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- PDB-4xrt: Crystal structure of the di-domain ARO/CYC StfQ from the steffimy... -

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Basic information

Entry
Database: PDB / ID: 4xrt
TitleCrystal structure of the di-domain ARO/CYC StfQ from the steffimycin biosynthetic pathway
ComponentsStfQ Aromatase/Cyclase
KeywordsLYASE / aromatase/cyclase / helix-grip fold / polyketide / polyketide synthase / natural products / dehydratase / ARO/CYC
Function / homologyCoenzyme Q-binding protein COQ10, START domain / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / FORMIC ACID / Aromatase
Function and homology information
Biological speciesStreptomyces steffisburgensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.952 Å
AuthorsTsai, S.C. / Caldara-Festin, G.M. / Jackson, D.R. / Aguilar, S. / Patel, A. / Nguyen, M. / Sasaki, E. / Valentic, T.R. / Barajas, J.F. / Vo, M. ...Tsai, S.C. / Caldara-Festin, G.M. / Jackson, D.R. / Aguilar, S. / Patel, A. / Nguyen, M. / Sasaki, E. / Valentic, T.R. / Barajas, J.F. / Vo, M. / Khanna, A. / Liu, H.-W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3R01GM076330-04S1 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural and functional analysis of two di-domain aromatase/cyclases from type II polyketide synthases.
Authors: Caldara-Festin, G. / Jackson, D.R. / Barajas, J.F. / Valentic, T.R. / Patel, A.B. / Aguilar, S. / Nguyen, M. / Vo, M. / Khanna, A. / Sasaki, E. / Liu, H.W. / Tsai, S.C.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Dec 30, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 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: StfQ Aromatase/Cyclase
B: StfQ Aromatase/Cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3154
Polymers74,2232
Non-polymers922
Water11,440635
1
A: StfQ Aromatase/Cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1582
Polymers37,1121
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: StfQ Aromatase/Cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1582
Polymers37,1121
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.976, 92.433, 138.529
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein StfQ Aromatase/Cyclase


Mass: 37111.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces steffisburgensis (bacteria)
Gene: stfQ / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2PA00
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.15 M sodium formate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 56825 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 24.3
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.952→47.29 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 2000 3.53 %Random selection
Rwork0.178 ---
obs0.1792 56649 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.952→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4811 0 6 635 5452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074942
X-RAY DIFFRACTIONf_angle_d1.0476733
X-RAY DIFFRACTIONf_dihedral_angle_d12.1541799
X-RAY DIFFRACTIONf_chiral_restr0.043730
X-RAY DIFFRACTIONf_plane_restr0.005886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9518-2.00060.27831390.24313795X-RAY DIFFRACTION98
2.0006-2.05470.28461400.21553838X-RAY DIFFRACTION100
2.0547-2.11510.24111400.19733839X-RAY DIFFRACTION100
2.1151-2.18340.20751420.18693860X-RAY DIFFRACTION100
2.1834-2.26140.2071410.1893844X-RAY DIFFRACTION100
2.2614-2.3520.23341420.18923876X-RAY DIFFRACTION100
2.352-2.4590.22961410.18813867X-RAY DIFFRACTION100
2.459-2.58860.23661420.19063880X-RAY DIFFRACTION100
2.5886-2.75080.24271440.19323910X-RAY DIFFRACTION100
2.7508-2.96320.24171420.19953912X-RAY DIFFRACTION100
2.9632-3.26130.22551440.18893927X-RAY DIFFRACTION100
3.2613-3.73310.17281450.16113963X-RAY DIFFRACTION100
3.7331-4.70260.1771450.14743982X-RAY DIFFRACTION100
4.7026-4.730420.19461530.16994156X-RAY DIFFRACTION100

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