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- PDB-3klu: Crystal structure of the protein yqbn. northeast structural genom... -

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Basic information

Entry
Database: PDB / ID: 3klu
TitleCrystal structure of the protein yqbn. northeast structural genomics consortium target sr445.
ComponentsUncharacterized protein yqbN
Keywordsstructural genomics / unknown function / NESG / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM
Function / homologyrbstp2171 - #30 / Phage-like element PBSX protein XkdN-like / Phage-like element PBSX protein XkdN-like superfamily / Phage XkdN-like tail assembly chaperone protein, TAC / rbstp2171 / 2-Layer Sandwich / Alpha Beta / : / Uncharacterized protein YqbN
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsKuzin, A.P. / Su, M. / Seetharaman, J. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, M. / Baran, M.C. ...Kuzin, A.P. / Su, M. / Seetharaman, J. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, M. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the protein yqbn. northeast structural genomics consortium target sr445.
Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, M. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionNov 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
SupersessionDec 8, 2009ID: 3DFD
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 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_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_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: Uncharacterized protein yqbN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3792
Polymers18,3241
Non-polymers551
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.101, 70.101, 59.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Uncharacterized protein yqbN


Mass: 18324.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yqbN, BSU26040 / References: UniProt: P45930
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG1000 20%, 0.1M MNCL2, 0.1M NAACETATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791, 0.9679, 0.9794
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: mirror
RadiationMonochromator: Si(222) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.96791
30.97941
ReflectionResolution: 2.2→50 Å / Num. obs: 16390 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 11.8 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 14.5
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.246 --
Rwork0.225 --
obs-16390 86 %
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 1 26 993

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