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- PDB-4aks: PatG macrocyclase domain -

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Basic information

Entry
Database: PDB / ID: 4aks
TitlePatG macrocyclase domain
ComponentsTHIAZOLINE OXIDASE/SUBTILISIN-LIKE PROTEASE
KeywordsHYDROLASE / 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 / Peptidase S8A, PatG / PatG/PatA-like domain / PatG domain / PatG, C-terminal / PatG Domain / PatG C-terminal / SagB-type dehydrogenase domain / Nitroreductase ...ThcOx helix turn helix domain / ThcOx helix turn helix domain / 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 / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiazoline oxidase/subtilisin-like protease
Similarity search - Component
Biological speciesPROCHLORON DIDEMNI (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,1492
Polymers77,1492
Non-polymers00
Water4,035224
1
A: THIAZOLINE OXIDASE/SUBTILISIN-LIKE PROTEASE


Theoretical massNumber of molelcules
Total (without water)38,5741
Polymers38,5741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: THIAZOLINE OXIDASE/SUBTILISIN-LIKE PROTEASE


Theoretical massNumber of molelcules
Total (without water)38,5741
Polymers38,5741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.080, 67.580, 97.340
Angle α, β, γ (deg.)90.00, 115.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 38574.445 Da / Num. of mol.: 2 / Fragment: MACROCYCLASE DOMAIN, RESIDUES 492-851
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.56 Å3/Da / Density % sol: 51.9 % / 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: 2.19→33.79 Å / Num. obs: 38196 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.7
Reflection shellResolution: 2.19→2.24 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.9 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→33.79 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.218 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22411 2016 5 %RANDOM
Rwork0.20277 ---
obs0.20386 38196 99.46 %-
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: 42.332 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.28 Å2
2--0 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.19→33.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4650 0 0 224 4874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194743
X-RAY DIFFRACTIONr_bond_other_d0.0030.023130
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.9816466
X-RAY DIFFRACTIONr_angle_other_deg1.0673.0017746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0535613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.13725.876194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45115775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8711519
X-RAY DIFFRACTIONr_chiral_restr0.0660.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215260
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02795
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: 2.186→2.242 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 145 -
Rwork0.355 2702 -
obs--98.72 %
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)
11.16720.52990.44621.81430.56790.80120.05230.04350.148-0.04670.0042-0.2766-0.03310.0512-0.05650.0716-0.04340.00080.1442-0.05950.196-38.05711.17448.187
21.55010.0565-0.40931.70020.35451.5128-0.0880.102-0.1071-0.05090.076-0.14030.21520.02460.0120.1217-0.0359-0.00770.1405-0.07940.1192-44.467-1.38245.259
31.5206-0.33170.29711.8107-0.2391.04750.0315-0.2449-0.21030.0775-0.0199-0.0956-0.04660.1386-0.01150.11310.0339-0.04230.16310.03030.0868-26.85839.61922.204
40.8810.3833-0.31122.1236-0.09821.8017-0.0110.061-0.0325-0.33260.0022-0.0114-0.01350.09420.00880.20370.0329-0.02440.09670.00450.0716-30.30245.6037.67
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A514 - 639
2X-RAY DIFFRACTION2A640 - 851
3X-RAY DIFFRACTION3B515 - 696
4X-RAY DIFFRACTION4B697 - 851

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