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- PDB-3ccf: Crystal structure of putative methyltransferase (YP_321342.1) fro... -

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Basic information

Entry
Database: PDB / ID: 3ccf
TitleCrystal structure of putative methyltransferase (YP_321342.1) from Anabaena variabilis ATCC 29413 at 1.90 A resolution
ComponentsCyclopropane-fatty-acyl-phospholipid synthase
KeywordsTRANSFERASE / YP_321342.1 / putative methyltransferase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


trans-aconitate 2-methyltransferase / trans-aconitate 2-methyltransferase activity / methylation
Similarity search - Function
Methyltransferase type 11 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZOIC ACID / Cyclopropane-fatty-acyl-phospholipid synthase
Similarity search - Component
Biological speciesAnabaena variabilis ATCC 29413 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative methyltransferase (YP_321342.1) from Anabaena variabilis ATCC 29413 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclopropane-fatty-acyl-phospholipid synthase
B: Cyclopropane-fatty-acyl-phospholipid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9764
Polymers63,7322
Non-polymers2442
Water7,080393
1
A: Cyclopropane-fatty-acyl-phospholipid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9882
Polymers31,8661
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cyclopropane-fatty-acyl-phospholipid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9882
Polymers31,8661
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.830, 67.230, 131.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLU / End label comp-ID: LYS / Refine code: 6 / Auth seq-ID: 28 - 258 / Label seq-ID: 47 - 277

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsAUTHORS STATE THAT THE SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION BUT CRYSTAL PACKING ANALYSIS DOES NOT REVEAL ANY INTERFACES THAT ARE LIKELY STABLE AS A DIMER.

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Components

#1: Protein Cyclopropane-fatty-acyl-phospholipid synthase


Mass: 31865.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis ATCC 29413 (bacteria)
Species: Anabaena variabilis / Strain: PCC 7937 / Gene: YP_321342.1, Ava_0823 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q3MEY9, trans-aconitate 2-methyltransferase
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
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: 1.97 Å3/Da / Density % sol: 37.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: NANODROP, 1.0M LiCl, 20.0% PEG 6000, 0.1M MES pH 6.0, 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: 0.91162, 0.97980, 0.97968
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 13, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.97981
30.979681
ReflectionResolution: 1.9→29.921 Å / Num. obs: 40355 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.041 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.39
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-1.970.5021.7140877587195.6
1.97-2.050.3862.2148347775199.8
2.05-2.140.3012.9139647330199.8
2.14-2.250.2313.8141907469199.6
2.25-2.390.1735.1147467678199.8
2.39-2.580.1256.5151667887199.7
2.58-2.840.0849.3147837635199.8
2.84-3.250.05114.4149137640199.8
3.25-4.080.03321.3146667553199.6
4.08-29.9210.02326.5152067711199

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.921 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.029 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.14
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. BENZOIC ACID (BEZ) HAS BEEN MODELED BASED ON THE DENSITY. THIS ASSIGNMENT IS SUPPORTED BY A SALT LINK WITH ARG 251. HOWEVER, IT COULD BE SOME OTHER COMPOUND.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2024 5 %RANDOM
Rwork0.18 ---
obs0.182 40297 99.38 %-
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 mean: 31.054 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2---2.4 Å20 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3754 0 18 393 4165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223896
X-RAY DIFFRACTIONr_bond_other_d0.0020.022555
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9445304
X-RAY DIFFRACTIONr_angle_other_deg1.5136226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1645486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60124.709189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5715610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4831517
X-RAY DIFFRACTIONr_chiral_restr0.1060.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214426
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02817
X-RAY DIFFRACTIONr_mcbond_it2.03432395
X-RAY DIFFRACTIONr_mcbond_other0.5953978
X-RAY DIFFRACTIONr_mcangle_it3.45553828
X-RAY DIFFRACTIONr_scbond_it5.94981501
X-RAY DIFFRACTIONr_scangle_it8.654111472
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2956 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.575
LOOSE THERMAL3.510
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 137 -
Rwork0.271 2668 -
all-2805 -
obs--94.7 %
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)
10.040.1694-0.2050.801-0.63361.71520.0041-0.03-0.0343-0.02020.02750.1127-0.0127-0.1569-0.0316-0.09460.01130.02150.00420.0016-0.1010.04721.00822.492
21.93390.1866-1.03160.5703-0.16062.03290.0733-0.24480.23780.03470.0004-0.0678-0.1060.1202-0.0737-0.11260.0027-0.0021-0.0187-0.0107-0.038428.83341.24912.811
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA22 - 25941 - 278
2X-RAY DIFFRACTION2BB19 - 26038 - 279

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