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- PDB-3exq: Crystal structure of a NUDIX family hydrolase from Lactobacillus ... -

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Basic information

Entry
Database: PDB / ID: 3exq
TitleCrystal structure of a NUDIX family hydrolase from Lactobacillus brevis
ComponentsNUDIX family hydrolase
KeywordsHYDROLASE / NUDIX / Protein Structure Initiative II(PSI II) / NYSGXRC / 11180k / Structural Genomics / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NUDIX family hydrolase
Similarity search - Component
Biological speciesLactobacillus brevis ATCC 367 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsPalani, K. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a NUDIX family hydrolase from Lactobacillus brevis
Authors: Palani, K. / Burley, S.K. / Swaminathan, S.
History
DepositionOct 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: NUDIX family hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1793
Polymers17,9871
Non-polymers1922
Water2,576143
1
A: NUDIX family hydrolase
hetero molecules

A: NUDIX family hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3586
Polymers35,9732
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4480 Å2
ΔGint-71 kcal/mol
Surface area15620 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.762, 82.477, 36.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein NUDIX family hydrolase


Mass: 17986.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis ATCC 367 (bacteria)
Gene: LVIS_0842 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03S37
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Sodium chloride, 0.1M HEPES, 1.6M Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 10, 2008 / Details: Mirrors
RadiationMonochromator: Si(III) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→35.1 Å / Num. all: 14576 / Num. obs: 14576 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 13 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.9
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 3 / Num. unique all: 1418 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→35.09 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 145595.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 700 5.1 %RANDOM
Rwork0.218 ---
all0.234 14576 --
obs0.218 13820 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.4253 Å2 / ksol: 0.366071 e/Å3
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1-6.3 Å20 Å20 Å2
2---4.08 Å20 Å2
3----2.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2→35.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 10 143 1393
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 102 4.6 %
Rwork0.21 2099 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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