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- PDB-3ef8: Crystal structure of Putative Scytalone Dehydratase (YP_496742.1)... -

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Basic information

Entry
Database: PDB / ID: 3ef8
TitleCrystal structure of Putative Scytalone Dehydratase (YP_496742.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.50 A resolution
ComponentsPutative Scyalone Dehydratase
KeywordsLYASE / YP_496742.1 / Putative Scytalone Dehydratase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / unknown function
Function / homology
Function and homology information


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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / SnoaL-like domain-containing protein
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans DSM 12444 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative Scyalone Dehydratase (YP_496742.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2017Group: Refinement description / Structure summary / Category: software / struct / struct_keywords
Item: _software.classification / _software.name ..._software.classification / _software.name / _struct.title / _struct_keywords.text
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Scyalone Dehydratase
B: Putative Scyalone Dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,07816
Polymers35,1462
Non-polymers1,93314
Water4,179232
1
A: Putative Scyalone Dehydratase
hetero molecules

A: Putative Scyalone Dehydratase
hetero molecules

A: Putative Scyalone Dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,13130
Polymers52,7183
Non-polymers3,41327
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6590 Å2
ΔGint-17 kcal/mol
Surface area18830 Å2
MethodPISA
2
B: Putative Scyalone Dehydratase
hetero molecules

B: Putative Scyalone Dehydratase
hetero molecules

B: Putative Scyalone Dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,10318
Polymers52,7183
Non-polymers2,38515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area6700 Å2
ΔGint-16 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.851, 59.851, 237.504
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-150-

MG

21A-277-

HOH

31A-278-

HOH

41A-279-

HOH

51B-265-

HOH

DetailsAUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TRIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative Scyalone Dehydratase


Mass: 17572.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans DSM 12444 (bacteria)
Gene: YP_496742.1, Saro_1465 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2G8B5

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Non-polymers , 5 types, 246 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2000M MgCl2, 20.0000% PEG-8000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97905 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 22, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 1.5→29.921 Å / Num. obs: 50820 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 12.779 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 3.731
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.545.60.8180.82136537830.81899.9
1.54-1.585.70.7290.82046536120.729100
1.58-1.635.70.60912020835640.609100
1.63-1.685.70.5231.21974934720.523100
1.68-1.735.70.4431.41916433610.443100
1.73-1.795.70.3751.71860232510.375100
1.79-1.865.70.3082.11791131220.308100
1.86-1.9480.2372.72415930200.237100
1.94-2.0290.1833.62614429070.183100
2.02-2.129.60.1594.12641027490.159100
2.12-2.249.60.1454.52525726340.145100
2.24-2.379.60.1344.72390524890.134100
2.37-2.549.60.1344.92223323140.134100
2.54-2.749.60.1245.22099921840.124100
2.74-39.60.1075.91932220140.107100
3-3.359.60.0916.61726717910.091100
3.35-3.879.60.08171532415880.081100
3.87-4.749.70.07571299913460.075100
4.74-6.719.50.0875.81008410570.087100
6.71-29.939.40.095.252825620.0999.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.5→29.921 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.047 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.069
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.A MAGNESIUM ION AND POLYETHYLENE GLYCOL FROM CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS HAVE BEEN MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 2579 5.1 %RANDOM
Rwork0.163 ---
obs0.164 50819 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.04 Å2 / Biso mean: 17.512 Å2 / Biso min: 2.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 93 269 2797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212610
X-RAY DIFFRACTIONr_bond_other_d0.0030.021836
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9623494
X-RAY DIFFRACTIONr_angle_other_deg1.04734421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4315315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.57422.459122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8815406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6231524
X-RAY DIFFRACTIONr_chiral_restr0.0860.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022871
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02571
X-RAY DIFFRACTIONr_mcbond_it1.71731538
X-RAY DIFFRACTIONr_mcbond_other0.4713624
X-RAY DIFFRACTIONr_mcangle_it2.76652488
X-RAY DIFFRACTIONr_scbond_it4.16381072
X-RAY DIFFRACTIONr_scangle_it6.085111006
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 205 -
Rwork0.185 3577 -
all-3782 -
obs--99.97 %

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