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- PDB-4akt: PatG macrocyclase in complex with peptide -

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Basic information

Entry
Database: PDB / ID: 4akt
TitlePatG macrocyclase in complex with peptide
Components
  • SUBSTRATE ANALOGUE
  • THIAZOLINE OXIDASE/SUBTILISIN-LIKE PROTEASE
KeywordsHYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX / HYDROLASE / PATELLAMIDE
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 / Peptidase S8/S53 domain / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiazoline oxidase/subtilisin-like protease
Similarity search - Component
Biological speciesPROCHLORON DIDEMNI (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsKoehnke, J. / Bent, A. / Houssen, W.E. / Zollman, D. / Morawitz, F. / Shirran, S. / Vendome, J. / Nneoyiegbe, A.F. / Trembleau, L. / Botting, C.H. ...Koehnke, J. / Bent, A. / Houssen, W.E. / Zollman, D. / Morawitz, F. / Shirran, S. / Vendome, J. / Nneoyiegbe, A.F. / Trembleau, L. / Botting, C.H. / Smith, M.C.M. / Jaspars, M. / Naismith, J.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: The Mechanism of Patellamide Macrocyclization Revealed by the Characterization of the Patg Macrocyclase Domain.
Authors: Koehnke, J. / Bent, A. / Houssen, W.E. / Zollman, D. / Morawitz, F. / Shirran, S. / Vendome, J. / Nneoyiegbe, A.F. / Trembleau, L. / Botting, C.H. / Smith, M.C. / Jaspars, M. / Naismith, J.H.
History
DepositionFeb 28, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Nov 6, 2013Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIAZOLINE OXIDASE/SUBTILISIN-LIKE PROTEASE
B: THIAZOLINE OXIDASE/SUBTILISIN-LIKE PROTEASE
C: SUBSTRATE ANALOGUE


Theoretical massNumber of molelcules
Total (without water)78,2183
Polymers78,2183
Non-polymers00
Water2,558142
1
A: THIAZOLINE OXIDASE/SUBTILISIN-LIKE PROTEASE
C: SUBSTRATE ANALOGUE


Theoretical massNumber of molelcules
Total (without water)39,7112
Polymers39,7112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-8.9 kcal/mol
Surface area13780 Å2
MethodPISA
2
B: THIAZOLINE OXIDASE/SUBTILISIN-LIKE PROTEASE


Theoretical massNumber of molelcules
Total (without water)38,5071
Polymers38,5071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.630, 67.320, 137.870
Angle α, β, γ (deg.)90.00, 116.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein THIAZOLINE OXIDASE/SUBTILISIN-LIKE PROTEASE / PATG


Mass: 38507.375 Da / Num. of mol.: 2 / Fragment: MACROCYCLASE DOMAIN, RESIDUES 492-851 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROCHLORON DIDEMNI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q52QJ1
#2: Protein/peptide SUBSTRATE ANALOGUE


Mass: 1203.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 618 TO ALA ENGINEERED RESIDUE IN CHAIN B, HIS 618 TO ALA

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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: 3.65 Å3/Da / Density % sol: 66.3 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.63→21.42 Å / Num. obs: 31502 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.1
Reflection shellResolution: 2.63→2.77 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→21.42 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.92 / SU B: 16.215 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21844 1676 5.1 %RANDOM
Rwork0.19024 ---
obs0.19168 31502 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20.18 Å2
2---0.19 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.63→21.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4966 0 0 142 5108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195073
X-RAY DIFFRACTIONr_bond_other_d0.0030.023346
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9786929
X-RAY DIFFRACTIONr_angle_other_deg1.0233.0028269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0635656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85325.924211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50515808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6641520
X-RAY DIFFRACTIONr_chiral_restr0.0640.2806
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215663
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02861
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.627→2.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 101 -
Rwork0.281 2113 -
obs--92.95 %
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)
12.84341.0631-0.30772.15210.69531.9153-0.26970.4654-0.3338-0.27790.11650.23480.1073-0.28890.15320.1089-0.094-0.01950.2337-0.05640.116623.88810.094-23.076
23.11811.1552-1.98581.2461-1.48938.1205-0.17210.0608-0.7743-0.2005-0.0249-0.25161.02220.38580.19710.225-0.04860.03210.1433-0.06050.22142.5838.358-18.786
31.2237-0.1526-0.16812.74350.40642.48-0.10550.13-0.02110.14820.06540.0696-0.0179-0.05540.04010.0236-0.00930.01840.0188-0.00740.03130.97715.663-7.584
42.96880.742-0.02322.69271.2722.48640.18060.06850.4586-0.40120.118-0.3969-0.33030.1806-0.29870.301-0.0950.18580.139-0.04310.241367.8317.858-43.073
55.6329-0.7837-5.24557.76710.783210.1474-0.1811-0.5804-0.38410.4862-0.0152-0.3930.95810.40.19630.2967-0.09240.07070.1437-0.02690.144255.2565.869-36.267
64.41550.5545-1.10965.55241.50494.76770.07950.1407-0.5838-0.11170.0213-0.56810.70020.2998-0.10080.4131-0.04550.15040.2154-0.12980.238968.0590.981-49.035
73.28238.1354-0.13528.9786-10.681520.49710.5144-0.3527-0.36890.1547-0.852-0.96851.5497-1.25690.33750.3993-0.15130.07050.4039-0.23410.683726.358-1.929-11.873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A515 - 650
2X-RAY DIFFRACTION2A658 - 697
3X-RAY DIFFRACTION3A698 - 851
4X-RAY DIFFRACTION4B515 - 642
5X-RAY DIFFRACTION5B643 - 712
6X-RAY DIFFRACTION6B713 - 850
7X-RAY DIFFRACTION7C4 - 12

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