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- PDB-4k0c: Crystal Structure of the computationally designed serine hydrolas... -

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Basic information

Entry
Database: PDB / ID: 4k0c
TitleCrystal Structure of the computationally designed serine hydrolase. Northeast Structural Genomics Consortium (NESG) Target OR317
Componentsdesigned serine hydrolase
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyLeucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å
AuthorsKuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. / Baker, D. ...Kuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / 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: Northeast Structural Genomics Consortium Target OR317
Authors: Kuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: designed serine hydrolase
B: designed serine hydrolase


Theoretical massNumber of molelcules
Total (without water)35,7462
Polymers35,7462
Non-polymers00
Water00
1
A: designed serine hydrolase


Theoretical massNumber of molelcules
Total (without water)17,8731
Polymers17,8731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: designed serine hydrolase


Theoretical massNumber of molelcules
Total (without water)17,8731
Polymers17,8731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.026, 76.032, 128.355
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein designed serine hydrolase


Mass: 17873.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 277 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 magnesium sulfate heptahydrate, 0.1 MES, PEG 400 40% v/v., microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 22, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 10205 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 48.52 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 9.7

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1269refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ESS

4ess


Resolution: 3.002→37.287 Å / Occupancy max: 1 / Occupancy min: 0.77 / FOM work R set: 0.816 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.257 491 4.83 %random
Rwork0.181 ---
obs0.184 10173 89.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.86 Å2 / Biso mean: 34.838 Å2 / Biso min: 9.25 Å2
Refinement stepCycle: LAST / Resolution: 3.002→37.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 0 0 2368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012395
X-RAY DIFFRACTIONf_angle_d1.323237
X-RAY DIFFRACTIONf_chiral_restr0.079381
X-RAY DIFFRACTIONf_plane_restr0.009426
X-RAY DIFFRACTIONf_dihedral_angle_d16.874893
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.002-3.3040.339970.2281876197370
3.304-3.7810.2811260.1892433255991
3.781-4.7620.2381380.172665280399
4.762-37.290.2311300.16827082838100

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