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- PDB-4n3p: Crystal Structure of De Novo designed Serine Hydrolase OSH18, Nor... -

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Basic information

Entry
Database: PDB / ID: 4n3p
TitleCrystal Structure of De Novo designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (NESG) Target OR396
ComponentsSerine Hydrolase OSH18
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / SER hydrolase
Function / homologyEnolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Alpha Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsKuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Kogan, S. / Maglaqui, M. / Everett, J.K. / Acton, T.B. ...Kuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Kogan, S. / Maglaqui, M. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of De Novo designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (NESG) Target OR396
Authors: Kuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Kogan, S. / Maglaqui, M. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast ...Authors: Kuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Kogan, S. / Maglaqui, M. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
History
DepositionOct 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine Hydrolase OSH18
B: Serine Hydrolase OSH18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,42022
Polymers94,8642
Non-polymers55520
Water1,18966
1
A: Serine Hydrolase OSH18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,68512
Polymers47,4321
Non-polymers25311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine Hydrolase OSH18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,73510
Polymers47,4321
Non-polymers3039
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Serine Hydrolase OSH18
hetero molecules

A: Serine Hydrolase OSH18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,42022
Polymers94,8642
Non-polymers55520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area2050 Å2
ΔGint-20 kcal/mol
Surface area34600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.119, 73.119, 163.975
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Serine Hydrolase OSH18


Mass: 47432.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 18 / 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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 4.6
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: NaAcetate - 0.1M, PEG 3350 - 16%, Microbatch Under Oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 17, 2013 / Details: mirror
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: 2.5→20 Å / Num. obs: 58285 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 44.87 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.6

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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: 1RF6

1rf6


Resolution: 2.501→19.736 Å / Occupancy max: 1 / Occupancy min: 0.57 / SU ML: 0.36 / σ(F): 1.44 / Phase error: 27.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 2905 4.99 %
Rwork0.1878 --
obs0.1911 58192 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.868 Å2
Refinement stepCycle: LAST / Resolution: 2.501→19.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6339 0 26 66 6431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086422
X-RAY DIFFRACTIONf_angle_d1.2058678
X-RAY DIFFRACTIONf_dihedral_angle_d16.3152406
X-RAY DIFFRACTIONf_chiral_restr0.0771053
X-RAY DIFFRACTIONf_plane_restr0.0051118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5011-2.5420.40991400.27692688X-RAY DIFFRACTION99
2.542-2.58580.30471460.24592663X-RAY DIFFRACTION100
2.5858-2.63270.31531340.22362646X-RAY DIFFRACTION100
2.6327-2.68320.35541380.22022661X-RAY DIFFRACTION100
2.6832-2.73780.30291260.22682583X-RAY DIFFRACTION100
2.7378-2.79720.27411380.21762694X-RAY DIFFRACTION100
2.7972-2.86210.33941420.20662665X-RAY DIFFRACTION100
2.8621-2.93340.29721420.21142654X-RAY DIFFRACTION100
2.9334-3.01250.3071400.21742617X-RAY DIFFRACTION100
3.0125-3.10080.32341370.23862618X-RAY DIFFRACTION100
3.1008-3.20050.32861440.22392638X-RAY DIFFRACTION100
3.2005-3.31440.28441340.20712689X-RAY DIFFRACTION99
3.3144-3.44640.33721370.21462576X-RAY DIFFRACTION99
3.4464-3.60230.28681470.20462586X-RAY DIFFRACTION98
3.6023-3.7910.24081290.1962628X-RAY DIFFRACTION98
3.791-4.02660.26761420.17572612X-RAY DIFFRACTION100
4.0266-4.33450.20371500.16612633X-RAY DIFFRACTION99
4.3345-4.76510.21651300.14682644X-RAY DIFFRACTION100
4.7651-5.4420.18641320.15562640X-RAY DIFFRACTION99
5.442-6.80920.20591370.17862616X-RAY DIFFRACTION99
6.8092-19.73670.17011400.14312536X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 21.8716 Å / Origin y: -12.7202 Å / Origin z: -5.7021 Å
111213212223313233
T0.3981 Å20.0052 Å20.0424 Å2-0.3294 Å2-0.0023 Å2--0.2536 Å2
L0.5216 °20.4954 °20.0564 °2-2.7409 °2-0.2829 °2--0.0975 °2
S0.0463 Å °-0.029 Å °-0.1501 Å °-0.2404 Å °-0.0969 Å °-0.2587 Å °0.0404 Å °0.0759 Å °0.0386 Å °
Refinement TLS groupSelection details: all

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