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- PDB-4v1u: Heterocyclase in complex with substrate and Cofactor -

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Basic information

Entry
Database: PDB / ID: 4v1u
TitleHeterocyclase in complex with substrate and Cofactor
Components
  • LYND
  • PATE
KeywordsHYDROLASE / HETEROCYCLASE / CYANOBACTINS
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
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 ...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 / 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 MONOPHOSPHATE / 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: 2.86 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.E. / 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 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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)187,27612
Polymers186,2914
Non-polymers9868
Water34219
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-108.1 kcal/mol
Surface area60870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.800, 152.810, 182.840
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: 6999.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) UNCULTURED PROCHLORON SP. (environmental samples)
Strain: PROCHLORON SP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: A0MHA3*PLUS

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Non-polymers , 4 types, 27 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.47 Å3/Da / Density % sol: 50.14 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.86→76.4 Å / Num. obs: 42149 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.1
Reflection shellResolution: 2.86→2.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BS9

4bs9


Resolution: 2.86→76.4 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.907 / SU B: 40.95 / SU ML: 0.339 / Cross valid method: THROUGHOUT / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25122 2131 5.1 %RANDOM
Rwork0.20096 ---
obs0.2035 40018 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.03 Å2
Baniso -1Baniso -2Baniso -3
1-2.49 Å20 Å20 Å2
2---1.57 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.86→76.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11884 0 52 19 11955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01912211
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211632
X-RAY DIFFRACTIONr_angle_refined_deg0.9131.9716657
X-RAY DIFFRACTIONr_angle_other_deg2.011326781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.20751501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94524.428551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21152000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6291574
X-RAY DIFFRACTIONr_chiral_restr0.0380.21893
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02113758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022722
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_it4.0016.4556040
X-RAY DIFFRACTIONr_mcbond_other4.0026.4556039
X-RAY DIFFRACTIONr_mcangle_it4.7479.6637529
X-RAY DIFFRACTIONr_mcangle_other4.7479.6637530
X-RAY DIFFRACTIONr_scbond_it3.6686.7326171
X-RAY DIFFRACTIONr_scbond_other3.6696.7326172
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.369.9529129
X-RAY DIFFRACTIONr_long_range_B_refined4.92651.11913529
X-RAY DIFFRACTIONr_long_range_B_other4.92651.1213529
X-RAY DIFFRACTIONr_rigid_bond_restr2.985323843
X-RAY DIFFRACTIONr_sphericity_free15.511511
X-RAY DIFFRACTIONr_sphericity_bonded22.617523576
LS refinement shellResolution: 2.86→2.934 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 156 -
Rwork0.335 2906 -
obs--98.11 %
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)
10.52970.47640.32890.43730.21382.7771-0.1313-0.11460.0067-0.0939-0.10690.0110.0011-0.12690.23830.16760.04090.01330.0384-0.03070.08044.3216-24.38289.0132
20.0511-0.04770.02470.0512-0.02990.01940.00150.02640.01110.0026-0.0141-0.01660.00620.00210.01260.2304-0.0039-0.0040.03730.01580.0575-2.4616-13.230750.8869
30.1344-0.1095-0.03110.128-0.06160.28170.004-0.005-0.00450.0114-0.0157-0.01280.00720.01460.01170.19520.001-0.00360.02250.01580.03627.496916.211232.1359
40.8988-0.8581-0.26171.0563-0.60143.14190.07870.05030.0201-0.0971-0.0411-0.01130.0927-0.0222-0.03760.1664-0.0177-0.00280.0286-0.01540.04513.174-28.051823.6165
50.5323-0.37270.10780.2646-0.11220.5419-0.01610.02410.04790.0198-0.0191-0.02930.0039-0.00350.03520.2161-0.0304-0.01170.0065-0.00550.06823.3165-28.357961.6567
60.08730.0627-0.05860.13360.03610.16640.02990.02810.016-0.0359-0.02490.02820.013-0.0584-0.00510.20130.0264-0.00340.0383-0.00320.031233.88078.871578.217
77.29293.361-8.750829.861-2.368610.5988-0.1966-0.0292-0.06490.49450.1179-0.11750.26110.04460.07870.1155-0.0088-0.05820.1285-0.02340.06016.9536-13.5103104.2481
80.4134-0.213.26040.57440.330234.16620.1239-0.1007-0.051-0.3310.30140.0289-0.19590.2383-0.42530.2582-0.10920.01150.22050.03380.091310.0536-12.119190.2449
90.40310.29542.1730.22951.665512.3248-0.16940.2149-0.0394-0.16720.18220.0023-1.3021.1623-0.01290.3163-0.0739-0.0850.23920.0170.195916.9333-19.30559.5451
105.38522.52072.43771.48590.88871.31290.195-0.3058-0.31570.1459-0.1758-0.29030.047-0.1265-0.01920.1102-0.0138-0.01320.2076-0.06090.162515.3978-15.211523.6397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 111
2X-RAY DIFFRACTION2A112 - 377
3X-RAY DIFFRACTION3A378 - 775
4X-RAY DIFFRACTION4B6 - 95
5X-RAY DIFFRACTION5B96 - 306
6X-RAY DIFFRACTION6B307 - 775
7X-RAY DIFFRACTION7C23 - 28
8X-RAY DIFFRACTION8C29 - 34
9X-RAY DIFFRACTION9D23 - 28
10X-RAY DIFFRACTION10D29 - 34

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