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- PDB-2wqd: Crystal structure of enzyme I of the phosphoenolpyruvate:sugar ph... -

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Basic information

Entry
Database: PDB / ID: 2wqd
TitleCrystal structure of enzyme I of the phosphoenolpyruvate:sugar phosphotransferase system in the dephosphorylated state
ComponentsPHOSPHOENOLPYRUVATE-PROTEIN PHOSPHOTRANSFERASEPhosphoenolpyruvate—protein phosphotransferase
KeywordsTRANSFERASE / KINASE / CYTOPLASM / TRANSPORT / MAGNESIUM / PEP-UTILISING ENZYME / PHOSPHOTRANSFERASE SYSTEM / METAL-BINDING / SUGAR TRANSPORT / PHOSPHOENOLPYRUVATE
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. / PEP-utilising enzyme, C-terminal ...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 speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOberholzer, A.E. / Schneider, P. / Siebold, C. / Baumann, U. / Erni, B.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal Structure of Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System in the Dephosphorylated State.
Authors: Oberholzer, A.E. / Schneider, P. / Siebold, C. / Baumann, U. / Erni, B.
History
DepositionAug 19, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOENOLPYRUVATE-PROTEIN PHOSPHOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2412
Polymers63,2011
Non-polymers401
Water2,792155
1
A: PHOSPHOENOLPYRUVATE-PROTEIN PHOSPHOTRANSFERASE
hetero molecules

A: PHOSPHOENOLPYRUVATE-PROTEIN PHOSPHOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4814
Polymers126,4012
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area3940 Å2
ΔGint-40.65 kcal/mol
Surface area47830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.340, 98.340, 105.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PHOSPHOENOLPYRUVATE-PROTEIN PHOSPHOTRANSFERASE / Phosphoenolpyruvate—protein phosphotransferase / PHOSPHOTRANSFERASE SYSTEM\ / ENZYME I


Mass: 63200.625 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-572 COMPND 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P51183
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 191 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 365 TO SER

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 46.99 % / Description: NONE
Crystal growDetails: 0.2M KCL 20% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→35.91 Å / Num. obs: 23409 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 19.1 % / Biso Wilson estimate: 36.07 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 29.6
Reflection shellResolution: 2.4→2.54 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 6.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→35.906 Å / SU ML: 0.26 / σ(F): 1.4 / Phase error: 30.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2951 1747 7.5 %
Rwork0.2282 --
obs0.2331 23406 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.786 Å2 / ksol: 0.283 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3899 Å2-0 Å2-0 Å2
2---0.3899 Å20 Å2
3----10.6178 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4324 0 1 155 4480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034377
X-RAY DIFFRACTIONf_angle_d0.6615931
X-RAY DIFFRACTIONf_dihedral_angle_d14.3091611
X-RAY DIFFRACTIONf_chiral_restr0.047702
X-RAY DIFFRACTIONf_plane_restr0.002783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47060.38511430.31031748X-RAY DIFFRACTION100
2.4706-2.55040.34971430.28541797X-RAY DIFFRACTION100
2.5504-2.64150.33511430.27441763X-RAY DIFFRACTION100
2.6415-2.74720.32781440.26251793X-RAY DIFFRACTION100
2.7472-2.87220.33481440.26011772X-RAY DIFFRACTION100
2.8722-3.02360.33571420.28051800X-RAY DIFFRACTION100
3.0236-3.21290.33361490.27181798X-RAY DIFFRACTION100
3.2129-3.46080.34691460.25031798X-RAY DIFFRACTION100
3.4608-3.80870.27441420.22581807X-RAY DIFFRACTION100
3.8087-4.3590.26781490.18491821X-RAY DIFFRACTION100
4.359-5.48870.22971490.17111836X-RAY DIFFRACTION100
5.4887-35.90950.24211530.19151926X-RAY DIFFRACTION100
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)
11.53240.15820.3205-0.27720.71341.6781-0.354-0.07160.1345-0.03780.04170.11180.1901-0.29260.24410.22450.03280.01730.3642-0.0530.3548-50.155921.9667-11.4602
21.02210.7383-0.81330.2196-1.01561.4125-0.25690.1554-0.2107-0.121-0.05250.0010.2347-0.52730.24250.1044-0.09340.09610.3481-0.2160.2749-56.67148.301-7.6553
32.0593-0.1631-0.15190.3067-0.16930.9691-0.1044-0.13790.18150.12140.0103-0.05780.24470.00220.08320.31540.02080.03950.15660.01950.2182-33.453319.6047-17.6017
40.50681.2928-0.33121.98731.60092.75810.3703-0.2957-0.0256-0.1426-0.2354-0.03280.0772-1.5334-0.15770.1661-0.1559-0.12260.87510.26950.226-26.8761-10.0027-8.967
50.41960.22351.01141.51191.44083.90150.3626-0.3548-0.109-0.0276-0.0233-0.06550.1256-1.619-0.2936-0.0133-0.1561-0.06790.70220.29020.1636-21.9244-5.99114.6727
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:39)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 40:157)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 158:252)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 253:343)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 344:572)

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