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- PDB-4lgq: Crystal structure of a putative polyketide cyclase (CV_0247) from... -

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Basic information

Entry
Database: PDB / ID: 4lgq
TitleCrystal structure of a putative polyketide cyclase (CV_0247) from Chromobacterium violaceum ATCC 12472 at 2.72 A resolution
ComponentsPutative polyketide cyclase
KeywordsLYASE / SnoaL-like / PF07366 family protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


polyketide metabolic process
Similarity search - Function
SnoaL-like polyketide cyclase / Polyketide cyclase SnoaL-like / 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 / Ester cyclase
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.72 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative polyketide cyclase (CV_0247) from Chromobacterium violaceum ATCC 12472 at 2.72 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 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 polyketide cyclase
B: Putative polyketide cyclase
C: Putative polyketide cyclase
D: Putative polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,16316
Polymers61,1904
Non-polymers97312
Water1,60389
1
A: Putative polyketide cyclase
B: Putative polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0557
Polymers30,5952
Non-polymers4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-21 kcal/mol
Surface area12090 Å2
MethodPISA
2
C: Putative polyketide cyclase
D: Putative polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1089
Polymers30,5952
Non-polymers5137
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-32 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.100, 98.076, 104.958
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative polyketide cyclase


Mass: 15297.509 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria)
Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757
Gene: CV_0247 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q7P1G6

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Non-polymers , 5 types, 101 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.77
Details: 0.300M sodium chloride, 22.00% polyethylene glycol 8000, 0.1M CAPS pH 10.77, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97872,0.97818
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978721
30.978181
ReflectionResolution: 2.72→49.038 Å / Num. obs: 18389 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 77.777 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.28
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.72-2.820.7391.664551886198.4
2.82-2.930.532.260731769198.2
2.93-3.060.3543.360331774197.8
3.06-3.220.2524.659001806197.1
3.22-3.420.1467.357841793196.4
3.42-3.690.09111.866691908198.4
3.69-4.060.06216.263321844198.1
4.06-4.640.0422259441811195.7
4.64-5.820.0423.559691821195.3
5.82-49.0380.0332962481927192.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.72→49.038 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.9193 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3.NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS). 4.EDO, PEG FRAGMENTS (PGE AND PEG) AND CL IONS MODELED WERE PRESENT IN PROTEIN/CYRO CONDITIONS. 5. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 949 5.17 %RANDOM
Rwork0.1781 ---
obs0.1802 18371 96.98 %-
Displacement parametersBiso max: 173.03 Å2 / Biso mean: 68.9634 Å2 / Biso min: 23.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.1902 Å20 Å20 Å2
2--4.775 Å20 Å2
3----4.5847 Å2
Refine analyzeLuzzati coordinate error obs: 0.386 Å
Refinement stepCycle: LAST / Resolution: 2.72→49.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4088 0 60 89 4237
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1926SINUSOIDAL6
X-RAY DIFFRACTIONt_trig_c_planes96HARMONIC2
X-RAY DIFFRACTIONt_gen_planes635HARMONIC5
X-RAY DIFFRACTIONt_it4245HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion553SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4697SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4245HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5728HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion2.38
LS refinement shellResolution: 2.72→2.88 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2938 169 5.67 %
Rwork0.2305 2809 -
all0.2343 2978 -
obs--96.98 %
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)
12.82180.30341.05291.75920.03684.69010.0814-0.2313-0.08590.54420.1752-0.5442-0.01390.5442-0.2566-0.18290.0079-0.152-0.0858-0.01080.004653.74088.3857127.983
21.69350.5906-0.41774.7693-0.18962.2635-0.06280.0493-0.122-0.30490.1189-0.12030.2988-0.2222-0.0561-0.0756-0.0095-0.0317-0.01370.0229-0.099537.82056.9386110.447
32.71711.3827-1.06143.43040.84133.7984-0.1872-0.2471-0.37920.39020.2135-0.54420.5440.5442-0.02630.00420.13260.0291-0.1393-0.0508-0.104668.86822.381287.1786
41.6454-0.1906-0.63742.67370.82783.73060.05610.1229-0.119-0.4715-0.00960.2872-0.2435-0.1251-0.0465-0.03120.0096-0.0345-0.0983-0.0225-0.061853.770620.210387.363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|5 - 138}A5 - 138
2X-RAY DIFFRACTION2{B|5 - 138}B5 - 138
3X-RAY DIFFRACTION3{C|5 - 138}C5 - 138
4X-RAY DIFFRACTION4{D|5 - 138}D5 - 138

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