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- PDB-3rd4: Crystal structure of PROPEN_03304 from Proteus penneri ATCC 35198... -

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Basic information

Entry
Database: PDB / ID: 3rd4
TitleCrystal structure of PROPEN_03304 from Proteus penneri ATCC 35198 Northeast Structural Genomics Consortium target id PvR55
Componentsuncharacterized protein
KeywordsStructural Genomics / Unknown function / PSI-Biology / Northeast Structural Genomics Consortium / NESG / PROPEN_03304
Function / homologyOB fold (Dihydrolipoamide Acetyltransferase, E2P) - #660 / Protein of unknown function DUF2500 / Protein of unknown function (DUF2500) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesProteus penneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsSeetharaman, J. / Min, S. / Kuzin, A. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. ...Seetharaman, J. / Min, S. / Kuzin, A. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of PROPEN_03304 from Proteus penneri ATCC 35198 Northeast Structural Genomics Consortium target id PvR55
Authors: Seetharaman, J. / Min, S. / Kuzin, A. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / ...Authors: Seetharaman, J. / Min, S. / Kuzin, A. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
History
DepositionMar 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: uncharacterized protein
D: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)47,7744
Polymers47,7744
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)11,9431
Polymers11,9431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)11,9431
Polymers11,9431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)11,9431
Polymers11,9431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)11,9431
Polymers11,9431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.415, 91.365, 52.198
Angle α, β, γ (deg.)90.00, 104.97, 90.00
Int Tables number5
Space group name H-MC121
DetailsTetramer

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Components

#1: Protein
uncharacterized protein


Mass: 11943.448 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus penneri (bacteria) / Strain: ATCC 35198 / Gene: PROPEN_03304 / Production host: Escherichia coli (E. coli) / References: UniProt: C0AZM8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.34 Å3/Da / Density % sol: 63.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES (pH 7.5), 30% PEG8k, and 0.1M, NaCl , VAPOR DIFFUSION, SITTING DROP, temperature 18K, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.707 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 10, 2011
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.707 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 26654 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.069 / Net I/σ(I): 9.9
Reflection shellResolution: 2.9→3 Å / Redundancy: 3 % / Num. unique all: 2024 / % possible all: 73.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→40.06 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 87091.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1314 5.8 %RANDOM
Rwork0.211 ---
obs0.211 22753 83 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.6028 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 50.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å210.35 Å2
2---11.72 Å20 Å2
3---11.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.9→40.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 0 76 2616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_improper_angle_d0.89
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 115 5 %
Rwork0.315 2179 -
obs--50 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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