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- PDB-4drt: Three dimensional structure of de novo designed serine hydrolase ... -

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Basic information

Entry
Database: PDB / ID: 4drt
TitleThree dimensional structure of de novo designed serine hydrolase OSH26, Northeast Structural Genomics Consortium (NESG) target OR89
Componentsde novo designed serine hydrolase, OR89
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homologyPeptidoglycan synthesis regulatory factor (PBP3), Domain 2 / D-Ala-D-Ala carboxypeptidase, C-terminal domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsKuzin, A. / Su, M. / Rajagopalan, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Baker, D. / Everett, J.K. / Acton, T.B. ...Kuzin, A. / Su, M. / Rajagopalan, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Baker, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Design of activated serine-containing catalytic triads with atomic-level accuracy.
Authors: Rajagopalan, S. / Wang, C. / Yu, K. / Kuzin, A.P. / Richter, F. / Lew, S. / Miklos, A.E. / Matthews, M.L. / Seetharaman, J. / Su, M. / Hunt, J.F. / Cravatt, B.F. / Baker, D.
History
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Sep 13, 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: de novo designed serine hydrolase, OR89
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1473
Polymers40,0881
Non-polymers582
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.114, 50.114, 134.205
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein de novo designed serine hydrolase, OR89


Mass: 40088.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 9
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 0.1M NH4H2PO4, 0.1m TAPS, PEG 8000 20% (w/v), microbatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 14, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.378
ReflectionResolution: 1.8→50 Å / Num. obs: 32295 / % possible obs: 92.5 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 38.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.411 / % possible all: 60.3

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-3000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MZF

3mzf


Resolution: 2.002→26.544 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.831 / Cross valid method: THROUGHOUT / σ(F): 2.08 / Phase error: 25 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.156 1294 5.11 %random
Rwork0.123 ---
obs0.123 25328 99.68 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.471 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 179.31 Å2 / Biso mean: 32.122 Å2 / Biso min: 11.01 Å2
Baniso -1Baniso -2Baniso -3
1--3.098 Å20 Å20 Å2
2---3.098 Å2-0 Å2
3---6.196 Å2
Refinement stepCycle: LAST / Resolution: 2.002→26.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2703 0 2 289 2994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072793
X-RAY DIFFRACTIONf_angle_d1.1693780
X-RAY DIFFRACTIONf_chiral_restr0.078420
X-RAY DIFFRACTIONf_plane_restr0.004498
X-RAY DIFFRACTIONf_dihedral_angle_d14.6691034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.003-2.0830.2041480.1782620276893
2.083-2.1770.191270.1722722284996
2.177-2.2920.1811430.1682668281195
2.292-2.4350.1771520.1542612276495
2.435-2.6230.1751570.1472708286595
2.623-2.8870.1861420.1342652279495
2.887-3.3030.1541550.1172670282595
3.303-4.1570.131320.0852687281995
4.157-21.8620.1331360.0962655279194
Refinement TLS params.Method: refined / Origin x: 15.2426 Å / Origin y: 5.2944 Å / Origin z: 0.3061 Å
111213212223313233
T0.1345 Å2-0.0427 Å20.0557 Å2-0.0701 Å20.0073 Å2--0.1479 Å2
L0.4846 °20.0533 °2-0.1437 °2-0.1213 °2-0.1519 °2--0.2994 °2
S0.0241 Å °-0.0209 Å °0.0207 Å °0.075 Å °-0.0534 Å °0.031 Å °-0.0354 Å °-0.0022 Å °0.0299 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 358
2X-RAY DIFFRACTION1allA1 - 872

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