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- PDB-4diu: Crystal Structure of Engineered Protein. Northeast Structural Gen... -

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Basic information

Entry
Database: PDB / ID: 4diu
TitleCrystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR94
ComponentsEngineered Protein PF00326
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeetharaman, J. / Lew, S. / Wang, D. / Kohan, E. / Patel, D. / Whitehead, T. / Fleishman, S. / Ciccosanti, C. / Xiao, R. / Everett, J.K. ...Seetharaman, J. / Lew, S. / Wang, D. / Kohan, E. / Patel, D. / Whitehead, T. / Fleishman, S. / Ciccosanti, C. / Xiao, R. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR94
Authors: Seetharaman, J. / Lew, S. / Wang, D. / Kohan, E. / Patel, D. / Whitehead, T. / Fleishman, S. / Ciccosanti, C. / Xiao, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJan 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Engineered Protein PF00326


Theoretical massNumber of molelcules
Total (without water)28,4531
Polymers28,4531
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.447, 95.595, 50.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Engineered Protein PF00326


Mass: 28453.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 6
Details: 2.03 M Lithium sulfate monohydrate .1M MES pH 6, Microbatch under oil, temperature 4 K, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 22, 2012
RadiationMonochromator: Bent single crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 17960 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.8 Å2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.66 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 213462.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2738 15.2 %RANDOM
Rwork0.214 ---
obs0.214 17960 81.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.6666 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1--12.4 Å20 Å20 Å2
2--11.45 Å20 Å2
3---0.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å-0.05 Å
Refinement stepCycle: LAST / Resolution: 2→30.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 0 142 2118
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.8
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 481 16.3 %
Rwork0.213 2464 -
obs--82.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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