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- PDB-7mw8: Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phos... -

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Basic information

Entry
Database: PDB / ID: 7mw8
TitleCrystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase
Components
  • Phosphodiesterase-nucleotide pyrophosphatase
  • pApG
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / transferase activity / hydrolase activity / metal ion binding / RNA / Phosphodiesterase-nucleotide pyrophosphatase
Function and homology information
Biological speciesXanthomonas citri (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsFernandez, D. / Li, L. / Brown, 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 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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

Downloads & links

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Assembly

Deposited unit
D: Phosphodiesterase-nucleotide pyrophosphatase
B: Phosphodiesterase-nucleotide pyrophosphatase
C: Phosphodiesterase-nucleotide pyrophosphatase
A: Phosphodiesterase-nucleotide pyrophosphatase
E: Phosphodiesterase-nucleotide pyrophosphatase
F: Phosphodiesterase-nucleotide pyrophosphatase
J: pApG
K: pApG
L: pApG
M: pApG
N: pApG
O: pApG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,52524
Polymers279,74012
Non-polymers78512
Water7,188399
1
D: Phosphodiesterase-nucleotide pyrophosphatase
K: pApG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7544
Polymers46,6232
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-84 kcal/mol
Surface area14730 Å2
MethodPISA
2
B: Phosphodiesterase-nucleotide pyrophosphatase
L: pApG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7544
Polymers46,6232
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-86 kcal/mol
Surface area14710 Å2
MethodPISA
3
C: Phosphodiesterase-nucleotide pyrophosphatase
M: pApG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7544
Polymers46,6232
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-87 kcal/mol
Surface area14980 Å2
MethodPISA
4
A: Phosphodiesterase-nucleotide pyrophosphatase
J: pApG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7544
Polymers46,6232
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-88 kcal/mol
Surface area14550 Å2
MethodPISA
5
E: Phosphodiesterase-nucleotide pyrophosphatase
N: pApG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7544
Polymers46,6232
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-85 kcal/mol
Surface area14820 Å2
MethodPISA
6
F: Phosphodiesterase-nucleotide pyrophosphatase
O: pApG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7544
Polymers46,6232
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-83 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.420, 66.719, 134.961
Angle α, β, γ (deg.)90.000, 116.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphodiesterase-nucleotide pyrophosphatase


Mass: 45993.855 Da / Num. of mol.: 6 / Mutation: T90A
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: RNA chain
pApG


Mass: 629.454 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.03 Å3/Da / Density % sol: 39.3 %
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: 1.18076 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2017
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: 1.18076 Å / Relative weight: 1
ReflectionResolution: 1.9→121.042 Å / Num. all: 155855 / Num. obs: 155855 / % possible obs: 95 % / Redundancy: 2.9 % / Rpim(I) all: 0.089 / Rrim(I) all: 0.16 / Rsym value: 0.132 / Net I/av σ(I): 2.1 / Net I/σ(I): 3.7 / Num. measured all: 449161
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
1.9-22.60.5961.156237212380.4070.7250.5961.189.1
2-2.122.70.411.656001207930.280.4980.411.792
2.12-2.272.60.2951.551002195620.210.3650.2952.292.5
2.27-2.4530.2522.357508192160.1680.3050.2522.997
2.45-2.693.10.207255156178580.1380.250.2073.998.3
2.69-330.1842.948939162300.1230.2220.1844.898.4
3-3.472.90.1443.740740140590.0980.1750.1445.996.6
3.47-4.253.20.1142.538840122430.0770.1380.1147.399.1
4.25-6.0130.0845.92803793410.0580.1030.0847.297
6.01-38.993.10.0743.71670153150.0480.0890.0746.798.3

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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: 1.9→30.04 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.479 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.303 7565 4.9 %RANDOM
Rwork0.2429 ---
obs0.2458 147590 94.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.72 Å2 / Biso mean: 37.325 Å2 / Biso min: 15.87 Å2
Baniso -1Baniso -2Baniso -3
1--3.83 Å20 Å20.24 Å2
2--1.26 Å2-0 Å2
3---1.56 Å2
Refinement stepCycle: final / Resolution: 1.9→30.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17587 0 127 399 18113
Biso mean--31.35 32.46 -
Num. residues----2301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01918319
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216951
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.94725047
X-RAY DIFFRACTIONr_angle_other_deg1.182338833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.13452302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55222.442823
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.039152630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3715173
X-RAY DIFFRACTIONr_chiral_restr0.0970.22648
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02121055
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024400
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 493 -
Rwork0.369 9995 -
all-10488 -
obs--87.33 %

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