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- PDB-3e56: The 2.0 Angstrom Resolution Crystal Structure of NpR1517, a Putat... -

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Basic information

Entry
Database: PDB / ID: 3.0E+56
TitleThe 2.0 Angstrom Resolution Crystal Structure of NpR1517, a Putative Heterocyst Differentiation Inhibitor from Nostoc punctiforme
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / alpha-beta sandwich / interlocked homodimer / ASR1734
Function / homologyUbiquitin-like (UB roll) / Ubiquitin-like (UB roll) - #10 / Npun R1517 / Npun R1517 / Other non-globular / Special / Npun R1517 domain-containing protein
Function and homology information
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / sulfur anomalous scattering / Resolution: 2.01 Å
AuthorsKennedy, M.A. / Ni, S. / Smola, M.J.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of Npun_R1517, a putative negative regulator of heterocyst differentiation from Nostoc punctiforme PCC 73102.
Authors: Ni, S. / Benning, M.M. / Smola, M.J. / Feldmann, E.A. / Kennedy, M.A.
History
DepositionAug 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,9171
Polymers12,9171
Non-polymers00
Water1,06359
1
A: Putative uncharacterized protein

A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)25,8332
Polymers25,8332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area4520 Å2
ΔGint-33 kcal/mol
Surface area9320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.336, 56.336, 56.491
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-123-

HOH

21A-149-

HOH

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Components

#1: Protein Putative uncharacterized protein


Mass: 12916.604 Da / Num. of mol.: 1 / Fragment: UNP residues 1-88
Source method: isolated from a genetically manipulated source
Details: cytosolic / Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Gene: Npun_R1517 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: B2IZS7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 1.74 Å3/Da / Density % sol: 29.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: .02M HEPES, 20% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: May 15, 2008 / Details: mirrors
RadiationMonochromator: Layered Montel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→39.9 Å / Num. all: 6345 / Num. obs: 6345 / % possible obs: 95.9 % / Observed criterion σ(I): 3 / Redundancy: 105.86 % / Biso Wilson estimate: 24.37 Å2 / Rsym value: 0.06 / Net I/σ(I): 76.22
Reflection shellResolution: 2.01→2.05 Å / Redundancy: 19.53 % / Mean I/σ(I) obs: 9.15 / Num. unique all: 1604 / Rsym value: 0.28 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PROTEUM2version 2data collection
SAINTdata reduction
SADABSdata scaling
SHELXSphasing
RefinementMethod to determine structure: sulfur anomalous scattering / Resolution: 2.01→39.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.475 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(I): 3 / ESU R: 2.082 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23683 291 4.6 %RANDOM
Rwork0.18795 ---
obs0.19007 6053 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.854 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.01→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms611 0 0 59 670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022616
X-RAY DIFFRACTIONr_angle_refined_deg1.5962.001825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.272574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.224.68832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.70215128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.471156
X-RAY DIFFRACTIONr_chiral_restr0.0950.296
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02449
X-RAY DIFFRACTIONr_nbd_refined0.2240.2199
X-RAY DIFFRACTIONr_nbtor_refined0.30.2412
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.233
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.210
X-RAY DIFFRACTIONr_mcbond_it1.3511.5387
X-RAY DIFFRACTIONr_mcangle_it2.1652599
X-RAY DIFFRACTIONr_scbond_it4.6443250
X-RAY DIFFRACTIONr_scangle_it5.5414.5226
X-RAY DIFFRACTIONr_rigid_bond_restr4.5373637
X-RAY DIFFRACTIONr_sphericity_free6.058359
X-RAY DIFFRACTIONr_sphericity_bonded3.0613611
LS refinement shellResolution: 2.01→2.063 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 21 -
Rwork0.191 389 -
obs-389 91.31 %

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