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- PDB-2xz7: CRYSTAL STRUCTURE OF THE PHOSPHOENOLPYRUVATE-BINDING DOMAIN OF EN... -

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Basic information

Entry
Database: PDB / ID: 2xz7
TitleCRYSTAL STRUCTURE OF THE PHOSPHOENOLPYRUVATE-BINDING DOMAIN OF ENZYME I IN COMPLEX WITH PHOSPHOENOLPYRUVATE FROM THE THERMOANAEROBACTER TENGCONGENSIS PEP-SUGAR PHOSPHOTRANSFERASE SYSTEM (PTS)
ComponentsPHOSPHOENOLPYRUVATE-PROTEIN KINASE (PTS SYSTEM EI COMPONENT IN BACTERIA)
KeywordsTRANSFERASE / THERMOPHILIC / PEP-UTILISING ENZYME
Function / homology
Function and homology information


phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / phosphorylation / 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 / Phosphoenolpyruvate-protein phosphotransferase
Similarity search - Component
Biological speciesTHERMOANAEROBACTER TENGCONGENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsWaltersperger, S.M. / Oberholzer, A.E. / Schneider, P. / Baumann, U. / Erni, B.
CitationJournal: Biochemistry / Year: 2011
Title: Phosphoenolpyruvate: Sugar Phosphotransferase System from the Hyperthermophilic Thermoanaerobacter Tengcongensis.
Authors: Navdaeva, V. / Zurbriggen, A. / Waltersperger, S.M. / Schneider, P. / Oberholzer, A.E. / Bahler, P. / Bachler, C. / Grieder, A. / Baumann, U. / Erni, B.
History
DepositionNov 23, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOENOLPYRUVATE-PROTEIN KINASE (PTS SYSTEM EI COMPONENT IN BACTERIA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4923
Polymers36,3001
Non-polymers1922
Water6,684371
1
A: PHOSPHOENOLPYRUVATE-PROTEIN KINASE (PTS SYSTEM EI COMPONENT IN BACTERIA)
hetero molecules

A: PHOSPHOENOLPYRUVATE-PROTEIN KINASE (PTS SYSTEM EI COMPONENT IN BACTERIA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9856
Polymers72,6002
Non-polymers3854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4730 Å2
ΔGint-40.5 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.499, 92.125, 47.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2068-

HOH

21A-2274-

HOH

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Components

#1: Protein PHOSPHOENOLPYRUVATE-PROTEIN KINASE (PTS SYSTEM EI COMPONENT IN BACTERIA)


Mass: 36300.027 Da / Num. of mol.: 1
Fragment: PHOSPHOENOLPYRUVATE-BINDING DOMAIN, RESIDUES 251-573
Source method: isolated from a genetically manipulated source
Details: COFACTOR-PHOSPHOENOLPYRUVATE
Source: (gene. exp.) THERMOANAEROBACTER TENGCONGENSIS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA (DE3)
References: UniProt: Q8R7R4, phosphoenolpyruvate-protein phosphotransferase
#2: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid


Mass: 168.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5O6P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→100 Å / Num. obs: 58115 / % possible obs: 93.6 % / Observed criterion σ(I): 2.05 / Redundancy: 1.8 % / Biso Wilson estimate: 8.16 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.17
Reflection shellResolution: 1.83→1.94 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.05 / % possible all: 87.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BG5

2bg5


Resolution: 1.83→61.868 Å / SU ML: 0.2 / σ(F): 1.99 / Phase error: 19.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1946 2891 5 %
Rwork0.1648 --
obs0.1663 58067 93.63 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.693 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 29.67 Å2
Baniso -1Baniso -2Baniso -3
1--5.9868 Å20 Å20 Å2
2--1.5731 Å20 Å2
3---4.4137 Å2
Refinement stepCycle: LAST / Resolution: 1.83→61.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 11 371 2914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032654
X-RAY DIFFRACTIONf_angle_d0.7623592
X-RAY DIFFRACTIONf_dihedral_angle_d13.0541060
X-RAY DIFFRACTIONf_chiral_restr0.052407
X-RAY DIFFRACTIONf_plane_restr0.003466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8289-1.85890.275930.25061873X-RAY DIFFRACTION66
1.8589-1.8910.31751440.25022686X-RAY DIFFRACTION96
1.891-1.92540.22841460.24072697X-RAY DIFFRACTION96
1.9254-1.96240.22791350.21442702X-RAY DIFFRACTION95
1.9624-2.00240.27191280.20242539X-RAY DIFFRACTION91
2.0024-2.0460.22461400.18392588X-RAY DIFFRACTION91
2.046-2.09360.2211380.17652641X-RAY DIFFRACTION97
2.0936-2.14590.22091430.17072789X-RAY DIFFRACTION98
2.1459-2.2040.21341450.17282704X-RAY DIFFRACTION98
2.204-2.26880.20351380.18782722X-RAY DIFFRACTION97
2.2688-2.34210.1981450.16122739X-RAY DIFFRACTION97
2.3421-2.42580.20531490.15772679X-RAY DIFFRACTION96
2.4258-2.52290.22431340.16082639X-RAY DIFFRACTION94
2.5229-2.63770.24661350.17462506X-RAY DIFFRACTION89
2.6377-2.77680.19181430.16962732X-RAY DIFFRACTION97
2.7768-2.95080.16491450.16132744X-RAY DIFFRACTION98
2.9508-3.17860.20581460.16652728X-RAY DIFFRACTION97
3.1786-3.49840.16881430.15022626X-RAY DIFFRACTION95
3.4984-4.00460.13471350.13722507X-RAY DIFFRACTION89
4.0046-5.0450.12441390.12412714X-RAY DIFFRACTION97
5.045-61.90350.18151270.14732621X-RAY DIFFRACTION93
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)
10.14270.40840.06061.22030.09011.95980.13190.46510.0941-0.1819-0.32760.28170.003-0.25880.14060.170.0404-0.02080.2934-0.02870.334612.649825.517410.7915
20.4907-0.12150.01241.3739-0.68340.52610.0618-0.05730.02890.038-0.03450.1868-0.0389-0.0837-0.0310.11860.0147-0.0110.1661-0.0350.144415.91434.548424.0882
30.79120.0597-0.21660.6403-0.27020.50110.06520.0582-0.1225-0.0201-0.06510.08950.0148-0.04790.00610.09090.0038-0.0110.0935-0.03250.116324.1937-7.271320.7197
41.08240.23450.88950.62720.44050.89390.0459-0.03170.15510.06-0.15850.08750.1278-0.11870.04540.13840.0275-0.00340.1393-0.01230.105236.73097.289715.1633
50.4686-0.0490.12690.2754-0.04820.30780.06460.06520.2125-0.2095-0.1301-0.0472-0.1168-0.01720.05670.20530.06160.00080.15930.01280.159725.639816.05698.9258
63.7021-1.69821.38971.1643-1.51282.6051-0.06430.37040.89-0.0528-0.2063-0.6987-0.4410.36640.2540.3108-0.00810.00680.17250.06380.363438.891721.29357.6164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 249:258)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 259:344)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 345:462)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 463:498)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 499:549)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 550:572)

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