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

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Entry
Database: PDB / ID: 4jbc
TitleCrystal Structure of the computationally designed serine hydrolase 3mmj_2, Northeast Structural Genomics Consortium (NESG) Target OR318
Componentsdesigned serine hydrolase 3mmj_2
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / serine hydrolase
Function / homologyAlpha-Beta Plaits - #1690 / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta / PHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 Å
AuthorsKuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Kuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Baker, D. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the computationally designed serine hydrolase 3mmj_2, Northeast Structural Genomics Consortium (NESG) Target OR318
Authors: Kuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Baker, D. / Hunt, J.F.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Structure summary
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: designed serine hydrolase 3mmj_2
B: designed serine hydrolase 3mmj_2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3786
Polymers74,9982
Non-polymers3804
Water9,188510
1
A: designed serine hydrolase 3mmj_2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5942
Polymers37,4991
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: designed serine hydrolase 3mmj_2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7844
Polymers37,4991
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-31 kcal/mol
Surface area28850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.243, 194.552, 46.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Detailsmonomer,42.52 kD,70.1%|heptamer,279.8 kD,22.8%

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Components

#1: Protein designed serine hydrolase 3mmj_2


Mass: 37499.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 10
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: Ammonium phosphate-monobasic 0.1M, CAPS 0.1M, PEG 2000 12% (w/v), VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97908 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 14, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 43119 / % possible obs: 85.4 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 15.83 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.9

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1269refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U26

1u26


Resolution: 2.005→29.732 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.812 / SU ML: 0.23 / σ(F): 1.43 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 1988 4.65 %
Rwork0.202 --
obs0.204 42747 84.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.33 Å2 / Biso mean: 26.531 Å2 / Biso min: 8.32 Å2
Refinement stepCycle: LAST / Resolution: 2.005→29.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5077 0 20 510 5607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085241
X-RAY DIFFRACTIONf_angle_d1.1747106
X-RAY DIFFRACTIONf_chiral_restr0.087723
X-RAY DIFFRACTIONf_plane_restr0.006922
X-RAY DIFFRACTIONf_dihedral_angle_d16.1771920
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.005-2.0560.281350.2072762289782
2.056-2.1110.2871430.2142923306687
2.111-2.1730.2861450.2352976312187
2.173-2.2430.497720.4061489156144
2.243-2.3230.591710.4071500157144
2.323-2.4170.2711530.2163147330092
2.417-2.5260.2771570.23200335795
2.526-2.660.2391620.2073324348697
2.66-2.8260.2461650.2043377354298
2.826-3.0440.271690.2083454362399
3.044-3.350.2571670.19634323599100
3.35-3.8340.2721020.1932074217659
3.834-4.8270.2091650.1523401356697
4.827-29.7350.1931820.16137003882100
Refinement TLS params.Method: refined / Origin x: -24.3843 Å / Origin y: 7.0721 Å / Origin z: -30.5696 Å
111213212223313233
T0.1014 Å2-0.003 Å20.0002 Å2-0.1268 Å20.0098 Å2--0.0926 Å2
L0.1512 °2-0.2126 °2-0.0873 °2-0.9763 °20.3052 °2--0.461 °2
S0.0113 Å °0.0015 Å °0.0144 Å °-0.0121 Å °0.0004 Å °-0.0196 Å °0.0148 Å °0.0824 Å °-0.009 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 315
2X-RAY DIFFRACTION1allB3 - 315
3X-RAY DIFFRACTION1allA - B1 - 403
4X-RAY DIFFRACTION1allA - B1 - 738

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