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- PDB-3hrl: Crystal structure of a putative endonuclease-like protein (ngo005... -

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Basic information

Entry
Database: PDB / ID: 3hrl
TitleCrystal structure of a putative endonuclease-like protein (ngo0050) from neisseria gonorrhoeae
ComponentsEndonuclease-Like Protein
Keywordsstructural genomics / unknown function / ENDONUCLEASE / NEISSERIA GONORRHOEAE / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyDomain of unknown function DUF559 / Protein of unknown function (DUF559) / Restriction endonuclease type II-like / methyltransferase activity / methylation / DNA (Cytosine-5-)-methyltransferase
Function and homology information
Biological speciesNeisseria gonorrhoeae FA 1090 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Cobb, G. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of a Putative Endonuclease-Like Protein (Ngo0050) from Neisseria Gonorrhoeae
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Cobb, G. / Joachimiak, A. / Anderson, W.F.
History
DepositionJun 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endonuclease-Like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2512
Polymers12,2151
Non-polymers351
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.922, 52.922, 102.295
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Endonuclease-Like Protein


Mass: 12215.399 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae FA 1090 (bacteria)
Gene: NGO0050 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21magic / References: UniProt: Q5FAH0
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.39 Å3/Da / Density % sol: 63.67 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3M NaCl, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 / Wavelength: 0.97872 Å
DetectorDetector: CCD / Date: May 29, 2009 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→22.33 Å / Num. all: 23330 / Num. obs: 23330 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 21.712
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 5.2 / Rsym value: 0.353 / % possible all: 98.7

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
ARP/wARPmodel building
Cootmodel building
REFMAC5.5.0051refinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→22.33 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.694 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 604 4.8 %RANDOM
Rwork0.18316 ---
obs0.18521 11984 99.83 %-
all-12588 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.925 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20.82 Å20 Å2
2--1.65 Å20 Å2
3----2.47 Å2
Refinement stepCycle: LAST / Resolution: 1.95→22.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms775 0 1 105 881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022790
X-RAY DIFFRACTIONr_bond_other_d0.0010.02539
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.9411066
X-RAY DIFFRACTIONr_angle_other_deg0.90131301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.733592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.823.57142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22315141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.846157
X-RAY DIFFRACTIONr_chiral_restr0.0980.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02170
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0871.5465
X-RAY DIFFRACTIONr_mcbond_other0.3141.5190
X-RAY DIFFRACTIONr_mcangle_it1.9972746
X-RAY DIFFRACTIONr_scbond_it3.5293325
X-RAY DIFFRACTIONr_scangle_it5.934.5320
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 37 -
Rwork0.19 839 -
obs--98.65 %
Refinement TLS params.Method: refined / Origin x: 34.4501 Å / Origin y: 22.4862 Å / Origin z: 20.4432 Å
111213212223313233
T0.0517 Å20.0085 Å20.0086 Å2-0.0852 Å20.0165 Å2--0.0103 Å2
L2.8971 °20.542 °20.9626 °2-0.9887 °20.4558 °2--1.4877 °2
S-0.0131 Å °0.1571 Å °-0.0196 Å °-0.0458 Å °0.0904 Å °0.0156 Å °-0.0181 Å °0.0068 Å °-0.0773 Å °

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