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- PDB-6v9k: CRYSTAL STRUCTURE OF THE HYBRID C-TERMINAL DOMAIN OF ENZYME I OF ... -

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Entry
Database: PDB / ID: 6v9k
TitleCRYSTAL STRUCTURE OF THE HYBRID C-TERMINAL DOMAIN OF ENZYME I OF THE BACTERIAL PHOSPHOTRANSFERASE SYSTEM FORMED BY HYBRIDIZING THE SCAFFOLD OF THE ESCHERICHIA COLI ENZYME WITH THE ACTIVE SITE LOOPS FROM THE THERMOANAEROBACTER TENGCONGENSIS 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 / N-acetylglucosamine transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / metal ion binding / identical protein binding / cytosol
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,9864
Polymers70,9372
Non-polymers492
Water10,413578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-38 kcal/mol
Surface area23340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.380, 69.530, 84.657
Angle α, β, γ (deg.)90.000, 108.730, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 35468.711 Da / Num. of mol.: 2
Mutation: V278P, R279K, F301Y, D305N, A306S, T309S, M334L, M345L, N346D, F347M, E351M, W357Y, G466M, D468E, M469H, I470V, S471K, H472E, L473Y, M477F, S478H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ptsI, E5E93_16640 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A4S4CN20, UniProt: P08839*PLUS, phosphoenolpyruvate-protein phosphotransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.0 and 20% w/v PEG 6000

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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 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 Å / Relative weight: 1
ReflectionResolution: 1.9→42.82 Å / Num. obs: 49363 / % possible obs: 99 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.044 / Rrim(I) all: 0.117 / Net I/σ(I): 15.3 / Num. measured all: 348445 / Scaling rejects: 389
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.9 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.940.8352223432120.7820.3420.9042.399.8
9.11-42.820.025324247310.010.02752.496.9

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Processing

Software
NameVersionClassification
PHENIX1.14.3260refinement
XDSdata reduction
Aimless0.7.2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xz7

2xz7


Resolution: 1.9→42.815 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 2471 5.02 %
Rwork0.1606 46796 -
obs0.1627 49267 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.01 Å2 / Biso mean: 28.1105 Å2 / Biso min: 9.17 Å2
Refinement stepCycle: final / Resolution: 1.9→42.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4868 0 2 578 5448
Biso mean--34.88 37.67 -
Num. residues----620
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9001-1.93660.25711350.2559261199
1.9366-1.97610.26871690.23042588100
1.9761-2.01910.2751430.2158257499
2.0191-2.06610.25781270.20362624100
2.0661-2.11770.21091400.19322627100
2.1177-2.1750.2181540.17592555100
2.175-2.2390.22521220.1725265199
2.239-2.31130.21341580.1623255399
2.3113-2.39390.21881350.15932627100
2.3939-2.48970.19791360.1568260399
2.4897-2.6030.19741630.1543257099
2.603-2.74020.19131300.1582260399
2.7402-2.91180.1835880.1453266099
2.9118-3.13660.20111530.1487258499
3.1366-3.45210.19121330.1416257798
3.4521-3.95140.19661390.1307254797
3.9514-4.97710.16411330.1251257096
4.9771-42.8150.19751130.1842267298
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)
10.47861.47180.00094.7644-0.64851.86890.05050.30960.4107-0.2146-0.04990.4841-0.25-0.2437-0.02570.20370.0687-0.00280.19310.00410.166414.87283.67826.8331
25.0561.01870.25394.7302-0.40963.0861-0.0098-0.11760.11430.1176-0.00280.6022-0.3186-0.5848-0.01890.18440.075-0.00980.2299-0.06270.20683.7143-8.7877.0456
30.6025-0.06741.31570.8816-0.1333.29370.05440.0193-0.057-0.0869-0.03110.09480.1425-0.2726-0.0180.1385-0.0027-0.01380.1529-0.00820.124711.7994-17.57688.0445
40.8944-0.17840.29411.6179-0.32471.7773-0.01880.02430.1570.0288-0.0322-0.129-0.27380.0470.02890.12230.0016-0.00080.09520.00590.14326.2282-0.332819.1962
53.1634-2.5643-1.86312.56341.71842.0366-0.1272-0.2447-0.31950.25640.01870.12580.20410.09860.10050.1517-0.0032-0.01490.11250.0160.159332.898-32.355945.2873
62.229-0.6788-1.97713.25420.89293.2901-0.0230.0719-0.19230.1334-0.0130.36270.0836-0.1986-0.06080.1352-0.0332-0.00980.11650.01540.156822.2687-22.125852.9442
70.4333-0.47170.59010.8962-0.37523.2555-0.0135-0.11060.00580.09950.02760.009-0.1405-0.06270.00070.1099-0.0029-0.00540.1093-0.00830.112326.3229-12.052147.8469
81.1428-0.60770.4621.1295-0.30561.53670.12880.1034-0.1696-0.1331-0.06260.05730.26010.0493-0.05210.13420.0144-0.00190.0996-0.0080.132332.5189-27.32728.5742
9-0000000000-027309.8242000.35580.04220.01630.5864-0.06020.446113.4189-10.75919.6352
100000-000001087776.37526538.80470.5462-0.16840.10760.42780.02080.287721.1005-19.693137.2879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 261 through 300 )A261 - 300
2X-RAY DIFFRACTION2chain 'A' and (resid 301 through 342 )A301 - 342
3X-RAY DIFFRACTION3chain 'A' and (resid 343 through 438 )A343 - 438
4X-RAY DIFFRACTION4chain 'A' and (resid 439 through 570 )A439 - 570
5X-RAY DIFFRACTION5chain 'B' and (resid 261 through 300 )B261 - 300
6X-RAY DIFFRACTION6chain 'B' and (resid 301 through 342 )B301 - 342
7X-RAY DIFFRACTION7chain 'B' and (resid 343 through 438 )B343 - 438
8X-RAY DIFFRACTION8chain 'B' and (resid 439 through 570 )B439 - 570
9X-RAY DIFFRACTION9chain 'A' and resi 859A261 - 859
10X-RAY DIFFRACTION10chain 'B' and resi 859B261 - 859

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