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- PDB-6le0: A nonspecific heme-binding cyclase catalyzes [4 + 2] cycloadditio... -

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Basic information

Entry
Database: PDB / ID: 6le0
TitleA nonspecific heme-binding cyclase catalyzes [4 + 2] cycloaddition during neoabyssomicin biosynthesis
ComponentsAbmU
KeywordsBIOSYNTHETIC PROTEIN / cyclase
Function / homologyAllene oxide cyclase barrel-like domain / Allene oxide cyclase barrel like domain / antibiotic biosynthetic process / isomerase activity / AbmU
Function and homology information
Biological speciesStreptomyces koyangensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsJu, J.J.
CitationJournal: Acs Omega / Year: 2020
Title: Nonspecific Heme-Binding Cyclase, AbmU, Catalyzes [4 + 2] Cycloaddition during Neoabyssomicin Biosynthesis.
Authors: Li, Q. / Ding, W. / Tu, J. / Chi, C. / Huang, H. / Ji, X. / Yao, Z. / Ma, M. / Ju, J.
History
DepositionNov 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AbmU
B: AbmU
C: AbmU
D: AbmU


Theoretical massNumber of molelcules
Total (without water)95,5714
Polymers95,5714
Non-polymers00
Water3,135174
1
A: AbmU
B: AbmU


Theoretical massNumber of molelcules
Total (without water)47,7862
Polymers47,7862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-37 kcal/mol
Surface area17040 Å2
MethodPISA
2
C: AbmU
D: AbmU


Theoretical massNumber of molelcules
Total (without water)47,7862
Polymers47,7862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-34 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.613, 65.349, 101.397
Angle α, β, γ (deg.)90.000, 90.189, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNSERSER(chain 'A' and (resid 2 through 32 or resid 41 through 206))AA4 - 313 - 30
12LEULEULEULEU(chain 'A' and (resid 2 through 32 or resid 41 through 206))AA41 - 10240 - 101
13TYRTYRSERSER(chain 'A' and (resid 2 through 32 or resid 41 through 206))AA105 - 147104 - 146
14ILEILETHRTHR(chain 'A' and (resid 2 through 32 or resid 41 through 206))AA149 - 205148 - 204
25ASNASNSERSER(chain 'B' and (resid 2 through 32 or resid 41 through 206))BB4 - 313 - 30
26LEULEULEULEU(chain 'B' and (resid 2 through 32 or resid 41 through 206))BB41 - 10240 - 101
27TYRTYRSERSER(chain 'B' and (resid 2 through 32 or resid 41 through 206))BB105 - 147104 - 146
28ILEILETHRTHR(chain 'B' and (resid 2 through 32 or resid 41 through 206))BB149 - 205148 - 204
39ASNASNSERSER(chain 'C' and (resid 2 through 32 or resid 41 through 206))CC4 - 313 - 30
310LEULEULEULEU(chain 'C' and (resid 2 through 32 or resid 41 through 206))CC41 - 10240 - 101
311TYRTYRSERSER(chain 'C' and (resid 2 through 32 or resid 41 through 206))CC105 - 147104 - 146
312ILEILETHRTHR(chain 'C' and (resid 2 through 32 or resid 41 through 206))CC149 - 205148 - 204
413ASNASNSERSER(chain 'D' and (resid 2 through 32 or resid 41 through 206))DD4 - 313 - 30
414LEULEULEULEU(chain 'D' and (resid 2 through 32 or resid 41 through 206))DD41 - 10240 - 101
415TYRTYRSERSER(chain 'D' and (resid 2 through 32 or resid 41 through 206))DD105 - 147104 - 146
416ILEILETHRTHR(chain 'D' and (resid 2 through 32 or resid 41 through 206))DD149 - 205148 - 204

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Components

#1: Protein
AbmU


Mass: 23892.865 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces koyangensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2P1BT29
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG 3350, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97893 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2.51→50 Å / Num. obs: 29528 / % possible obs: 98.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 41.68 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.04 / Net I/σ(I): 13.9
Reflection shellResolution: 2.51→2.58 Å / Rmerge(I) obs: 0.498 / Num. unique obs: 1020 / Rpim(I) all: 0.219

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.51→27.88 Å / SU ML: 0.331 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.6494
RfactorNum. reflection% reflection
Rfree0.2451 1457 4.94 %
Rwork0.1996 --
obs0.2019 29510 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 50.81 Å2
Refinement stepCycle: LAST / Resolution: 2.51→27.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6245 0 0 174 6419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01016425
X-RAY DIFFRACTIONf_angle_d1.25748769
X-RAY DIFFRACTIONf_chiral_restr0.072933
X-RAY DIFFRACTIONf_plane_restr0.00961171
X-RAY DIFFRACTIONf_dihedral_angle_d14.10863741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.60.33411420.25572790X-RAY DIFFRACTION98.99
2.6-2.70.2881280.24582820X-RAY DIFFRACTION98.96
2.7-2.830.30421300.23992828X-RAY DIFFRACTION98.96
2.83-2.980.29291490.24442797X-RAY DIFFRACTION99.19
2.98-3.160.30361510.23852803X-RAY DIFFRACTION98.76
3.16-3.410.27871410.21822740X-RAY DIFFRACTION96.74
3.41-3.750.23721610.20362846X-RAY DIFFRACTION99.24
3.75-4.290.21521460.17632832X-RAY DIFFRACTION99.33
4.29-5.40.19571010.16242835X-RAY DIFFRACTION96.99
5.4-27.880.21812080.17752762X-RAY DIFFRACTION95.74

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