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- PDB-6rn5: PptA from Streptomyces chartreusis -

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Basic information

Entry
Database: PDB / ID: 6rn5
TitlePptA from Streptomyces chartreusis
ComponentsCHAD domain protein
KeywordsUNKNOWN FUNCTION / Polyphosphate-binding protein
Function / homologyCHAD domain superfamily / CHAD domain / CHAD / CHAD domain / CHAD domain profile. / CARBONATE ION / COPPER (II) ION / CHAD domain protein
Function and homology information
Biological speciesStreptomyces chartreusis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.037 Å
AuthorsWerten, S. / Rustmeier, N.H. / Hinrichs, W.
CitationJournal: FEBS Lett / Year: 2019
Title: Structural and biochemical analysis of a phosin from Streptomyces chartreusis reveals a combined polyphosphate- and metal-binding fold.
Authors: Sebastiaan Werten / Nils Hinnerk Rustmeier / Maximilian Gemmer / Marie-Joëlle Virolle / Winfried Hinrichs /
Abstract: X-ray crystallographic analysis of a phosin (PptA) from Steptomyces chartreusis reveals a metal-associated, lozenge-shaped fold featuring a 5-10 Å wide, positively charged tunnel that traverses the ...X-ray crystallographic analysis of a phosin (PptA) from Steptomyces chartreusis reveals a metal-associated, lozenge-shaped fold featuring a 5-10 Å wide, positively charged tunnel that traverses the protein core. Two distinct metal-binding sites were identified in which the predominant metal ion was Cu . In solution, PptA forms stable homodimers that bind with nanomolar affinity to polyphosphate, a stress-related biopolymer acting as a phosphate and energy reserve in conditions of nutrient depletion. A single protein dimer interacts with 14-15 consecutive phosphate moieties within the polymer. Our observations suggest that PptA plays a role in polyphosphate metabolism, mobilisation or sensing, possibly by acting in concert with polyphosphate kinase (Ppk). Like Ppk, phosins may influence antibiotic synthesis by streptomycetes.
History
DepositionMay 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Aug 12, 2020Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle / struct_conn
Item: _audit_author.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._audit_author.name / _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_symmetry
Revision 1.3May 15, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHAD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,29110
Polymers39,6491
Non-polymers6429
Water2,414134
1
A: CHAD domain protein
hetero molecules

A: CHAD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,58220
Polymers79,2972
Non-polymers1,28518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area5110 Å2
ΔGint-234 kcal/mol
Surface area27520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.303, 132.233, 116.398
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-402-

CU

21A-631-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CHAD domain protein


Mass: 39648.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces chartreusis (bacteria) / Gene: SCNRRL3882_4295 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2N9BBV4

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Non-polymers , 5 types, 143 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM MES/HCl pH 6.5, 1.6 M MgSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.905002 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905002 Å / Relative weight: 1
ReflectionResolution: 2.037→46.196 Å / Num. obs: 24547 / % possible obs: 98.9 % / Redundancy: 12.3 % / Biso Wilson estimate: 38.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.111 / Rsym value: 0.106 / Net I/σ(I): 19.2
Reflection shellResolution: 2.037→2.16 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.916 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 3733 / CC1/2: 0.711 / Rrim(I) all: 0.971 / Rsym value: 0.916 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0218 2018/15/02refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.037→46.196 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.617 / SU ML: 0.142 / Cross valid method: FREE R-VALUE / ESU R: 0.161 / ESU R Free: 0.155
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1228 5 %Random selection
Rwork0.191 ---
all0.193 ---
obs0.193 24546 98.944 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.16 Å2
Baniso -1Baniso -2Baniso -3
1-5.127 Å20 Å2-0 Å2
2---2.613 Å20 Å2
3----2.515 Å2
Refinement stepCycle: LAST / Resolution: 2.037→46.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 28 134 2317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192213
X-RAY DIFFRACTIONr_bond_other_d0.0010.022112
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9623008
X-RAY DIFFRACTIONr_angle_other_deg0.81634827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5525278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.15720.94795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8615344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9481530
X-RAY DIFFRACTIONr_chiral_restr0.080.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212454
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02476
X-RAY DIFFRACTIONr_nbd_refined0.2290.2532
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1590.21975
X-RAY DIFFRACTIONr_nbtor_refined0.180.21095
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21109
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2103
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0550.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1840.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0760.29
X-RAY DIFFRACTIONr_nbd_other0.1360.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0790.24
X-RAY DIFFRACTIONr_mcbond_it3.2434.0631127
X-RAY DIFFRACTIONr_mcbond_other3.2394.0611126
X-RAY DIFFRACTIONr_mcangle_it4.8216.0481400
X-RAY DIFFRACTIONr_mcangle_other4.826.0511401
X-RAY DIFFRACTIONr_scbond_it4.2054.6231086
X-RAY DIFFRACTIONr_scbond_other4.2024.6041068
X-RAY DIFFRACTIONr_scangle_it6.4566.7561608
X-RAY DIFFRACTIONr_scangle_other6.4716.7261582
X-RAY DIFFRACTIONr_lrange_it8.25249.3852546
X-RAY DIFFRACTIONr_lrange_other8.24949.2672521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.037-2.090.412820.3681547X-RAY DIFFRACTION90.2993
2.09-2.1470.356860.3291646X-RAY DIFFRACTION97.6875
2.147-2.2090.264850.2731603X-RAY DIFFRACTION99.8226
2.209-2.2770.312830.2441584X-RAY DIFFRACTION99.7606
2.277-2.3510.279810.2211545X-RAY DIFFRACTION99.6324
2.351-2.4340.239780.1921475X-RAY DIFFRACTION99.7431
2.434-2.5250.22750.1831418X-RAY DIFFRACTION99.7328
2.525-2.6280.266720.1821380X-RAY DIFFRACTION99.7938
2.628-2.7450.211700.1851334X-RAY DIFFRACTION99.7868
2.745-2.8780.281670.1881263X-RAY DIFFRACTION99.7749
2.878-3.0330.312640.2031215X-RAY DIFFRACTION100
3.033-3.2160.243600.191148X-RAY DIFFRACTION99.8347
3.216-3.4370.278570.1881083X-RAY DIFFRACTION99.6503
3.437-3.7110.198540.1651028X-RAY DIFFRACTION100
3.711-4.0620.237490.156925X-RAY DIFFRACTION99.8974
4.062-4.5370.191460.151865X-RAY DIFFRACTION100
4.537-5.2310.206400.164761X-RAY DIFFRACTION99.5031
5.231-6.3860.215340.202658X-RAY DIFFRACTION100
6.386-8.9460.176280.142519X-RAY DIFFRACTION99.8175
8.946-46.1960.153170.185321X-RAY DIFFRACTION99.705

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