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- PDB-4uvq: PatG Domain of Unknown Function -

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Basic information

Entry
Database: PDB / ID: 4uvq
TitlePatG Domain of Unknown Function
ComponentsTHIAZOLINE OXIDASE/SUBTILISIN-LIKE PROTEASE
KeywordsHYDROLASE / PATELLAMIDES / CYANOBACTINS / PROCHLORON.
Function / homology
Function and homology information


oxidoreductase activity / serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
ThcOx helix turn helix domain / ThcOx helix turn helix domain / Cyanobactin oxidase ThcOx, / Peptidase S8A, PatG / PatG/PatA-like domain / PatG domain / PatG, C-terminal / PatG Domain / PatG C-terminal / SagB-type dehydrogenase domain ...ThcOx helix turn helix domain / ThcOx helix turn helix domain / Cyanobactin oxidase ThcOx, / Peptidase S8A, PatG / PatG/PatA-like domain / PatG domain / PatG, C-terminal / PatG Domain / PatG C-terminal / SagB-type dehydrogenase domain / : / Nitroreductase / Nitroreductase family / Nitroreductase-like / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
Thiazoline oxidase/subtilisin-like protease
Similarity search - Component
Biological speciesPROCHLORON SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.724 Å
AuthorsMann, G. / Koehnke, J. / Bent, A.F. / Graham, R. / Schwarz-Linek, U. / Naismith, J.H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: The Structure of the Cyanobactin Domain of Unknown Function from Patg in the Patellamide Gene Cluster
Authors: Mann, G. / Koehnke, J. / Bent, A.F. / Graham, R. / Schwarz-Linek, U. / Naismith, J.H.
History
DepositionAug 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: THIAZOLINE OXIDASE/SUBTILISIN-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3872
Polymers31,3211
Non-polymers651
Water4,846269
1
A: THIAZOLINE OXIDASE/SUBTILISIN-LIKE PROTEASE
hetero molecules

A: THIAZOLINE OXIDASE/SUBTILISIN-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7734
Polymers62,6422
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2250 Å2
ΔGint-81.7 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.110, 95.190, 40.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2181-

HOH

21A-2183-

HOH

31A-2186-

HOH

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Components

#1: Protein THIAZOLINE OXIDASE/SUBTILISIN-LIKE PROTEASE


Mass: 31321.184 Da / Num. of mol.: 1 / Fragment: DOMAIN OF UNKNOWN FUNCTION, RESIDUES 913-1185 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROCHLORON SP. (bacteria) / Description: DAVIES REEF / Plasmid: PHISTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q52QJ1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 1.98 Å3/Da / Density % sol: 37.88 % / Description: NONE
Crystal growDetails: 0.04 M POTASSIUM PHOSPHATE, 16 % (W/V) PEG 8000, AND 20 % (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.72→53.17 Å / Num. obs: 26646 / % possible obs: 99.9 % / Observed criterion σ(I): 3.4 / Redundancy: 14 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.1
Reflection shellResolution: 1.72→1.77 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALEPACKdata scaling
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.724→53.175 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 20.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1995 1345 5.1 %
Rwork0.1751 --
obs0.1764 25301 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 1.724→53.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 1 269 2379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092184
X-RAY DIFFRACTIONf_angle_d0.9322967
X-RAY DIFFRACTIONf_dihedral_angle_d12.82799
X-RAY DIFFRACTIONf_chiral_restr0.032328
X-RAY DIFFRACTIONf_plane_restr0.004393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7243-1.7860.29471190.23932503X-RAY DIFFRACTION100
1.786-1.85750.28351250.21352467X-RAY DIFFRACTION100
1.8575-1.9420.23261390.19312515X-RAY DIFFRACTION100
1.942-2.04440.21241320.18142478X-RAY DIFFRACTION100
2.0444-2.17250.18981330.16712490X-RAY DIFFRACTION100
2.1725-2.34020.17761330.15692522X-RAY DIFFRACTION100
2.3402-2.57570.22161430.16672513X-RAY DIFFRACTION100
2.5757-2.94840.21331320.17552541X-RAY DIFFRACTION100
2.9484-3.71460.18741390.16622576X-RAY DIFFRACTION100
3.7146-53.19980.17351500.17252697X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.43641.40730.06682.4336-0.58930.69740.05330.258-0.1842-0.0708-0.00110.06190.0551-0.0418-0.01790.11990.0217-0.04920.1374-0.01960.105437.712127.960524.8496
21.2589-0.34851.61062.14740.67795.25740.2082-0.2445-0.71370.2055-0.0780.42180.4768-0.2838-0.18430.227-0.0504-0.07540.22630.01410.438126.520612.348732.7975
32.63140.30280.49984.7002-0.84513.12760.199-0.1917-0.34920.1105-0.10130.10430.33070.0836-0.07380.1272-0.014-0.02950.1337-0.00240.18534.90719.236533.8777
45.204-0.78312.07553.9538-1.02324.64410.19820.5009-0.4053-0.54-0.28840.09080.30270.39910.02880.21460.01260.00710.19240.00750.148441.200725.172923.7909
51.29760.1692-0.23291.3802-0.01541.82420.0432-0.0066-0.0722-0.01980.0384-0.03390.02940.1428-0.05820.12670.0187-0.02440.11680.00040.139940.063327.637230.7579
60.91991.48131.8782.86873.54364.53340.25340.07980.17271.0944-0.1039-0.2441-0.23870.7423-0.39730.4542-0.1292-0.12010.2769-0.05930.183744.692547.619950.376
72.4350.35231.35713.09890.79345.6016-0.053-0.24930.03810.3193-0.1279-0.0571-0.2576-0.1879-0.05310.1499-0.0146-0.00160.14380.00340.163537.441748.564141.2216
84.17570.008-0.99453.23770.66154.70.06820.25260.1208-0.1075-0.1658-0.12750.1310.0611-0.03560.1190.01260.00910.07870.00760.121643.392542.271226.8984
91.8427-0.9467-1.81663.88591.60663.2040.1212-0.00330.0506-0.30160.1191-0.4928-0.12150.1886-0.23220.1403-0.03070.01650.1817-0.03710.219948.950152.783730.5886
101.3148-0.9684-0.63483.62232.15224.02580.0211-0.06010.257-0.10460.0198-0.1042-0.2958-0.0713-0.17010.1476-0.0026-0.0120.20030.00340.209143.913460.562934.9871
110.0453-0.0323-0.18225.97113.49152.3335-0.1246-0.13680.0586-0.00580.4632-0.5023-0.10760.327-0.31480.16060.0042-0.00340.2183-0.04450.202152.586250.204929.6763
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 10 THROUGH 26 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 27 THROUGH 42 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 43 THROUGH 68 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 69 THROUGH 80 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 81 THROUGH 142 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 143 THROUGH 160 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 161 THROUGH 179 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 180 THROUGH 200 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 201 THROUGH 231 )
10X-RAY DIFFRACTION10CHAIN A AND (RESID 232 THROUGH 248 )
11X-RAY DIFFRACTION11CHAIN A AND (RESID 249 THROUGH 274 )

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