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- PDB-6p77: 2.5 Angstrom structure of Caci_6494 from Catenulispora Acidiphila -

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Basic information

Entry
Database: PDB / ID: 6p77
Title2.5 Angstrom structure of Caci_6494 from Catenulispora Acidiphila
ComponentsAromatic-ring-hydroxylating dioxygenase beta subunit
KeywordsUNKNOWN FUNCTION / NTF2 Superfamily
Function / homology
Function and homology information


dioxygenase activity
Similarity search - Function
SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Aromatic-ring-hydroxylating dioxygenase beta subunit
Similarity search - Component
Biological speciesCatenulispora acidiphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.501 Å
AuthorsVuksanovic, N. / Silvaggi, N.R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structural characterization of three noncanonical NTF2-like superfamily proteins: implications for polyketide biosynthesis.
Authors: Vuksanovic, N. / Zhu, X. / Serrano, D.A. / Siitonen, V. / Metsa-Ketela, M. / Melancon 3rd, C.E. / Silvaggi, N.R.
History
DepositionJun 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aromatic-ring-hydroxylating dioxygenase beta subunit
B: Aromatic-ring-hydroxylating dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2818
Polymers33,4522
Non-polymers8296
Water48627
1
A: Aromatic-ring-hydroxylating dioxygenase beta subunit
hetero molecules

A: Aromatic-ring-hydroxylating dioxygenase beta subunit
hetero molecules

A: Aromatic-ring-hydroxylating dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,18112
Polymers50,1783
Non-polymers1,0039
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6810 Å2
ΔGint-50 kcal/mol
Surface area21140 Å2
MethodPISA
2
B: Aromatic-ring-hydroxylating dioxygenase beta subunit
hetero molecules

B: Aromatic-ring-hydroxylating dioxygenase beta subunit
hetero molecules

B: Aromatic-ring-hydroxylating dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,66212
Polymers50,1783
Non-polymers1,4849
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation12_665-y+1,-z+1,x1
Buried area9800 Å2
ΔGint-17 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.260, 159.260, 159.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

21B-505-

HOH

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Components

#1: Protein Aromatic-ring-hydroxylating dioxygenase beta subunit


Mass: 16726.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catenulispora acidiphila (strain DSM 44928 / NRRL B-24433 / NBRC 102108 / JCM 14897) (bacteria)
Strain: DSM 44928 / NRRL B-24433 / NBRC 102108 / JCM 14897 / Gene: Caci_6494 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7PWR4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 4.8 Å3/Da / Density % sol: 74.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 1.4 M K2HPO4 0.07 M Na2H2PO4 pH 8.3 5% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→46.02 Å / Num. obs: 23351 / % possible obs: 99.97 % / Redundancy: 21.7 % / Biso Wilson estimate: 48.08 Å2 / Rmerge(I) obs: 0.1958 / Net I/σ(I): 28.48
Reflection shellResolution: 2.501→2.591 Å / Rmerge(I) obs: 1.358 / Num. unique obs: 2330

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.501→45.97 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.922 / SU B: 12.141 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22456 2004 8.6 %RANDOM
Rwork0.20232 ---
obs0.20422 23351 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.58 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.501→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 55 27 2310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0182325
X-RAY DIFFRACTIONr_bond_other_d0.0020.022105
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.8513130
X-RAY DIFFRACTIONr_angle_other_deg1.062.8494841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2655271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35822.656128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2915338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0291528
X-RAY DIFFRACTIONr_chiral_restr0.0840.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022575
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02517
X-RAY DIFFRACTIONr_mcbond_it3.5733.411102
X-RAY DIFFRACTIONr_mcbond_other3.563.4071101
X-RAY DIFFRACTIONr_mcangle_it5.1945.0761367
X-RAY DIFFRACTIONr_mcangle_other5.1965.0791368
X-RAY DIFFRACTIONr_scbond_it5.7164.311223
X-RAY DIFFRACTIONr_scbond_other5.7154.3111224
X-RAY DIFFRACTIONr_scangle_other8.3176.1431764
X-RAY DIFFRACTIONr_long_range_B_refined9.88341.8572380
X-RAY DIFFRACTIONr_long_range_B_other9.87841.8362379
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 147 -
Rwork0.257 1559 -
obs--100 %
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)
12.57960.6828-0.07853.93140.36182.422-0.01670.20980.1666-0.26250.03550.2298-0.2267-0.1195-0.01880.07420.0017-0.04150.02630.01420.057748.32965.746.815
22.4242-0.91960.0683.5536-0.62591.77150.10210.1347-0.2462-0.3704-0.00450.32990.1847-0.3413-0.09760.137-0.0062-0.08420.08820.00330.087143.29898.23642.455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 148
2X-RAY DIFFRACTION2B4 - 148

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