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- PDB-4v1t: Heterocyclase in complex with substrate and Cofactor -

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Basic information

Entry
Database: PDB / ID: 4v1t
TitleHeterocyclase in complex with substrate and Cofactor
Components
  • LYND
  • PATE
KeywordsHYDROLASE / CYANOBACTINS
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
Double Stranded RNA Binding Domain - #660 / Herpes Virus-1 - #250 / Outer Surface Protein A; domain 3 - #60 / Microcyclamide/patellamide bacteriocin family, leader peptide / Protein of unknown function (DUF5837) / Family of unknown function (DUF5837) / Bacteriocin biosynthesis, cyclodehydratase domain / Thiazole/oxazole-forming peptide maturase, SagD family component / : / Winged Helix-turn-helix domain ...Double Stranded RNA Binding Domain - #660 / Herpes Virus-1 - #250 / Outer Surface Protein A; domain 3 - #60 / Microcyclamide/patellamide bacteriocin family, leader peptide / Protein of unknown function (DUF5837) / Family of unknown function (DUF5837) / Bacteriocin biosynthesis, cyclodehydratase domain / Thiazole/oxazole-forming peptide maturase, SagD family component / : / Winged Helix-turn-helix domain / YcaO-like domain / YcaO cyclodehydratase, ATP-ad Mg2+-binding / YcaO domain profile. / Outer Surface Protein A; domain 3 / Herpes Virus-1 / Double Stranded RNA Binding Domain / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Patellamide protein / YcaO domain-containing protein
Similarity search - Component
Biological speciesLYNGBYA AESTUARII (bacteria)
UNCULTURED PROCHLORON SP. (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsKoehnke, J. / Naismith, J.H.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: Structural Analysis of Leader Peptide Binding Enables Leader-Free Cyanobactin Processing
Authors: Koehnke, J. / Mann, G. / Bent, A.F. / Ludewig, H. / Shirran, S. / Botting, C. / Lebl, T. / Houssen, W. / Jaspars, M. / Naismith, J.H.
History
DepositionOct 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jul 1, 2015Group: Database references
Revision 1.3Aug 5, 2015Group: Database references
Revision 1.4Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.5Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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
Revision 1.6May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYND
B: LYND
C: PATE
D: PATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,54716
Polymers186,2264
Non-polymers1,32112
Water10,323573
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12780 Å2
ΔGint-149.5 kcal/mol
Surface area60650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.760, 116.150, 183.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein LYND


Mass: 86145.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LYNGBYA AESTUARII (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: A0YXD2
#2: Protein PATE


Mass: 6967.765 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) UNCULTURED PROCHLORON SP. (environmental samples)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: A0MHA3*PLUS

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Non-polymers , 5 types, 585 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.34 Å3/Da / Density % sol: 47.43 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.14→47.35 Å / Num. obs: 95581 / % possible obs: 98.8 % / Observed criterion σ(I): 2.2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.5
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.2 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→47.35 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 15.482 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24442 4791 5 %RANDOM
Rwork0.19792 ---
obs0.20025 90749 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.189 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.14→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12008 0 72 573 12653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01912358
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211743
X-RAY DIFFRACTIONr_angle_refined_deg1.0711.97216869
X-RAY DIFFRACTIONr_angle_other_deg2.198327048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75251521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33324.45555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.882152018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8031574
X-RAY DIFFRACTIONr_chiral_restr0.0490.21914
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113924
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022748
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_it2.9654.4456111
X-RAY DIFFRACTIONr_mcbond_other2.9654.4456110
X-RAY DIFFRACTIONr_mcangle_it3.366.6537623
X-RAY DIFFRACTIONr_mcangle_other3.366.6537624
X-RAY DIFFRACTIONr_scbond_it3.2724.966247
X-RAY DIFFRACTIONr_scbond_other3.2734.9596240
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5357.2219235
X-RAY DIFFRACTIONr_long_range_B_refined3.86636.89214547
X-RAY DIFFRACTIONr_long_range_B_other3.87836.70614353
X-RAY DIFFRACTIONr_rigid_bond_restr6.273324101
X-RAY DIFFRACTIONr_sphericity_free6.9555196
X-RAY DIFFRACTIONr_sphericity_bonded18.603524200
LS refinement shellResolution: 2.14→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 364 -
Rwork0.284 6582 -
obs--98.02 %
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)
10.4401-0.2136-1.09840.1060.51992.8219-0.0509-0.0362-0.04330.00860.00530.03040.15350.13540.04560.2411-0.021-0.02070.14560.01420.059348.1755-10.85352.0706
20.04670.15770.02470.54480.08810.1280.0085-0.00330.0090.0202-0.03210.00990.0226-0.00190.02360.1649-0.00560.01320.1266-0.00070.066241.105-19.1049-36.3868
30.00630.00260.00040.00190.00020.0001-0.01530.0110.0163-0.00760.01390.00350.00220.00210.00130.19-0.0003-0.00560.13420.00030.06045.6758-10.6769-50.707
40.00710.0077-0.01860.023-0.03130.10820.0150.00220.01030.01250.0081-0.01450.0205-0.0782-0.02310.1921-0.0003-0.0030.14810.00380.066950.29284.7302-51.8779
50.064-0.05580.05450.1149-0.06440.0514-0.0018-0.0163-0.00410.0145-0.0026-0.0094-0.0131-0.01140.00440.18880.00140.00170.1552-0.00360.049636.112210.7039-19.4994
60.0591-0.06560.04950.0737-0.0560.0432-0.0061-0.0085-0.00440.00440.01610.0108-0.0123-0.0169-0.00990.1783-0.0170.00510.1513-0.00430.06347.621312.9995-3.0853
79.5251-3.0893-6.10121.4748-0.191413.87050.17930.0995-1.0643-0.3596-0.02940.5261.2627-0.0882-0.14990.2302-0.0125-0.13090.09370.00040.214437.4599-12.625820.6233
87.2261-6.67652.95277.1673-5.804610.6876-0.1275-0.33070.08690.14330.42320.0295-0.1513-0.4805-0.29570.1965-0.1199-0.04130.14870.04090.046535.2623-6.41665.5661
92.06720.14582.334813.02142.01172.9142-0.00630.09490.1804-0.595-0.1411-0.1328-0.07680.02120.14740.07960.01160.00820.30990.12150.060134.8157.9252-76.4829
100.03380.0447-0.11863.3828-5.74139.8060.05660.03160.05190.16630.44520.2679-0.3535-0.7516-0.50180.10210.01580.06130.1510.09330.103433.75222.018-62.6838
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 113
2X-RAY DIFFRACTION2A114 - 329
3X-RAY DIFFRACTION3A330 - 775
4X-RAY DIFFRACTION4B4 - 148
5X-RAY DIFFRACTION5B149 - 405
6X-RAY DIFFRACTION6B406 - 775
7X-RAY DIFFRACTION7C21 - 27
8X-RAY DIFFRACTION8C28 - 35
9X-RAY DIFFRACTION9D21 - 27
10X-RAY DIFFRACTION10D28 - 34

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