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- PDB-3trc: Structure of the GAF domain from a phosphoenolpyruvate-protein ph... -

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Basic information

Entry
Database: PDB / ID: 3trc
TitleStructure of the GAF domain from a phosphoenolpyruvate-protein phosphotransferase (ptsP) from Coxiella burnetii
ComponentsPhosphoenolpyruvate-protein phosphotransferase
KeywordsTRANSFERASE / Signal transduction
Function / homology
Function and homology information


phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / membrane / metal ion binding / cytoplasm
Similarity search - Function
Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / : / PEP-utilising enzyme, N-terminal / 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 ...Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / : / PEP-utilising enzyme, N-terminal / 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 / GAF domain / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / phosphoenolpyruvate--protein phosphotransferase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Feb 10, 2016Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Phosphoenolpyruvate-protein phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0433
Polymers18,9251
Non-polymers1182
Water3,477193
1
A: Phosphoenolpyruvate-protein phosphotransferase
hetero molecules

A: Phosphoenolpyruvate-protein phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0876
Polymers37,8512
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2850 Å2
ΔGint-57 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.869, 54.869, 105.256
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phosphoenolpyruvate-protein phosphotransferase


Mass: 18925.365 Da / Num. of mol.: 1 / Mutation: UNP RESIDUES 8-175
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_1550, ptsP / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q83BF9, phosphoenolpyruvate-protein phosphotransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 295 K / pH: 7.5
Details: 0.1M HEPES pH 7.5, 1.4M tri-sodium citrate, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 28, 2011
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 20101 / Num. obs: 19760 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Rmerge(I) obs: 0.051 / Χ2: 1.067 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.682.60.3518880.373191.4
1.68-1.713.50.3249360.374196.9
1.71-1.744.20.2849410.369196.8
1.74-1.784.30.2419520.361194.7
1.78-1.824.40.2329240.42195
1.82-1.864.50.1789510.39196
1.86-1.94.60.159420.431196.4
1.9-1.964.70.1329710.526198.1
1.96-2.015.30.1189950.764199.9
2.01-2.0860.1149861.03199.9
2.08-2.1570.1039931.1561100
2.15-2.247.50.0929901.1761100
2.24-2.3480.08210061.1331100
2.34-2.4690.0729921.0811100
2.46-2.6210.60.06210210.9241100
2.62-2.8212.30.05310000.9331100
2.82-3.1112.50.04410351.0191100
3.11-3.5512.60.04210331.3241100
3.55-4.4816.80.04610531.6271100
4.48-5014.60.04211511.451199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→31.229 Å / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.8733 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 1003 5.09 %RANDOM
Rwork0.1855 ---
all0.1869 21173 --
obs0.1869 19702 97.79 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.755 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 62.31 Å2 / Biso mean: 22.7042 Å2 / Biso min: 8.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.6145 Å2-0 Å20 Å2
2---0.6145 Å20 Å2
3---1.2291 Å2
Refinement stepCycle: LAST / Resolution: 1.65→31.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1291 0 6 193 1490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051379
X-RAY DIFFRACTIONf_angle_d0.9331874
X-RAY DIFFRACTIONf_chiral_restr0.063215
X-RAY DIFFRACTIONf_plane_restr0.004248
X-RAY DIFFRACTIONf_dihedral_angle_d14.026517
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.73480.28981390.27492410254991
1.7348-1.84350.21891680.21682536270495
1.8435-1.98580.23641270.18282626275398
1.9858-2.18560.21211500.175427002850100
2.1856-2.50180.19841500.179327252875100
2.5018-3.15150.21881380.183227542892100
3.1515-31.23480.20511310.17929483079100
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)
10.10210.11650.01970.3242-0.02080.06470.20590.08960.03980.22460.1505-0.21970.1201-0.05810.10980.05990.231-0.0752-0.17970.0330.161224.018624.222846.5361
20.48120.08770.26350.6730.14910.46630.03170.1386-0.0027-0.1062-0.0184-0.0080.12130.1132-0.00680.14830.02320.00040.12-0.00930.129224.877336.91941.2709
30.1241-0.01460.03730.15350.05440.3706-0.00340.01320.0276-0.0389-0.006-0.0199-0.03260.03420.00690.1588-0.0207-0.00970.11450.00270.121117.888948.073346.495
40.5858-0.10720.03950.4539-0.06360.16280.0652-0.1215-0.07440.1920.01790.09120.0137-0.0036-0.04630.15180.00680.01950.1090.01290.13289.468441.516856.8564
52.1730.84-0.12462.0399-0.10110.0745-0.0160.31330.0995-0.32230.08080.08180.0128-0.0259-0.04810.2480.0270.03140.24370.00320.23133.564247.853151.2746
62.026-0.5515-0.03410.66260.75051.48190.04070.04570.1832-0.12760.11110.0736-0.2942-0.1235-0.10360.19560.02150.01710.25080.10230.29064.83445.017540.8002
70.3076-0.2134-0.0490.3852-0.14420.2759-0.061-0.181-0.09470.04910.0245-0.0110.05490.13850.0210.11140.0056-0.00440.14930.00210.077218.665340.448154.0428
80.41640.1163-0.15760.58010.1780.4523-0.08230.0214-0.07450.06360.0645-0.02760.1112-0.06190.02110.1306-0.02860.00180.09860.01530.15155.116331.22347.8123
90.57690.37360.23760.42050.07610.1234-0.07340.085-0.26730.0860.1511-0.23740.07850.0668-0.01930.09830.0133-0.01820.0983-0.03180.146726.59437.60852.4681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq -2:16)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 17:34)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 35:74)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 75:94)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 95:101)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 102:110)A0
7X-RAY DIFFRACTION7chain 'A' and (resseq 111:131)A0
8X-RAY DIFFRACTION8chain 'A' and (resseq 132:138)A0
9X-RAY DIFFRACTION9chain 'A' and (resseq 139:165)A0

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