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- PDB-3f8h: Crystal structure of a putative polyketide cyclase (tm1040_3560) ... -

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Basic information

Entry
Database: PDB / ID: 3f8h
TitleCrystal structure of a putative polyketide cyclase (tm1040_3560) from silicibacter sp. tm1040 at 2.00 A resolution
Componentsputative polyketide cyclase
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Conserved hypothetical protein CHP02096 / 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
ACETATE ION / SnoaL-like domain-containing protein
Similarity search - Component
Biological speciesSilicibacter sp. TM1040 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative polyketide cyclase (YP_611791.1) from SILICIBACTER SP. TM1040 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: 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 1.4Feb 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 / _pdbx_struct_conn_angle.value / _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 1.5Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative polyketide cyclase
B: putative polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,26012
Polymers34,2742
Non-polymers98510
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-17 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.310, 63.310, 196.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPHISHISAA3 - 3122 - 50
21ASPASPHISHISBB3 - 3122 - 50
12ILEILEILEILEAA37 - 6456 - 83
22ILEILEILEILEBB37 - 6456 - 83
13THRTHRSERSERAA71 - 13090 - 149
23THRTHRSERSERBB71 - 13090 - 149
DetailsAUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein putative polyketide cyclase


Mass: 17137.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter sp. TM1040 (bacteria) / Gene: TM1040_3560, YP_611791.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1GLD7

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Non-polymers , 5 types, 280 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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.

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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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.0200M CaCl2, 30.0000% MPD, 0.1M Acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97967,0.94645
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979671
20.946451
ReflectionResolution: 2→29.501 Å / Num. obs: 28101 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.871 Å2 / Rmerge(I) obs: 0.169 / Net I/σ(I): 7.58
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.070.011.9228814849195.9
2.07-2.150.012.6282425007199.8
2.15-2.250.013.2307825326199.8
2.25-2.370.014.1302205225199.8
2.37-2.520.015301695203199.8
2.52-2.710.016.6294655066199.9
2.71-2.990.018.33083353241100
2.99-3.420.0111.6295625112199.9
3.42-4.30.0115.3294885150199.7
4.3-29.5010.0117296865202199.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.501 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 5.825 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.133
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. CA ION, 2-METHYLPENTANE-2,4-DIOL AND ACETATE IONS HAVE BEEN MODELED FROM THE CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1408 5 %RANDOM
Rwork0.167 ---
obs0.169 28016 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 81.87 Å2 / Biso mean: 44.739 Å2 / Biso min: 24.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2--0.73 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2→29.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 65 270 2471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222283
X-RAY DIFFRACTIONr_bond_other_d0.0030.021473
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.9573109
X-RAY DIFFRACTIONr_angle_other_deg1.58233569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9655286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.72224.087115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.75315346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2791513
X-RAY DIFFRACTIONr_chiral_restr0.0920.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022584
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02495
X-RAY DIFFRACTIONr_mcbond_it1.3521382
X-RAY DIFFRACTIONr_mcbond_other0.2882565
X-RAY DIFFRACTIONr_mcangle_it2.46242206
X-RAY DIFFRACTIONr_scbond_it4.3316901
X-RAY DIFFRACTIONr_scangle_it6.1058896
LS refinement shellResolution: 1.997→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 84 -
Rwork0.207 1950 -
all-2034 -
obs--99.56 %
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)
10.50310.2396-0.13160.6027-0.28512.08210.01230.01550.06160.01080.0221-0.0578-0.25170.007-0.0345-0.2224-0.01130.0068-0.2067-0.014-0.17579.0929.18522.357
20.9160.1125-0.74350.6930.21471.8565-0.0277-0.026-0.00520.04970.03990.0193-0.07190.0312-0.0122-0.24680.0092-0.0008-0.2139-0.0141-0.19742.54322.73441.893
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 131
2X-RAY DIFFRACTION2B-5 - 131

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