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- PDB-3jsr: X-Ray structure of All0216 protein from Nostoc sp. PCC 7120 at th... -

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Basic information

Entry
Database: PDB / ID: 3jsr
TitleX-Ray structure of All0216 protein from Nostoc sp. PCC 7120 at the resolution 1.8A. Northeast Structural Genomics Consortium target NsR236
ComponentsAll0216 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / NsR236
Function / homologyUncharacterised protein family Ycf54 / Ycf54 protein / Ycf54-like superfamily / Ycf54 protein / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / : / All0216 protein
Function and homology information
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKuzin, A.P. / Chen, Y. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-Ray structure of All0216 protein from Nostoc sp. PCC 7120 at the resolution 1.8A
Authors: Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: All0216 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0362
Polymers13,9971
Non-polymers391
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.603, 57.603, 97.554
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-200-

HOH

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Components

#1: Protein All0216 protein


Mass: 13996.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: all0216 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8Z082
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
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: 2.89 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 293 K / pH: 9
Details: 8.64 M potassium acetate, 0.1 M TAPS, pH 9.0, microbatch, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→29 Å / Num. obs: 15602 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 27.7 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 75.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 28.8 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 13.4 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.4_115)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→28.8 Å / SU ML: 0.18 / σ(F): 0.16 / Phase error: 20.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 1560 10 %
Rwork0.222 --
obs0.222 15600 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.24 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7126 Å2-0 Å20 Å2
2---2.7126 Å2-0 Å2
3---5.4253 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms887 0 1 135 1023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006912
X-RAY DIFFRACTIONf_angle_d1.281241
X-RAY DIFFRACTIONf_dihedral_angle_d19.094338
X-RAY DIFFRACTIONf_chiral_restr0.094136
X-RAY DIFFRACTIONf_plane_restr0.007159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.85810.22991380.24351248X-RAY DIFFRACTION98
1.8581-1.92450.27811380.22791232X-RAY DIFFRACTION98
1.9245-2.00160.23791360.22881235X-RAY DIFFRACTION98
2.0016-2.09260.26231380.22611259X-RAY DIFFRACTION99
2.0926-2.20290.24311410.22751263X-RAY DIFFRACTION98
2.2029-2.34090.21871390.24221265X-RAY DIFFRACTION99
2.3409-2.52150.21251430.22831288X-RAY DIFFRACTION99
2.5215-2.77510.2241420.21941272X-RAY DIFFRACTION99
2.7751-3.17620.25331440.23861304X-RAY DIFFRACTION99
3.1762-40.20561480.20261310X-RAY DIFFRACTION99
4-28.80520.2011530.19661364X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 16.276 Å / Origin y: 23.1833 Å / Origin z: 35.2722 Å
111213212223313233
T0.1635 Å2-0.0069 Å2-0.0239 Å2-0.0885 Å20.006 Å2--0.0969 Å2
L0.0631 °2-0.1105 °20.145 °2-1.3517 °2-0.522 °2--0.5423 °2
S-0.005 Å °-0.003 Å °0.0117 Å °-0.2181 Å °-0.0578 Å °0.0818 Å °0.0117 Å °0.0314 Å °0.0427 Å °
Refinement TLS groupSelection details: ALL

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