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- PDB-4jgk: Crystal Structure of the evolved variant of the computationally d... -

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Basic information

Entry
Database: PDB / ID: 4jgk
TitleCrystal Structure of the evolved variant of the computationally designed serine hydrolase, Northeast Structural Genomics Consortium (NESG) Target OR275
Componentsevolved variant of a designed serine hydrolase
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / serine hydrolase
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: 1.883 Å
AuthorsKuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. / Baker, D. ...Kuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Mao, L. / 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: Crystal Structure of the evolved variant of the computationally designed serine hydrolase, Northeast Structural Genomics Consortium (NESG) Target OR275
Authors: Kuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMar 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Source and taxonomy
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: evolved variant of a designed serine hydrolase
B: evolved variant of a designed serine hydrolase
C: evolved variant of a designed serine hydrolase
D: evolved variant of a designed serine hydrolase


Theoretical massNumber of molelcules
Total (without water)70,9054
Polymers70,9054
Non-polymers00
Water8,017445
1
A: evolved variant of a designed serine hydrolase


Theoretical massNumber of molelcules
Total (without water)17,7261
Polymers17,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: evolved variant of a designed serine hydrolase


Theoretical massNumber of molelcules
Total (without water)17,7261
Polymers17,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: evolved variant of a designed serine hydrolase


Theoretical massNumber of molelcules
Total (without water)17,7261
Polymers17,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: evolved variant of a designed serine hydrolase


Theoretical massNumber of molelcules
Total (without water)17,7261
Polymers17,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.618, 30.155, 128.732
Angle α, β, γ (deg.)90.000, 90.870, 90.000
Int Tables number4
Space group name H-MP1211
Detailsmonomer,15.59 kD,93.3%

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Components

#1: Protein
evolved variant of a designed serine hydrolase


Mass: 17726.230 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.1 Å3/Da / Density % sol: 41.35 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 7
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:DL-malic acid 0.15M, PEG 3350 20%, microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 2, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.883→50 Å / Num. obs: 44664 / % possible obs: 92.2 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 16.48 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 49.1

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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 4ETJ

4etj


Resolution: 1.883→49.65 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.854 / SU ML: 0.2 / σ(F): 1.34 / Phase error: 21.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2249 5.04 %random
Rwork0.177 ---
obs0.179 44651 91.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.06 Å2 / Biso mean: 20.864 Å2 / Biso min: 8.17 Å2
Refinement stepCycle: LAST / Resolution: 1.883→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4912 0 0 445 5357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065033
X-RAY DIFFRACTIONf_angle_d0.9756814
X-RAY DIFFRACTIONf_chiral_restr0.063782
X-RAY DIFFRACTIONf_plane_restr0.004893
X-RAY DIFFRACTIONf_dihedral_angle_d12.7141834
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.883-1.9240.278740.1941377145149
1.924-1.9690.2751000.1871788188862
1.969-2.0190.2541250.1762071219672
2.019-2.0730.2391350.1782612274792
2.073-2.1340.2611620.1722812297498
2.134-2.2030.2181470.1672780292798
2.203-2.2820.231510.16228793030100
2.282-2.3730.2411450.1762790293597
2.373-2.4810.2441440.18228923036100
2.481-2.6120.2581440.1962800294498
2.612-2.7750.2351640.1922871303599
2.775-2.990.2561400.19429073047100
2.99-3.290.2361480.1962907305599
3.29-3.7660.2161590.17629243083100
3.766-4.7450.2091430.15429303073100
4.745-49.6670.1791680.1663062323099
Refinement TLS params.Method: refined / Origin x: 8.4627 Å / Origin y: 23.3499 Å / Origin z: 32.3973 Å
111213212223313233
T0.113 Å20.0107 Å20.0021 Å2-0.0824 Å20.0017 Å2--0.1287 Å2
L0.0605 °20.0513 °2-0.0116 °2-0.0664 °2-0.056 °2--0.15 °2
S0.0113 Å °0.0032 Å °0.0092 Å °-0.0225 Å °0.0033 Å °0.0298 Å °0.0123 Å °-0.019 Å °-0.0146 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 165
2X-RAY DIFFRACTION1allB2 - 166
3X-RAY DIFFRACTION1allC2 - 166
4X-RAY DIFFRACTION1allD2 - 167
5X-RAY DIFFRACTION1allB1 - 445

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