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- PDB-4loa: X-ray structure of the de-novo design amidase at the resolution 1... -

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Basic information

Entry
Database: PDB / ID: 4loa
TitleX-ray structure of the de-novo design amidase at the resolution 1.8A, Northeast Structural Genomics Consortium (NESG) Target OR398
ComponentsDe-novo design amidase
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG) / de novo design / amidase
Function / homologyP-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.819 Å
AuthorsKuzin, A. / Lew, S. / Vorobiev, S.M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Maglaqui, M. / Kogan, S. / Khersonsky, O. / Everett, J.K. ...Kuzin, A. / Lew, S. / Vorobiev, S.M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Maglaqui, M. / Kogan, S. / Khersonsky, O. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target OR398
Authors: Kuzin, A. / Lew, S. / Vorobiev, S.M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Maglaqui, M. / Kogan, S. / Khersonsky, O. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJul 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 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_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 1.2Dec 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 design amidase
B: De-novo design amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6534
Polymers40,5122
Non-polymers1422
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-20 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.485, 44.335, 57.515
Angle α, β, γ (deg.)71.070, 75.970, 86.860
Int Tables number1
Space group name H-MP1
Detailsdimer,39.56 kD,98.8%

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Components

#1: Protein De-novo design amidase


Mass: 20255.766 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) artificial gene (others)
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 1.99 Å3/Da / Density % sol: 38.23 %
Crystal growTemperature: 277 K / pH: 7.5
Details: Protein solution - 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution - 100mM HEPES, 42% PEG 200, microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 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: 1.8→33.5 Å / Num. all: 78543 / Num. obs: 27069 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 27.42 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 12.5

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Processing

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

1via


Resolution: 1.819→33.445 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.806 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.99 / Phase error: 26.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2669 5.04 %random
Rwork0.203 ---
obs0.205 27069 94.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.26 Å2 / Biso mean: 38.123 Å2 / Biso min: 12.94 Å2
Refinement stepCycle: LAST / Resolution: 1.819→33.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 0 8 68 2630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072659
X-RAY DIFFRACTIONf_angle_d0.9533568
X-RAY DIFFRACTIONf_chiral_restr0.068381
X-RAY DIFFRACTIONf_plane_restr0.003450
X-RAY DIFFRACTIONf_dihedral_angle_d13.742991
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.819-1.8520.311230.3092595271893
1.852-1.8880.3051210.2892602272395
1.888-1.9270.311360.2782761289794
1.927-1.9690.2891410.2392599274095
1.969-2.0140.2531730.2282693286696
2.014-2.0650.2371350.2232666280196
2.065-2.1210.3011540.2212671282596
2.121-2.1830.2861360.2172710284696
2.183-2.2530.2591470.2042629277696
2.253-2.3340.2941730.1982726289997
2.334-2.4270.2941260.2082691281796
2.427-2.5380.2881520.2052679283196
2.538-2.6710.2031340.1992705283996
2.671-2.8390.2551270.212713284096
2.839-3.0580.2731400.2042690283096
3.058-3.3650.231270.1932654278194
3.365-3.8520.1911580.1922600275893
3.852-4.850.2291510.1642586273792
4.85-33.4510.2131150.2092341245683
Refinement TLS params.Method: refined / Origin x: 0.3225 Å / Origin y: 0.6305 Å / Origin z: 0.3564 Å
111213212223313233
T0.1435 Å20.0056 Å20.0066 Å2-0.1367 Å2-0.0134 Å2--0.1962 Å2
L0.4963 °20.2073 °2-0.3004 °2-1.8107 °2-1.6017 °2--2.4346 °2
S0.0378 Å °-0.0618 Å °0.0377 Å °0.0563 Å °0.0881 Å °0.1087 Å °-0.1504 Å °-0.071 Å °-0.0729 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 166
2X-RAY DIFFRACTION1allB5 - 172
3X-RAY DIFFRACTION1allB - A1 - 326
4X-RAY DIFFRACTION1allA1 - 201
5X-RAY DIFFRACTION1allB1 - 201

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