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.85 / Details: 13-21% PEG3350 and 0.1 M Na HEPES pH 7.85

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.25→40.003 Å / Num. obs: 69911 / % possible obs: 98.8 % / Redundancy: 13.4 % / CC1/2: 0.998 / Rpim(I) all: 0.046 / Net I/σ(I): 8.8
Reflection shellResolution: 2.25→2.3 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4372 / CC1/2: 0.703 / Rpim(I) all: 0.825

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AM8
Resolution: 2.25→40.003 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 29.015 / SU ML: 0.292 / Cross valid method: FREE R-VALUE / ESU R: 0.378 / ESU R Free: 0.252
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2666 3482 4.982 %
Rwork0.2273 66413 -
all0.229 --
obs-69895 98.448 %
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: 63.805 Å2
Baniso -1Baniso -2Baniso -3
1--0.161 Å20 Å20 Å2
2--3.811 Å2-0 Å2
3----3.649 Å2
Refinement stepCycle: LAST / Resolution: 2.25→40.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11156 0 36 20 11212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01311440
X-RAY DIFFRACTIONr_bond_other_d0.0020.01710551
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.63615587
X-RAY DIFFRACTIONr_angle_other_deg1.1781.57624086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59251530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96322.282482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.142151629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3771552
X-RAY DIFFRACTIONr_chiral_restr0.0420.21503
X-RAY DIFFRACTIONr_chiral_restr_other1.7950.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022546
X-RAY DIFFRACTIONr_nbd_refined0.1740.22194
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.29977
X-RAY DIFFRACTIONr_nbtor_refined0.1520.25564
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.24833
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2236
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.210
X-RAY DIFFRACTIONr_nbd_other0.1960.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2750.22
X-RAY DIFFRACTIONr_mcbond_it0.8723.5066114
X-RAY DIFFRACTIONr_mcbond_other0.8733.5066113
X-RAY DIFFRACTIONr_mcangle_it1.4325.2597634
X-RAY DIFFRACTIONr_mcangle_other1.4325.2597635
X-RAY DIFFRACTIONr_scbond_it0.9013.6075326
X-RAY DIFFRACTIONr_scbond_other0.9013.6075327
X-RAY DIFFRACTIONr_scangle_it1.4855.3747949
X-RAY DIFFRACTIONr_scangle_other1.4855.3747950
X-RAY DIFFRACTIONr_lrange_it3.11941.88412220
X-RAY DIFFRACTIONr_lrange_other3.11641.8812219
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
2.25-2.3080.3982430.38147780.38251050.4480.46598.35460.353
2.308-2.3710.3622250.35247000.35250050.5670.58198.40160.32
2.371-2.440.3542240.33646520.33749470.6370.64698.56480.306
2.44-2.5150.3712430.30644190.30947310.7180.73698.54150.275
2.515-2.5970.3442160.28543540.28846310.7420.7998.68280.255
2.597-2.6870.3462230.26742020.27144760.8020.83898.86060.237
2.687-2.7880.2732080.25940620.25943220.8470.86698.79690.229
2.788-2.9020.2882100.2539190.25241730.8640.87498.94560.219
2.902-3.030.3261990.24337290.24739690.8550.88798.9670.214
3.03-3.1770.2562000.21833850.2238570.910.92292.94790.196
3.177-3.3480.2541820.20734260.20936370.920.93199.20260.192
3.348-3.5490.2791730.21833110.22135070.890.92399.34420.207
3.549-3.7920.2541630.20830850.2132680.9250.93599.3880.199
3.792-4.0930.2431300.19129170.19330640.9340.94899.44520.19
4.093-4.4790.2051560.18226680.18328380.9510.95799.50670.187
4.479-50.2071300.17924330.1825690.9570.95799.76640.194
5-5.7580.2741240.22121760.22423120.9030.9399.4810.234
5.758-7.0160.297950.23117740.23419870.9030.92394.06140.252
7.016-9.7730.272800.20714880.2115740.9390.94999.61880.242
9.773-40.0030.228570.2639200.2619860.9530.93999.08720.324
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)
12.87050.743-0.74581.36310.31253.27330.0021-0.1284-0.19670.157-0.08470.01470.461-0.32820.08260.3684-0.0273-0.0440.07410.02730.0664-10.085831.5635-81.3486
27.52450.24910.97811.96-0.07197.35070.0938-0.01340.13920.1163-0.05620.25880.0885-0.7318-0.03760.2817-0.0461-0.01350.2618-0.02850.0975-22.061433.6058-82.0187
32.9550.198-0.72859.4226-1.78145.7916-0.21270.06620.6694-0.29550.38410.5473-0.6903-0.4424-0.17140.38560.0088-0.01780.46060.00570.3715-26.102942.6991-85.0082
43.8422-0.09180.84224.98487.243713.3308-0.192-0.18941.12550.1398-0.16960.4854-0.82450.12650.36160.7313-0.02150.05540.5198-0.10290.6391-26.918545.5051-81.2251
59.47564.1951-3.36713.9923-0.41452.57510.2359-0.45210.57330.2556-0.22611.0487-0.0583-0.6047-0.00980.40960.00340.07350.71650.14230.3815-26.601434.5289-73.1793
61.89550.5058-0.80471.14450.41572.17110.124-0.3354-0.24330.2018-0.1561-0.22550.18930.13150.03210.3446-0.0749-0.03530.07670.05310.0575-2.079334.1481-78.4888
70.34921.6601-0.96228.0153-4.40423.30760.103-0.0308-0.01650.5278-0.0652-0.2165-0.2575-0.0111-0.03780.4173-0.02790.02680.3225-0.06230.2504-9.172449.7161-66.9449
85.5395-0.4305-0.24180.6912-1.19755.6909-0.2571-0.36660.25230.5234-0.04970.1851-0.8131-0.52290.30680.5601-0.07060.04930.2308-0.10360.3724-12.627454.2858-74.1959
91.7998-0.2163-1.14031.42670.05044.68550.2601-0.23120.28380.1116-0.1457-0.2023-0.16760.2441-0.11440.3102-0.0608-0.00950.0642-0.02390.08240.346645.267-82.3552
109.312-2.5286-1.756217.7746-2.77670.95490.20910.29360.17170.3805-0.16650.154-0.1397-0.0626-0.04260.40010.02720.00650.3509-0.03240.3387-12.112653.0883-92.9584
111.8328-0.34880.14920.0707-0.07641.8483-0.0072-0.3158-0.09190.00460.0452-0.01660.07430.2156-0.03810.570.0920.03680.47120.08640.42423.7375-6.4144-111.1435
124.5307-1.5388-0.48232.8805-0.31073.1634-0.1801-0.25810.13270.01370.0635-0.1772-0.32820.08070.11660.4539-0.0025-0.00080.19840.0060.030719.99066.9138-135.0302
1310.0025-1.38641.12014.5371-0.22915.37220.04970.0085-0.16220.1389-0.022-0.29420.17340.5451-0.02780.46950.09860.08310.21910.06720.126126.7505-9.8483-127.7389
146.99183.1177-1.67395.3518-2.32196.70890.01440.0014-0.2435-0.0714-0.04980.36630.345-0.38670.03540.51870.05520.0620.23770.01470.194816.1442-14.2086-134.5145
153.1070.80180.00321.51561.79293.04490.0056-0.8795-0.70720.5055-0.27360.19880.7055-0.24480.26810.7905-0.05470.16920.52850.1640.425813.6954-18.4991-124.6974
162.4679-0.89520.47932.4613-0.82333.4568-0.3137-0.40980.01780.27180.2606-0.148-0.3992-0.0150.0530.51840.09560.00640.28080.02820.01718.43335.2031-123.8074
175.57184.3487-6.82213.4168-5.34558.40270.3681-0.43940.2270.2139-0.19620.2145-0.27170.4403-0.1720.7553-0.07260.21080.9850.17010.622-4.1746-1.6557-121.3491
189.76781.53914.93850.32820.74812.58430.096-0.9248-0.32420.04550.02320.14890.1549-0.6796-0.11910.88190.04520.25710.7840.18740.56344.4366-5.5387-112.9587
191.1551-0.10580.26240.5116-0.52756.5742-0.1769-0.3108-0.01950.13090.170.2172-0.1451-1.12020.0070.48130.13370.0620.4380.07710.16653.51445.5226-127.695
204.06361.6512.21087.08911.30313.5566-0.1093-0.12190.0350.05310.06310.7398-0.0333-0.58470.04620.4240.07190.10260.40930.07230.13674.96367.427-135.5102
217.2333-1.0681.6231.7239-0.80680.58520.11080.12580.2655-0.3467-0.06220.20070.0785-0.015-0.04860.53370.030.01750.5410.03020.316313.16118.9238-178.3528
223.5802-1.43710.22032.6702-0.93172.6410.07260.30750.1007-0.1247-0.1207-0.1237-0.17180.06460.04820.4327-0.03610.04910.24690.04750.053420.58257.811-153.4776
234.91631.65971.26634.9659-4.66026.3775-0.14490.3154-0.0081-0.20340.1027-0.05860.0807-0.19110.04220.48710.11060.0150.45890.05220.06135.118611.3056-157.1715
244.64441.772-1.03575.04462.69026.78590.11040.4078-0.7821-0.4189-0.07630.41631.0509-0.2693-0.03410.79430.0246-0.19540.52140.00850.4472-1.5036-1.2413-155.2673
250.01950.09420.23590.49751.18762.90980.01670.01080.0035-0.0245-0.06320.02760.06870.01650.04640.62780.0478-0.0150.5217-0.00810.6216-1.4409-2.7676-168.848
269.2106-5.03-1.88182.89440.84450.87220.28350.9354-0.5496-0.2624-0.230.4482-0.15-0.6009-0.05340.71610.0142-0.07230.74410.20480.20266.007210.4786-167.9862
272.57-0.0876-0.65562.31980.0923.3807-0.00480.26620.0507-0.2843-0.0758-0.3714-0.15140.4220.08060.46980.00050.06710.31760.09490.083228.85613.5621-160.0324
280.1710.2210.34648.4221-0.96361.9437-0.05210.0666-0.1906-0.25910.13780.01220.1595-0.095-0.08570.4879-0.03310.04310.486-0.05560.384816.9112-6.3522-175.2281
291.4822-0.4481-0.23142.9278-2.01236.6995-0.02390.4367-0.3575-0.44740.00610.1010.6047-0.43150.01780.52210.00960.07440.318-0.08560.167421.4529-8.2987-162.3609
304.35960.9549-0.02452.8959-0.63553.39210.08760.3797-0.68990.0649-0.1816-0.22360.44520.02920.0940.59620.02590.09420.3035-0.00670.158726.0731-8.781-153.7942
317.5973-0.8384-1.06330.13620.25830.66720.19150.8917-0.00720.038-0.1157-0.05620.2893-0.1717-0.07590.7318-0.0830.02710.68270.04330.2755-3.460938.6431-131.5571
323.12271.3697-1.08142.917-1.05774.44950.02920.36540.0114-0.21190.0294-0.0270.2062-0.2378-0.05860.3866-0.0236-0.03020.1663-0.03440.0273-4.619435.4967-108.1914
333.7362-3.22791.35176.3615-2.5141.01230.1480.61490.3242-0.3652-0.1542-0.03880.1356-0.02850.00620.69850.12220.0430.89270.10710.6494-15.329956.1098-110.2662
342.14171.70971.90152.55610.72128.5814-0.49910.42250.6984-0.4947-0.34730.5025-0.8584-1.35760.84640.80990.2815-0.04711.21990.11980.2594-8.246653.9532-113.775
353.52121.7904-2.1522.307-1.65345.0518-0.07470.4122-0.0791-0.2960.047-0.01310.5884-0.44460.02780.5289-0.085-0.01030.3321-0.05920.0125-8.136531.3244-115.5485
367.3683-1.092-1.3256.13891.29072.37790.21460.6964-0.1833-0.464-0.2405-0.2510.3947-0.46140.02580.6778-0.1451-0.06340.6844-0.09560.0506-21.446825.635-118.178
377.2237-1.823-3.56020.61950.48752.87380.13270.1391-0.0169-0.08980.03650.12650.0461-0.2811-0.16920.5192-0.0084-0.06710.56910.01550.4117-20.543639.1454-128.3358
380.2989-0.00323.0090.0339-0.248432.9136-0.00470.06870.0115-0.05680.01580.0634-0.1158-0.0837-0.0110.55870.0773-0.03520.59770.02130.5276-24.880346.3205-129.1408
392.37860.1718-1.74370.60080.15397.1895-0.10530.68410.0428-0.23410.09290.32770.1831-1.09680.01240.5276-0.1288-0.13150.70030.04630.182-24.155233.7812-112.4624
404.73841.4279-1.21064.6780.37563.4981-0.1640.70210.287-0.4280.35860.62450.2119-1.0695-0.19460.5146-0.1266-0.11580.73950.07390.1262-24.31231.4848-105.6869
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 81
2X-RAY DIFFRACTION2ALLA82 - 117
3X-RAY DIFFRACTION3ALLA118 - 140
4X-RAY DIFFRACTION4ALLA141 - 169
5X-RAY DIFFRACTION5ALLA170 - 187
6X-RAY DIFFRACTION6ALLA188 - 256
7X-RAY DIFFRACTION7ALLA257 - 283
8X-RAY DIFFRACTION8ALLA284 - 300
9X-RAY DIFFRACTION9ALLA301 - 373
10X-RAY DIFFRACTION10ALLA374 - 384
11X-RAY DIFFRACTION11ALLB1 - 27
12X-RAY DIFFRACTION12ALLB28 - 84
13X-RAY DIFFRACTION13ALLB85 - 108
14X-RAY DIFFRACTION14ALLB109 - 146
15X-RAY DIFFRACTION15ALLB147 - 171
16X-RAY DIFFRACTION16ALLB172 - 250
17X-RAY DIFFRACTION17ALLB251 - 263
18X-RAY DIFFRACTION18ALLB264 - 294
19X-RAY DIFFRACTION19ALLB295 - 359
20X-RAY DIFFRACTION20ALLB360 - 384
21X-RAY DIFFRACTION21ALLC1 - 15
22X-RAY DIFFRACTION22ALLC16 - 86
23X-RAY DIFFRACTION23ALLC87 - 124
24X-RAY DIFFRACTION24ALLC125 - 153
25X-RAY DIFFRACTION25ALLC154 - 169
26X-RAY DIFFRACTION26ALLC170 - 196
27X-RAY DIFFRACTION27ALLC197 - 256
28X-RAY DIFFRACTION28ALLC257 - 281
29X-RAY DIFFRACTION29ALLC282 - 352
30X-RAY DIFFRACTION30ALLC353 - 384
31X-RAY DIFFRACTION31ALLD1 - 20
32X-RAY DIFFRACTION32ALLD21 - 128
33X-RAY DIFFRACTION33ALLD129 - 139
34X-RAY DIFFRACTION34ALLD140 - 170
35X-RAY DIFFRACTION35ALLD171 - 238
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