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- PDB-3pe5: Three-dimensional Structure of protein A7VV38_9CLOT from Clostrid... -

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Basic information

Entry
Database: PDB / ID: 3pe5
TitleThree-dimensional Structure of protein A7VV38_9CLOT from Clostridium leptum DSM 753, Northeast Structural Genomics Consortium Target QlR103
ComponentsUncharacterized protein
KeywordsStructural genomics / Unknown function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyLCP protein / : / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / Aminopeptidase / 3-Layer(aba) Sandwich / membrane / Alpha Beta / Cell envelope-like function transcriptional attenuator common domain protein
Function and homology information
Biological speciesClostridium leptum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.381 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be published
Title: Northeast Structural Genomics Consortium Target QlR103
Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionOct 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Nov 20, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)89,7542
Polymers89,7542
Non-polymers00
Water1,15364
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)44,8771
Polymers44,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)44,8771
Polymers44,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.778, 49.617, 105.282
Angle α, β, γ (deg.)90.000, 106.350, 90.000
Int Tables number4
Space group name H-MP1211
Detailsmonomer,40.22 kD,95.6%

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Components

#1: Protein Uncharacterized protein


Mass: 44876.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium leptum (bacteria) / Strain: DSM 753 / Gene: CLOLEP_02443 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: A7VV38
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 6
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution:0.1M MgCl2, 0.1M MES, PEG 4000 20% /w/v), microbatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97903 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 52123 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 13.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.6 / % possible all: 85

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.381→35.397 Å / FOM work R set: 0.726 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1366 5.01 %RANDOM
Rwork0.211 ---
obs0.214 28649 95.77 %-
Solvent computationShrinkage radii: 0.72 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.344 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 187.72 Å2 / Biso mean: 51.36 Å2 / Biso min: 14.01 Å2
Baniso -1Baniso -2Baniso -3
1-25.204 Å20 Å2-17.895 Å2
2---15.592 Å20 Å2
3----9.612 Å2
Refinement stepCycle: LAST / Resolution: 2.381→35.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4338 0 0 64 4402
Refinement TLS params.Method: refined / Origin x: -22.1897 Å / Origin y: 35.9299 Å / Origin z: 75.5461 Å
111213212223313233
T0.1558 Å2-0.016 Å20.0282 Å2-0.1714 Å20.0167 Å2--0.1457 Å2
L0.5303 °2-0.2648 °20.5291 °2-0.263 °2-0.212 °2--0.398 °2
S0.0087 Å °-0.0165 Å °-0.0129 Å °0.0313 Å °0.004 Å °0.0256 Å °-0.0407 Å °-0.0031 Å °-0 Å °
Refinement TLS groupSelection details: all

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