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- PDB-4gvw: Three-dimensional structure of the de novo designed serine hydrol... -

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Basic information

Entry
Database: PDB / ID: 4gvw
TitleThree-dimensional structure of the de novo designed serine hydrolase 2bfq_3, Northeast Structural Genomics Consortium (NESG) Target OR248
ComponentsDe novo designed serine hydrolase
KeywordsDE NOVO PROTEIN / HYDROLASE / Structural Genomics / 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 / ACETIC ACID / PHOSPHATE ION
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / BALBES / Resolution: 2.113 Å
AuthorsKuzin, A. / Lew, S. / Seetharaman, J. / Rajagopalan, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target OR248
Authors: Kuzin, A. / Lew, S. / Seetharaman, J. / Rajagopalan, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionAug 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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_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

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Assembly

Deposited unit
A: De novo designed serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0804
Polymers21,7301
Non-polymers3503
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.644, 62.052, 107.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Detailsbiological unit is the same as asym.

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Components

#1: Protein De novo designed serine hydrolase


Mass: 21729.865 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growMethod: 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 Ammonium Sulfate, 0.1M MES, 40% PEG 8000, microbatch under oil

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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: Jun 5, 2012 / 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: 2.1→50 Å / Num. obs: 10802 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 37

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Processing

Software
NameVersionClassificationNB
PHENIXdev_988refinement
PDB_EXTRACT3.1data extraction
msr165data collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: BALBES
Starting model: 2BFR

2bfr


Resolution: 2.113→41.427 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.839 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.239 520 4.82 %random
Rwork0.172 ---
obs0.175 10795 98.31 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.836 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 102.19 Å2 / Biso mean: 32.397 Å2 / Biso min: 10.78 Å2
Baniso -1Baniso -2Baniso -3
1--4.39 Å2-0 Å20 Å2
2---3.212 Å20 Å2
3---7.603 Å2
Refinement stepCycle: LAST / Resolution: 2.113→41.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1456 0 21 75 1552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081517
X-RAY DIFFRACTIONf_angle_d1.0032044
X-RAY DIFFRACTIONf_chiral_restr0.073225
X-RAY DIFFRACTIONf_plane_restr0.005262
X-RAY DIFFRACTIONf_dihedral_angle_d15.144564
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 (%)
2.113-2.3260.2821230.1972391251493
2.326-2.6620.2541300.18425732703100
2.662-3.3540.2551350.17126022737100
3.354-41.4350.2121320.16127092841100
Refinement TLS params.Method: refined / Origin x: -12.6994 Å / Origin y: -15.0508 Å / Origin z: -16.0012 Å
111213212223313233
T0.1356 Å20.0064 Å20.0041 Å2-0.1769 Å2-0.0398 Å2--0.1887 Å2
L2.3216 °2-0.056 °2-0.0637 °2-2.7582 °2-0.8577 °2--2.7186 °2
S-0.0635 Å °-0.3642 Å °0.1322 Å °0.3806 Å °0.0271 Å °-0.0096 Å °-0.1355 Å °-0.1266 Å °0.0366 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 192
2X-RAY DIFFRACTION1allA1 - 375
3X-RAY DIFFRACTION1allA1 - 201
4X-RAY DIFFRACTION1allA1 - 202
5X-RAY DIFFRACTION1allA1 - 203

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