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- PDB-4u13: Crystal structure of putative polyketide cyclase (protein SMa1630... -

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Basic information

Entry
Database: PDB / ID: 4u13
TitleCrystal structure of putative polyketide cyclase (protein SMa1630) from Sinorhizobium meliloti at 2.3 A resolution
Componentsputative polyketide cyclase SMa1630
KeywordsTRANSFERASE / PSI-Biology / NYSGRC / putative polyketide cyclase / protein SMa1630 / Structural Genomics / New York Structural Genomics Research Consortium
Function / homologySnoaL-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 / SnoaL-like domain-containing protein
Function and homology information
Biological speciesSinorhizobium meliloti 1021 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShabalin, I.G. / Bacal, P. / Osinski, T. / Cooper, D.R. / Szlachta, K. / Stead, M. / Grabowski, M. / Hammonds, J. / Ahmed, M. / Hillerich, B.S. ...Shabalin, I.G. / Bacal, P. / Osinski, T. / Cooper, D.R. / Szlachta, K. / Stead, M. / Grabowski, M. / Hammonds, J. / Ahmed, M. / Hillerich, B.S. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH-5U54GM094662-04 United States
CitationJournal: to be published
Title: Crystal structure of a putative polyketide cyclase (protein SMa1630) from Sinorhizobium meliloti at 2.3 A resolution
Authors: Shabalin, I.G. / Bacal, P. / Osinski, T. / Cooper, D.R. / Szlachta, K. / Stead, M. / Grabowski, M. / Hammonds, J. / Ahmed, M. / Hillerich, B.S. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W.
History
DepositionJul 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Refinement description / Structure summary
Revision 1.2Aug 26, 2015Group: Data collection
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative polyketide cyclase SMa1630
B: putative polyketide cyclase SMa1630


Theoretical massNumber of molelcules
Total (without water)24,0602
Polymers24,0602
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-4 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.764, 42.295, 62.287
Angle α, β, γ (deg.)90.000, 111.830, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: -2 - 106 / Label seq-ID: 1 - 109

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
Detailsbiological unit is the same as asym.

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Components

#1: Protein putative polyketide cyclase SMa1630


Mass: 12030.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein was expressed with HIS-tag but was subjected to limited proteolysis with chymotrypsin.
Source: (gene. exp.) Sinorhizobium meliloti 1021 (bacteria) / Gene: SMa1630 / Plasmid: pSGC-His / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): RIL / References: UniProt: Q92YJ1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 ul of 18 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG condition #96 (0.2 M Lithium Sulfate, 0.1 M ...Details: 0.2 ul of 18 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG condition #96 (0.2 M Lithium Sulfate, 0.1 M HEPES:NaOH pH 7.5, 25% (w/v) PEG 3350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours.
Temp details: Rigaku Gallery 700

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 10379 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Χ2: 1.244 / Net I/av σ(I): 20.149 / Net I/σ(I): 12.9 / Num. measured all: 38669
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.3-2.343.20.6742.14800.91792.5
2.34-2.383.20.5735100.95997.1
2.38-2.433.60.6184950.84999
2.43-2.483.80.715211.02599.8
2.48-2.533.90.6325070.929100
2.53-2.5940.3785091.005100
2.59-2.6640.3575431.146100
2.66-2.7340.2774871.138100
2.73-2.8140.265501.429100
2.81-2.940.2015021.392100
2.9-33.90.1585391.417100
3-3.123.90.115051.487100
3.12-3.263.90.0885231.369100
3.26-3.443.80.0775201.43199.8
3.44-3.653.70.0595231.551100
3.65-3.933.80.0575241.39599.8
3.93-4.333.60.0495241.326100
4.33-4.953.60.0475241.20399.8
4.95-6.243.60.0435461.408100
6.24-503.30.0495471.29398.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data reduction
HKL-3000phasing
HKL-3000data scaling
PHENIXROSETTA-MRphasing
REFMAC5.8.0073refinement
Cootmodel building
PDB_EXTRACT3.14data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3fh1

3fh1


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2313 / WRfactor Rwork: 0.2045 / FOM work R set: 0.7849 / SU B: 18.364 / SU ML: 0.195 / SU R Cruickshank DPI: 0.3262 / SU Rfree: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.326 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 535 5.2 %RANDOM
Rwork0.1926 9813 --
obs0.1942 10348 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.47 Å2 / Biso mean: 65.057 Å2 / Biso min: 43.15 Å2
Baniso -1Baniso -2Baniso -3
1-2.65 Å2-0 Å21.2 Å2
2---1.72 Å20 Å2
3----1.44 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 0 21 1656
Biso mean---58.62 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191670
X-RAY DIFFRACTIONr_bond_other_d0.0040.021561
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.9532276
X-RAY DIFFRACTIONr_angle_other_deg0.99233568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0465216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95323.13467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34915237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0381512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211902
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02378
X-RAY DIFFRACTIONr_mcbond_it2.6523.484870
X-RAY DIFFRACTIONr_mcbond_other2.6483.482869
X-RAY DIFFRACTIONr_mcangle_it4.0215.2081084
Refine LS restraints NCS

Ens-ID: 1 / Number: 5738 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 32 -
Rwork0.284 646 -
all-678 -
obs--87.71 %
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)
18.35261.54136.72754.39141.527920.60320.32920.0307-1.098-0.3320.2366-0.49920.50520.1281-0.56570.44070.15420.1180.1779-0.00720.357817.10624.24341.956
23.42962.3460.09792.00740.32725.85430.2254-0.2394-0.09370.2158-0.23520.085-0.09790.50490.00970.33830.05830.04340.2680.02070.211315.78835.72653.839
31.3331-0.204-0.48490.7990.6182.83450.1075-0.0114-0.09150.1247-0.07250.0899-0.08030.332-0.0350.37430.06360.09040.25150.03910.258914.50336.95544.847
45.27240.7522-0.17554.13182.96485.56560.12260.39260.3315-0.2433-0.2317-0.2597-0.9969-0.35260.10920.45570.14850.01610.24060.06450.1979-0.78526.95836.769
52.83190.2082-1.64.2270.78164.09020.27240.0898-0.14160.0338-0.46370.1271-0.0875-0.32780.19130.38330.06530.0050.2252-0.02080.1687-7.01417.5945.085
62.0232-0.2751-0.56581.75240.37472.25570.180.13-0.0093-0.1962-0.2632-0.0208-0.0735-0.24920.08330.42070.1050.03620.2453-0.02730.1967-2.23115.02439.376
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 9
2X-RAY DIFFRACTION2A10 - 45
3X-RAY DIFFRACTION3A46 - 106
4X-RAY DIFFRACTION4B-2 - 12
5X-RAY DIFFRACTION5B13 - 37
6X-RAY DIFFRACTION6B38 - 106

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