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- PDB-7n1s: Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phos... -

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Basic information

Entry
Database: PDB / ID: 7n1s
TitleCrystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase
ComponentsPhosphodiesterase-nucleotide pyrophosphatase
KeywordsHYDROLASE / enzyme / nucleotide / pyrophosphatase / phosphodiesterase / bacterial
Function / homologyType I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Alkaline-phosphatase-like, core domain superfamily / transferase activity / Prokaryotic membrane lipoprotein lipid attachment site profile. / hydrolase activity / metal ion binding / Phosphodiesterase-nucleotide pyrophosphatase
Function and homology information
Biological speciesXanthomonas citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsFernandez, D. / Li, L. / Brown, J.A. / Carozza, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1209045-100-PAMNF United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: ENPP1's regulation of extracellular cGAMP is a ubiquitous mechanism of attenuating STING signaling.
Authors: Carozza, J.A. / Cordova, A.F. / Brown, J.A. / AlSaif, Y. / Bohnert, V. / Cao, X. / Mardjuki, R.E. / Skariah, G. / Fernandez, D. / Li, L.
History
DepositionMay 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphodiesterase-nucleotide pyrophosphatase
B: Phosphodiesterase-nucleotide pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0176
Polymers83,4982
Non-polymers5194
Water1,78399
1
A: Phosphodiesterase-nucleotide pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0093
Polymers41,7491
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphodiesterase-nucleotide pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0093
Polymers41,7491
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.204, 77.712, 129.292
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 45 - 425 / Label seq-ID: 2 - 382

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Phosphodiesterase-nucleotide pyrophosphatase


Mass: 41749.039 Da / Num. of mol.: 2 / Mutation: H214A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas citri (bacteria) / Gene: XAC3562_610174 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U5FM15
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.92 Å3/Da / Density % sol: 35.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 3350, bis-tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2018
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→66.606 Å / Num. all: 45218 / Num. obs: 45218 / % possible obs: 100 % / Redundancy: 7.3 % / Rpim(I) all: 0.041 / Rrim(I) all: 0.109 / Rsym value: 0.101 / Net I/av σ(I): 4.9 / Net I/σ(I): 9.7 / Num. measured all: 328450
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.117.21.1920.74694765280.4731.2851.1921.8100
2.11-2.247.30.7311.14471161340.2880.7870.7312.7100
2.24-2.397.20.5381.44206858040.2130.5790.5383.6100
2.39-2.587.50.3772.14068154160.1460.4050.3774.8100
2.58-2.837.20.2293.43620750100.0910.2460.2297100
2.83-3.167.30.1385.43342245550.0550.1490.13810.7100
3.16-3.657.30.088.42939040280.0320.0860.0817.4100
3.65-4.477.30.05311.72515034350.0210.0570.05326100
4.47-6.327.10.04611.91929427320.0190.050.04627.9100
6.32-38.8566.70.0347.61058015760.0150.0380.03429.399.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0135refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSU

2gsu


Resolution: 2→30.61 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2386 / WRfactor Rwork: 0.1957 / FOM work R set: 0.7108 / SU B: 7.608 / SU ML: 0.193 / SU R Cruickshank DPI: 0.2435 / SU Rfree: 0.1945 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 2185 4.8 %RANDOM
Rwork0.2139 ---
obs0.2161 42956 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.41 Å2 / Biso mean: 44.528 Å2 / Biso min: 23.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--4.2 Å2-0 Å2
3----4.25 Å2
Refinement stepCycle: final / Resolution: 2→30.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5845 0 28 99 5972
Biso mean--48.96 41.5 -
Num. residues----765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196041
X-RAY DIFFRACTIONr_bond_other_d0.0060.025633
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.9398239
X-RAY DIFFRACTIONr_angle_other_deg1.245312904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6275763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28222.5272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53515870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7121557
X-RAY DIFFRACTIONr_chiral_restr0.1030.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216951
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021446
Refine LS restraints NCS

Ens-ID: 1 / Number: 45434 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 178 -
Rwork0.398 3114 -
all-3292 -
obs--100 %

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