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- PDB-5vog: Crystal Structure of a Hypothetical Protein from Neisseria gonorr... -

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Basic information

Entry
Database: PDB / ID: 5vog
TitleCrystal Structure of a Hypothetical Protein from Neisseria gonorrhoeae with bound ppGpp
ComponentsPutative phosphoribosyltransferase
KeywordsTRANSFERASE / SSGCID / ppGpp / possible Phosphoribosyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


nucleoside metabolic process / glycosyltransferase activity
Similarity search - Function
Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / Phosphoribosyltransferase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Hypothetical Protein from Neisseria gonorrhoeae with bound ppGpp
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMay 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Data collection
Revision 1.2Jul 5, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7536
Polymers20,9771
Non-polymers7765
Water3,621201
1
A: Putative phosphoribosyltransferase
hetero molecules

A: Putative phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,50612
Polymers41,9542
Non-polymers1,55210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+1/2,y,-z+1/21
Buried area6090 Å2
ΔGint-48 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.270, 103.930, 105.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-428-

HOH

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Components

#1: Protein Putative phosphoribosyltransferase


Mass: 20977.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria)
Gene: ESCNG_40048, WHOF_00431, WHOF_02526C, WHOG_01129, WHOG_02374C, WHOK_01250, WHOK_02372C, WHOM_00300, WHOM_02380C, WHON_00453, WHON_02375C, WHOU_01208, WHOU_02454C, WHOV_00719, WHOV_02442C, WHOW_ ...Gene: ESCNG_40048, WHOF_00431, WHOF_02526C, WHOG_01129, WHOG_02374C, WHOK_01250, WHOK_02372C, WHOM_00300, WHOM_02380C, WHON_00453, WHON_02375C, WHOU_01208, WHOU_02454C, WHOV_00719, WHOV_02442C, WHOW_01101, WHOW_02437C, WHOX_00398, WHOX_02372C, WHOZ_01227, WHOZ_02445C
Plasmid: NegoA.19192.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1D3HIA2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O17P4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: NegoA.19192.a.B1.PS38045 at 17 mg/ml mixed 1:1 with Morpheus(a2): 10% (w/v) PEG-8000, 20% (v/v) ethylene glycol, 0.1 M MES/imidazole, pH = 5.5, 0.03 M each magnesium chloride and calcium chloride, direct cryo

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 29, 2017
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→40.635 Å / Num. obs: 35700 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.493 % / Biso Wilson estimate: 24.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rrim(I) all: 0.034 / Χ2: 0.993 / Net I/σ(I): 26.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.545.5650.4033.6926190.940.44599.9
1.54-1.585.4460.2944.9225570.9680.32599.5
1.58-1.635.2540.2286.2924660.9760.25399.2
1.63-1.685.4970.1748.3324030.9840.192100
1.68-1.735.6570.12711.4323530.9910.14100
1.73-1.795.6060.09814.3322700.9950.108100
1.79-1.865.4790.07418.7521880.9970.08199.9
1.86-1.945.2080.0622.7420960.9970.06699.4
1.94-2.025.5480.04728.6220160.9990.05299.9
2.02-2.125.7060.03934.1919560.9990.043100
2.12-2.245.6620.03339.4518360.9990.03699.9
2.24-2.375.4290.03241.3117570.9990.03699.8
2.37-2.545.2240.0343.6616440.9990.03399.9
2.54-2.745.7940.02848.9215430.9990.03199.9
2.74-35.6870.02851.1614120.9990.03199.8
3-3.355.4020.02852.0712920.9990.03199.6
3.35-3.875.2160.02853.0411360.9980.03199.1
3.87-4.745.6840.02755.79710.9990.02998.9
4.74-6.715.2260.02953.567520.9990.03298.3
6.71-40.6355.3140.02954.414330.9990.03295.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX(dev_2744: ???)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JKZ

2jkz


Resolution: 1.5→40.635 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.19
RfactorNum. reflection% reflection
Rfree0.1765 1921 5.38 %
Rwork0.1492 --
obs0.1507 35688 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.28 Å2 / Biso mean: 35.5166 Å2 / Biso min: 18.86 Å2
Refinement stepCycle: final / Resolution: 1.5→40.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 46 204 1630
Biso mean--28.89 45.1 -
Num. residues----176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051531
X-RAY DIFFRACTIONf_angle_d0.8692108
X-RAY DIFFRACTIONf_chiral_restr0.055237
X-RAY DIFFRACTIONf_plane_restr0.004277
X-RAY DIFFRACTIONf_dihedral_angle_d9.454919
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.53750.20281380.161823892527100
1.5375-1.57910.20551250.1472401252699
1.5791-1.62560.1731600.14182356251699
1.6256-1.6780.18971470.13423632510100
1.678-1.7380.17141390.13224042543100
1.738-1.80760.15911270.126924082535100
1.8076-1.88990.18861290.135724102539100
1.8899-1.98950.19051420.147623912533100
1.9895-2.11410.18341210.151224362557100
2.1141-2.27740.16911270.143924122539100
2.2774-2.50650.17881380.152824162554100
2.5065-2.86910.18551390.151824472586100
2.8691-3.61450.1761430.15324242567100
3.6145-40.64990.16971460.15152510265698

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