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- PDB-4qgo: Crystal structure of NucA from Streptococcus agalactiae with no m... -

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Basic information

Entry
Database: PDB / ID: 4qgo
TitleCrystal structure of NucA from Streptococcus agalactiae with no metal bound
ComponentsDNA-entry nuclease (Competence-specific nuclease)
KeywordsHYDROLASE / Beta beta alpha / nuclease
Function / homologyExtracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesStreptococcus agalactiae ILRI112 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPedersen, L.C. / Moon, A.F. / Gaudu, P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural characterization of the virulence factor nuclease A from Streptococcus agalactiae.
Authors: Moon, A.F. / Gaudu, P. / Pedersen, L.C.
History
DepositionMay 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-entry nuclease (Competence-specific nuclease)
B: DNA-entry nuclease (Competence-specific nuclease)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,61017
Polymers50,4792
Non-polymers1,13115
Water11,764653
1
A: DNA-entry nuclease (Competence-specific nuclease)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8539
Polymers25,2401
Non-polymers6138
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA-entry nuclease (Competence-specific nuclease)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7578
Polymers25,2401
Non-polymers5177
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.591, 57.131, 62.422
Angle α, β, γ (deg.)109.40, 97.08, 90.16
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA-entry nuclease (Competence-specific nuclease)


Mass: 25239.607 Da / Num. of mol.: 2 / Fragment: catalytic domain / Mutation: H148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae ILRI112 (bacteria)
Gene: SAIL_8320 / Production host: Escherichia coli (E. coli) / References: UniProt: R5A2Y6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.6M ammonium sulfate, 0.1M sodium citrate and 0.2M NaCl, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 5, 2013
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 74966 / Num. obs: 74966 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 10.18 Å2 / Rsym value: 0.058 / Net I/σ(I): 10.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.4 % / Rsym value: 0.26 / % possible all: 91.4

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3OWA

3owa


Resolution: 1.5→30.555 Å / SU ML: 0.13 / σ(F): 1.48 / Phase error: 17.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1803 2344 3.13 %
Rwork0.1531 --
obs0.154 74953 96.03 %
all-74966 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→30.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3395 0 57 653 4105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063707
X-RAY DIFFRACTIONf_angle_d1.0625081
X-RAY DIFFRACTIONf_dihedral_angle_d14.3831347
X-RAY DIFFRACTIONf_chiral_restr0.079539
X-RAY DIFFRACTIONf_plane_restr0.004696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.498-1.52860.23141220.18583831X-RAY DIFFRACTION87
1.5286-1.56180.24191330.17394194X-RAY DIFFRACTION94
1.5618-1.59810.17881310.17244166X-RAY DIFFRACTION94
1.5981-1.63810.1971440.16544227X-RAY DIFFRACTION95
1.6381-1.68240.17211360.15584216X-RAY DIFFRACTION95
1.6824-1.73190.18491370.15094250X-RAY DIFFRACTION96
1.7319-1.78780.17661430.14874308X-RAY DIFFRACTION96
1.7878-1.85170.19681310.15224265X-RAY DIFFRACTION96
1.8517-1.92580.16831420.15384272X-RAY DIFFRACTION97
1.9258-2.01340.19291350.15354317X-RAY DIFFRACTION97
2.0134-2.11960.19641440.14974291X-RAY DIFFRACTION97
2.1196-2.25230.15831360.14654339X-RAY DIFFRACTION98
2.2523-2.42620.20281390.15584348X-RAY DIFFRACTION98
2.4262-2.67020.19861440.164372X-RAY DIFFRACTION98
2.6702-3.05630.16181420.16214378X-RAY DIFFRACTION98
3.0563-3.84940.17141440.1424410X-RAY DIFFRACTION99
3.8494-30.56170.15961410.1444425X-RAY DIFFRACTION99

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