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- PDB-4kyb: Crystal Structure of de novo designed serine hydrolase OSH55.14_E... -

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Basic information

Entry
Database: PDB / ID: 4kyb
TitleCrystal Structure of de novo designed serine hydrolase OSH55.14_E3, Northeast Structural Genomics Consortium Target OR342
ComponentsDesigned Protein OR342
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG) Target OR342
Function / homologyLeucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.909 Å
AuthorsKuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Lee, D. / Raja, S. / Everett, J.K. / Acton, T.B. ...Kuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Lee, D. / Raja, S. / 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 OR342
Authors: Kuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Lee, D. / Raja, S. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMay 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Designed Protein OR342
B: Designed Protein OR342
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8546
Polymers35,4752
Non-polymers3804
Water543
1
A: Designed Protein OR342
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9273
Polymers17,7371
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Designed Protein OR342
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9273
Polymers17,7371
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.054, 76.401, 132.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsmonomer,. kD,0%

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Components

#1: Protein Designed Protein OR342


Mass: 17737.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.15 Å3/Da / Density % sol: 42.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:0.1 M Potassium phosphate-monobasic (KH2PO4) 0.1 M HEPES, PEG 8000 40% (w/v) , VAPOR DIFFUSION, ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:0.1 M Potassium phosphate-monobasic (KH2PO4) 0.1 M HEPES, PEG 8000 40% (w/v) , VAPOR DIFFUSION, HANGING DROP, 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 CCD 165 mm / Detector: CCD / Date: Jan 22, 2013
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: 2.9→30 Å / Num. obs: 6944 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 10.9

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Processing

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

4ess


Resolution: 2.909→29.31 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.753 / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 29.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.301 346 5.03 %random
Rwork0.201 ---
obs0.206 6875 95.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.78 Å2 / Biso mean: 51.146 Å2 / Biso min: 23.78 Å2
Refinement stepCycle: LAST / Resolution: 2.909→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 20 3 2361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092403
X-RAY DIFFRACTIONf_angle_d2.1433248
X-RAY DIFFRACTIONf_chiral_restr0.074374
X-RAY DIFFRACTIONf_plane_restr0.008426
X-RAY DIFFRACTIONf_dihedral_angle_d18.46886
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.909-3.6640.3541620.2293070323292
3.664-29.3120.2691840.1843459364398
Refinement TLS params.Method: refined / Origin x: -15.5275 Å / Origin y: 11.1258 Å / Origin z: -36.5875 Å
111213212223313233
T0.287 Å20.0072 Å2-0.0064 Å2-0.3116 Å2-0.001 Å2--0.3051 Å2
L1.0483 °20.1307 °20.5918 °2-0.2967 °20.0773 °2--1.5236 °2
S0.0306 Å °-0.069 Å °-0.0111 Å °-0.0701 Å °-0.036 Å °0.0177 Å °-0.0194 Å °0.1258 Å °-0.0183 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 164
2X-RAY DIFFRACTION1allB2 - 156
3X-RAY DIFFRACTION1all1 - 4
4X-RAY DIFFRACTION1allN1
5X-RAY DIFFRACTION1allA - B1 - 202
6X-RAY DIFFRACTION1allT1
7X-RAY DIFFRACTION1allG1

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