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- PDB-6ipv: Crystal structure of CqsB2 from Streptomyces exfoliatus 2419-SVT2... -

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Basic information

Entry
Database: PDB / ID: 6ipv
TitleCrystal structure of CqsB2 from Streptomyces exfoliatus 2419-SVT2 (apo form)
ComponentsCqsB2
KeywordsBIOSYNTHETIC PROTEIN / Carquinostatin A biosynthesis / polyketide aromatase/cyclase
Function / homologySTART-like domain superfamily / Uncharacterized protein
Function and homology information
Biological speciesStreptomyces exfoliatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsTomita, T. / Kobayashi, M. / Nishiyama, M. / Kuzuyama, T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: An Unprecedented Cyclization Mechanism in the Biosynthesis of Carbazole Alkaloids in Streptomyces.
Authors: Kobayashi, M. / Tomita, T. / Shin-Ya, K. / Nishiyama, M. / Kuzuyama, T.
History
DepositionNov 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CqsB2
B: CqsB2
C: CqsB2
D: CqsB2


Theoretical massNumber of molelcules
Total (without water)110,5804
Polymers110,5804
Non-polymers00
Water7,098394
1
A: CqsB2
B: CqsB2


Theoretical massNumber of molelcules
Total (without water)55,2902
Polymers55,2902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-48 kcal/mol
Surface area19050 Å2
MethodPISA
2
C: CqsB2
D: CqsB2


Theoretical massNumber of molelcules
Total (without water)55,2902
Polymers55,2902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-49 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.687, 127.687, 125.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein
CqsB2


Mass: 27645.105 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces exfoliatus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL-CodonPlus / References: UniProt: A0A5A4PV77*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence has been deposited to DDBJ with accession code LC406090.

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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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl (pH8.5), 30% (w/v) PEG 4000, 0.2M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→125.72 Å / Num. obs: 53154 / % possible obs: 100 % / Redundancy: 14.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.054 / Net I/σ(I): 21.9
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.278 / Num. unique obs: 2605 / CC1/2: 0.879 / Rpim(I) all: 0.266

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→125.72 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.757 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22913 2665 5 %RANDOM
Rwork0.18134 ---
obs0.18369 50461 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.843 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.2→125.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7212 0 0 394 7606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197408
X-RAY DIFFRACTIONr_bond_other_d0.0010.026720
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.93110052
X-RAY DIFFRACTIONr_angle_other_deg0.796315452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8385880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.79423.878392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.814151228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1071552
X-RAY DIFFRACTIONr_chiral_restr0.0840.21028
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021804
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_it1.8343.0673532
X-RAY DIFFRACTIONr_mcbond_other1.8283.0673531
X-RAY DIFFRACTIONr_mcangle_it2.7954.5924408
X-RAY DIFFRACTIONr_mcangle_other2.7974.5924409
X-RAY DIFFRACTIONr_scbond_it2.1633.2793876
X-RAY DIFFRACTIONr_scbond_other2.1623.2793877
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5664.8125645
X-RAY DIFFRACTIONr_long_range_B_refined4.9824.5828890
X-RAY DIFFRACTIONr_long_range_B_other4.96524.5748862
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 215 -
Rwork0.227 3605 -
obs--99.53 %

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