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- PDB-5f2v: Crystal structure of the small alarmone synthethase 1 from Bacill... -

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Basic information

Entry
Database: PDB / ID: 5f2v
TitleCrystal structure of the small alarmone synthethase 1 from Bacillus subtilis bound to AMPCPP
ComponentsGTP pyrophosphokinase YjbM
KeywordsTRANSFERASE / (p)ppGpp / alarmone / stringent response / allosteric regulator
Function / homology
Function and homology information


GTP diphosphokinase / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / kinase activity / GTP binding / ATP binding / metal ion binding
Similarity search - Function
Nucleotidyltransferase / : / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Helix Hairpins / 2-Layer Sandwich ...Nucleotidyltransferase / : / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / GTP pyrophosphokinase YjbM
Similarity search - Component
Biological speciesBacillus subtilis PY79 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSteinchen, W. / Schuhmacher, J.S. / Altegoer, F. / Bange, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Catalytic mechanism and allosteric regulation of an oligomeric (p)ppGpp synthetase by an alarmone.
Authors: Steinchen, W. / Schuhmacher, J.S. / Altegoer, F. / Fage, C.D. / Srinivasan, V. / Linne, U. / Marahiel, M.A. / Bange, G.
History
DepositionDec 2, 2015Deposition site: RCSB / Processing site: PDBE
SupersessionDec 16, 2015ID: 5DEE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
V: GTP pyrophosphokinase YjbM
X: GTP pyrophosphokinase YjbM
T: GTP pyrophosphokinase YjbM
S: GTP pyrophosphokinase YjbM
Y: GTP pyrophosphokinase YjbM
O: GTP pyrophosphokinase YjbM
Z: GTP pyrophosphokinase YjbM
W: GTP pyrophosphokinase YjbM
U: GTP pyrophosphokinase YjbM
P: GTP pyrophosphokinase YjbM
R: GTP pyrophosphokinase YjbM
Q: GTP pyrophosphokinase YjbM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,31936
Polymers293,96512
Non-polymers6,35424
Water2,936163
1
V: GTP pyrophosphokinase YjbM
T: GTP pyrophosphokinase YjbM
S: GTP pyrophosphokinase YjbM
U: GTP pyrophosphokinase YjbM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,10612
Polymers97,9884
Non-polymers2,1188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13000 Å2
ΔGint-105 kcal/mol
Surface area36920 Å2
MethodPISA
2
X: GTP pyrophosphokinase YjbM
Y: GTP pyrophosphokinase YjbM
Z: GTP pyrophosphokinase YjbM
W: GTP pyrophosphokinase YjbM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,10612
Polymers97,9884
Non-polymers2,1188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-103 kcal/mol
Surface area36120 Å2
MethodPISA
3
O: GTP pyrophosphokinase YjbM
P: GTP pyrophosphokinase YjbM
R: GTP pyrophosphokinase YjbM
Q: GTP pyrophosphokinase YjbM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,10612
Polymers97,9884
Non-polymers2,1188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-104 kcal/mol
Surface area36050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.671, 103.631, 138.290
Angle α, β, γ (deg.)90.00, 104.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GTP pyrophosphokinase YjbM / (p)ppGpp synthase YjbM / Small alarmone synthase 1 / SAS 1


Mass: 24497.084 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis PY79 (bacteria) / Gene: yjbM, BSU11600 / Plasmid: pET24d(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O31611, GTP diphosphokinase
#2: Chemical
ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C11H18N5O12P3 / Source: (gene. exp.) Bacillus subtilis PY79 (bacteria) / Gene: yjbM, BSU11600 / Plasmid: pET24d(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: Mg / Source: (gene. exp.) Bacillus subtilis PY79 (bacteria) / Gene: yjbM, BSU11600 / Plasmid: pET24d(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M KSCN, 20% (W/V) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97934 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.8→48.31 Å / Num. obs: 78602 / % possible obs: 0.995 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 2.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.8 / % possible all: 0.895

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Processing

Software
NameVersionClassification
PHENIX1.9_1685refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DEC

5dec


Resolution: 2.8→48.31 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 1998 2.55 %
Rwork0.1925 --
obs0.1943 78506 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18390 0 32 163 18585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918751
X-RAY DIFFRACTIONf_angle_d1.17225358
X-RAY DIFFRACTIONf_dihedral_angle_d17.5577106
X-RAY DIFFRACTIONf_chiral_restr0.0412835
X-RAY DIFFRACTIONf_plane_restr0.0043151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.32321410.24745407X-RAY DIFFRACTION100
2.87-2.94760.35311430.25215464X-RAY DIFFRACTION100
2.9476-3.03430.31861400.23845380X-RAY DIFFRACTION100
3.0343-3.13220.31491430.23355462X-RAY DIFFRACTION100
3.1322-3.24420.34661420.22445419X-RAY DIFFRACTION100
3.2442-3.3740.31331420.22055459X-RAY DIFFRACTION100
3.374-3.52750.30891430.21635432X-RAY DIFFRACTION100
3.5275-3.71350.29091420.20255481X-RAY DIFFRACTION100
3.7135-3.9460.27661430.20155427X-RAY DIFFRACTION100
3.946-4.25050.25591420.1725479X-RAY DIFFRACTION100
4.2505-4.6780.21711430.16135477X-RAY DIFFRACTION100
4.678-5.35410.2751430.17075491X-RAY DIFFRACTION100
5.3541-6.74270.24971450.19725516X-RAY DIFFRACTION100
6.7427-48.32010.17371460.15955614X-RAY DIFFRACTION100

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