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- PDB-5xnx: Crystallographic structure of the enzymatically active N-terminal... -

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Basic information

Entry
Database: PDB / ID: 5xnx
TitleCrystallographic structure of the enzymatically active N-terminal domain of the Rel protein from Mycobacterium tuberculosis
ComponentsBifunctional (p)ppGpp synthase/hydrolase RelA
KeywordsHYDROLASE / TRANSFERASE / RelA / Mycobacterium tuberculosis / HD DOMAIN / HELIX BUNDLE / Synthetase domain / (p)ppGpp / Stringent response
Function / homology
Function and homology information


guanosine-3',5'-bis(diphosphate) 3'-diphosphatase / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / GTP diphosphokinase / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / stringent response / peptidoglycan-based cell wall / kinase activity / manganese ion binding / GTP binding ...guanosine-3',5'-bis(diphosphate) 3'-diphosphatase / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / GTP diphosphokinase / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / stringent response / peptidoglycan-based cell wall / kinase activity / manganese ion binding / GTP binding / ATP binding / plasma membrane
Similarity search - Function
RelA/SpoT, AH and RIS domains / RelA/SpoT, AH and RIS domains / RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / HD domain / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain ...RelA/SpoT, AH and RIS domains / RelA/SpoT, AH and RIS domains / RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / HD domain / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / Hypothetical protein af1432 / Hypothetical protein af1432 / ACT domain profile. / ACT domain / HD domain profile. / ACT-like domain / TGS-like / TGS domain profile. / TGS / HD domain / Beta Polymerase, domain 2 / Beta-grasp domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Bifunctional (p)ppGpp synthase/hydrolase RelA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsSingal, B. / Balakrishna, A.M. / Manimekalai, M.S.S. / Nartey, W. / Gruber, G.
CitationJournal: FEBS Lett. / Year: 2017
Title: Crystallographic and solution structure of the N-terminal domain of the Rel protein from Mycobacterium tuberculosis
Authors: Singal, B. / Balakrishna, A.M. / Nartey, W. / Manimekalai, M.S.S. / Jeyakanthan, J. / Gruber, G.
History
DepositionMay 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional (p)ppGpp synthase/hydrolase RelA
B: Bifunctional (p)ppGpp synthase/hydrolase RelA
C: Bifunctional (p)ppGpp synthase/hydrolase RelA
D: Bifunctional (p)ppGpp synthase/hydrolase RelA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,6787
Polymers178,6054
Non-polymers733
Water00
1
A: Bifunctional (p)ppGpp synthase/hydrolase RelA
hetero molecules

D: Bifunctional (p)ppGpp synthase/hydrolase RelA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3514
Polymers89,3022
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_764-y+2,x-y+1,z-1/31
Buried area2010 Å2
ΔGint-27.7 kcal/mol
Surface area36370 Å2
MethodPISA
2
B: Bifunctional (p)ppGpp synthase/hydrolase RelA
C: Bifunctional (p)ppGpp synthase/hydrolase RelA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3273
Polymers89,3022
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-20.6 kcal/mol
Surface area35930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.710, 161.710, 75.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 4 / Auth seq-ID: 14 - 344 / Label seq-ID: 14 - 344

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.505483, -0.86281, 0.006756), (-0.862676, -0.505525, -0.015355), (0.016664, 0.001933, -0.999859)160.64583, 280.89453, 22.03163
3given(0.497242, -0.867576, -0.007904), (0.867599, 0.497164, 0.009983), (-0.004731, -0.011821, 0.999919)162.5316, 0.1541, -49.22021
4given(-0.4967, -0.86788, 0.008597), (-0.867917, 0.496638, -0.008486), (0.003095, -0.011677, -0.999927)242.09531, 140.41252, -0.22162

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Components

#1: Protein
Bifunctional (p)ppGpp synthase/hydrolase RelA


Mass: 44651.188 Da / Num. of mol.: 4 / Fragment: UNP residues 1-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: relA, Rv2583c, MTCY227.18 / Plasmid: pET9D / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P9WHG9, GTP diphosphokinase, guanosine-3',5'-bis(diphosphate) 3'-diphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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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: 3.19 Å3/Da / Density % sol: 61.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.8M succinic acid, pH 7.0, 0.2M MgCl2, 0.2-0.4M Trimethylamin-N-oxide, 20% w/v Benzamidine hydrochloride hydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2017 / Details: mirrors
RadiationMonochromator: Double Crystal Si(111) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.247
11-K, -H, -L20.252
11K, H, -L30.249
11-h,-k,l40.252
ReflectionResolution: 3.7→20 Å / Num. obs: 23372 / % possible obs: 99.2 % / Redundancy: 11.1 % / CC1/2: 0.9874 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.6
Reflection shellResolution: 3.7→3.83 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 3.9 / CC1/2: 0.962 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vj7

1vj7


Resolution: 3.7→10.02 Å / Cor.coef. Fo:Fc: 0.741 / Cor.coef. Fo:Fc free: 0.733 / SU B: 112.217 / SU ML: 0.771 / Cross valid method: THROUGHOUT / ESU R Free: 0.2 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.36765 1104 5 %RANDOM
Rwork0.3502 ---
obs0.35105 21004 94.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 107.249 Å2
Baniso -1Baniso -2Baniso -3
1--12.14 Å2-0 Å2-0 Å2
2---12.14 Å2-0 Å2
3---24.28 Å2
Refinement stepCycle: 1 / Resolution: 3.7→10.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9446 0 3 0 9449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0199610
X-RAY DIFFRACTIONr_bond_other_d0.0030.028990
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.95713083
X-RAY DIFFRACTIONr_angle_other_deg0.954320510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39651258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.67523.281381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.997151472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1621570
X-RAY DIFFRACTIONr_chiral_restr0.0590.21554
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110900
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022070
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2047.5645086
X-RAY DIFFRACTIONr_mcbond_other0.2047.5655085
X-RAY DIFFRACTIONr_mcangle_it0.39111.3526326
X-RAY DIFFRACTIONr_mcangle_other0.39111.3516327
X-RAY DIFFRACTIONr_scbond_it0.067.6464524
X-RAY DIFFRACTIONr_scbond_other0.067.6454525
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.16711.4586758
X-RAY DIFFRACTIONr_long_range_B_refined3.01871.35636865
X-RAY DIFFRACTIONr_long_range_B_other3.01871.35536866
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3697 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.570.5
Bmedium positional0.660.5
Cmedium positional0.590.5
Dmedium positional0.570.5
Amedium thermal5.222
Bmedium thermal6.282
Cmedium thermal9.192
Dmedium thermal2.852
LS refinement shellResolution: 3.7→3.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 86 -
Rwork0.348 1624 -
obs--99.36 %
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)
10.39230.26570.03963.64330.48221.3655-0.10460.1637-0.09930.12110.1558-0.23040.1650.0706-0.05120.257-0.06380.06190.42660.01920.0579142.2875113.3291-4.3515
23.14681.39070.38171.44740.09922.1344-0.1244-0.0083-0.14960.2480.0040.0816-0.09590.02860.12050.2178-0.03420.05070.30990.03160.0467134.4082100.911428.9108
33.78990.94360.30581.7624-0.39951.38670.0769-0.1502-0.0976-0.0554-0.31010.0162-0.0001-0.04850.23330.2254-0.09090.04980.2454-0.04040.074787.924373.245346.6956
43.4254-1.4376-0.32821.76420.27730.87980.10930.2328-0.16810.1377-0.10690.05520.02240.1394-0.00240.2977-0.10510.07490.26820.01540.059673.377373.29663.4291
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 382
2X-RAY DIFFRACTION2B12 - 373
3X-RAY DIFFRACTION3C11 - 373
4X-RAY DIFFRACTION4D11 - 374

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