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- PDB-6vbj: CRYSTAL STRUCTURE OF THE HYBRID C-TERMINAL DOMAIN OF ENZYME I OF ... -

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Entry
Database: PDB / ID: 6vbj
TitleCRYSTAL STRUCTURE OF THE HYBRID C-TERMINAL DOMAIN OF ENZYME I OF THE BACTERIAL PHOSPHOTRANSFERASE SYSTEM FORMED BY HYBRIDIZING THE SCAFFOLD OF THE THERMOANAEROBACTER TENGCONGENSIS ENZYME WITH THE ACTIVE SITE LOOPS FROM THE ESCHERICHIA COLI ENZYME
ComponentsPhosphoenolpyruvate-protein phosphotransferase
KeywordsTRANSFERASE / phosphoenolpyruvate-protein phosphotransferase PtsI / Hybrid / bacterial phosphotransferase
Function / homology
Function and homology information


phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / metal ion binding / cytoplasm
Similarity search - Function
Phosphotransferase system, enzyme I / Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / : / PEP-utilising enzyme, N-terminal / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. ...Phosphotransferase system, enzyme I / Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / : / PEP-utilising enzyme, N-terminal / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Phosphoenolpyruvate-protein phosphotransferase
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStewart Jr., C.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133488 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Hybrid Thermophilic/Mesophilic Enzymes Reveal a Role for Conformational Disorder in Regulation of Bacterial Enzyme I.
Authors: Dotas, R.R. / Nguyen, T.T. / Stewart Jr., C.E. / Ghirlando, R. / Potoyan, D.A. / Venditti, V.
History
DepositionDec 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: 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 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoenolpyruvate-protein phosphotransferase
B: Phosphoenolpyruvate-protein phosphotransferase


Theoretical massNumber of molelcules
Total (without water)69,7832
Polymers69,7832
Non-polymers00
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-17 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.430, 85.420, 95.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Phosphoenolpyruvate-protein phosphotransferase / Phosphotransferase system / enzyme I


Mass: 34891.395 Da / Num. of mol.: 2
Mutation: P278V, K279R, Y301F, N305D, S306A, S309T, L334M, L345M, D346N, M347F, M351E, Y357W, M466G, E468D, H469M, V470I, K471S, E472H, Y473L, F477M, H478S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Gene: PtsA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8R7R4, phosphoenolpyruvate-protein phosphotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITED SEQUENCE IS A HYBRID C-TERMINAL DOMAIN OF ENZYME I OF THE BACTERIAL ...THE DEPOSITED SEQUENCE IS A HYBRID C-TERMINAL DOMAIN OF ENZYME I OF THE BACTERIAL PHOSPHOTRANSFERASE SYSTEM FORMED BY HYBRIDIZING THE SCAFFOLD OF THE THERMOANAEROBACTER TENGCONGENSIS ENZYME WITH THE ACTIVE SITE LOOPS FROM THE ESCHERICHIA COLI ENZYME

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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: 43.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.03 M Sodium nitrate, 0.03 M Sodium phosphate dibasic, 0.03 M Ammonium sulfate, 0.1 M Tris-Bicine pH 8.5 and 12.5% MPD, 12.5%PEG 1000, 12.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 20, 2018 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.8→48.37 Å / Num. obs: 48831 / % possible obs: 85.6 % / Redundancy: 10.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.031 / Rrim(I) all: 0.108 / Net I/σ(I): 14.4 / Num. measured all: 513772 / Scaling rejects: 347
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.843.52.32366510350.4261.4242.7420.331.7
9-48.3712.80.04870045470.9990.0140.05140.799.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.2data scaling
PHASERphasing
PHENIX1.14refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XZ7

2xz7


Resolution: 2→42.71 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2295 1997 4.88 %
Rwork0.1911 38891 -
obs0.193 40888 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.77 Å2 / Biso mean: 38.9642 Å2 / Biso min: 13.82 Å2
Refinement stepCycle: final / Resolution: 2→42.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4862 0 0 433 5295
Biso mean---36.68 -
Num. residues----626
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.050.30431280.276230983
2.05-2.10550.271290.2384255191
2.1055-2.16740.25841500.2159272497
2.1674-2.23740.25461420.2022781100
2.2374-2.31730.25311350.1962831100
2.3173-2.41010.22261450.19312787100
2.4101-2.51980.22231440.18792827100
2.5198-2.65260.29361390.19882815100
2.6526-2.81880.25831360.20582815100
2.8188-3.03640.25741440.2162832100
3.0364-3.34180.21281390.1922851100
3.3418-3.82510.20781520.17292855100
3.8251-4.81820.19561700.15122872100
4.8182-42.710.21891440.19543041100
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)
11.62660.8840.3351.5-0.25161.4478-0.3149-0.0094-0.05450.0094-0.2656-0.22850.0240.10670.34320.20390.04410.01290.29250.01360.379838.95723.051840.0776
22.14250.3950.56081.79540.32721.3264-0.05150.3366-0.2612-0.14130.0745-0.25680.10490.06430.00270.2768-0.0050.09090.2349-0.03930.258529.475816.818124.7217
31.75820.2763-0.24322.13940.68351.2381-0.01760.28730.1619-0.3649-0.05050.0342-0.1038-0.11590.15080.23430.00060.04040.22160.03180.214224.629924.026623.1937
41.12130.6631-0.34152.89520.06240.2411-0.03040.20730.1813-0.19030.08090.1426-0.2533-0.1004-0.06740.27080.0134-0.03990.22810.03560.157614.915532.671120.9142
50.97620.0101-0.29981.4964-0.12071.5999-0.04950.1559-0.0832-0.15790.16280.00530.0491-0.1107-0.05210.1672-0.02140.01280.1505-0.01110.158219.909817.303630.1004
61.0064-0.68830.32868.2281.41711.2297-0.052-0.0486-0.11370.2110.03830.7466-0.10120.1145-0.03680.2154-0.01070.03540.2260.02230.291610.474816.805232.9265
70.2534-0.39450.31763.57490.65541.037-0.0728-0.05240.01460.25040.1619-0.28910.05970.0718-0.110.1505-0.0080.03760.1884-0.02070.157118.748820.794236.6897
80.6792-0.38650.46532.5418-0.70051.2021-0.03990.02570.00350.0167-0.026-0.2196-0.0354-0.01340.06480.12810.00750.0080.1887-0.00490.152924.353438.386837.3711
91.1019-0.51570.48940.9283-0.35891.9285-0.15380.08490.17850.0320.0236-0.21570.17660.02570.04780.17770.0179-0.02510.2312-0.0040.241733.273932.330842.3279
101.6685-0.23680.49142.01270.41051.83510.0745-0.14360.0730.1854-0.0987-0.3909-0.15080.10380.04070.2-0.0174-0.05150.18620.01940.273239.711735.774548.8051
115.9373-1.908-0.1623.36330.53433.3169-0.071-0.40911.0514-0.1392-0.1876-0.6799-0.49670.55710.12920.3307-0.0402-0.05840.35180.00130.577740.818647.687844.3531
120.99060.979-1.25321.0096-1.68735.06190.0031-0.06960.00170.2861-0.1720.1973-0.4433-0.12040.02960.35170.03060.04820.1574-0.00970.2941-1.544161.915541.8317
131.36440.0724-0.24971.6138-0.09040.6724-0.02310.17930.1159-0.2961-0.00580.1773-0.1216-0.03130.04090.2422-0.0136-0.04630.2109-0.00950.17588.36667.925424.728
140.62170.13250.37551.5205-0.3630.5664-0.04550.09810.0271-0.24490.0173-0.2368-0.01490.05960.04650.2083-0.01520.02840.1854-0.01970.184220.256262.22124.9107
150.438-0.82850.16223.6427-0.92430.2458-0.10360.01820.10030.21540.1205-0.51760.0036-0.01920.00520.198-0.0168-0.0180.1858-0.03110.198522.537867.251835.2567
160.5481-0.8048-0.4812.67050.65090.993-0.09170.02470.02260.1590.00980.20680.1157-0.01610.06320.180.008-0.0010.19360.01930.157312.123447.771736.7593
171.5128-0.02830.02871.80260.18091.2968-0.087-0.0296-0.16070.29380.07720.32760.0231-0.11980.02250.21430.03020.0450.18910.02250.2672-0.674552.705543.4671
186.0455-1.9612-0.56783.84860.17272.8051-0.38560.4804-1.18270.1930.14310.79390.5386-0.29580.19730.3491-0.06170.0820.3093-0.05820.6414-4.797339.240341.7295
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 260 through 286 )A260 - 286
2X-RAY DIFFRACTION2chain 'A' and (resid 287 through 323 )A287 - 323
3X-RAY DIFFRACTION3chain 'A' and (resid 324 through 347 )A324 - 347
4X-RAY DIFFRACTION4chain 'A' and (resid 348 through 366 )A348 - 366
5X-RAY DIFFRACTION5chain 'A' and (resid 367 through 395 )A367 - 395
6X-RAY DIFFRACTION6chain 'A' and (resid 396 through 415 )A396 - 415
7X-RAY DIFFRACTION7chain 'A' and (resid 416 through 438 )A416 - 438
8X-RAY DIFFRACTION8chain 'A' and (resid 439 through 495 )A439 - 495
9X-RAY DIFFRACTION9chain 'A' and (resid 496 through 526 )A496 - 526
10X-RAY DIFFRACTION10chain 'A' and (resid 527 through 554 )A527 - 554
11X-RAY DIFFRACTION11chain 'A' and (resid 555 through 572 )A555 - 572
12X-RAY DIFFRACTION12chain 'B' and (resid 260 through 278 )B260 - 278
13X-RAY DIFFRACTION13chain 'B' and (resid 279 through 342 )B279 - 342
14X-RAY DIFFRACTION14chain 'B' and (resid 343 through 395 )B343 - 395
15X-RAY DIFFRACTION15chain 'B' and (resid 396 through 438 )B396 - 438
16X-RAY DIFFRACTION16chain 'B' and (resid 439 through 495 )B439 - 495
17X-RAY DIFFRACTION17chain 'B' and (resid 496 through 554 )B496 - 554
18X-RAY DIFFRACTION18chain 'B' and (resid 555 through 572 )B555 - 572

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