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- PDB-3cvo: Crystal structure of a methyltransferase-like protein (spo2022) f... -

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Basic information

Entry
Database: PDB / ID: 3cvo
TitleCrystal structure of a methyltransferase-like protein (spo2022) from silicibacter pomeroyi dss-3 at 1.80 A resolution
ComponentsMethyltransferase-like protein of unknown function
KeywordsTRANSFERASE / Rossmann fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyVaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Class I SAM-dependent methyltransferase
Function and homology information
Biological speciesSilicibacter pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of methyltransferase-like protein of unknown function (YP_167254.1) from Silicibacter pomeroyi DSS-3 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 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 1.5Feb 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
Revision 1.6Nov 20, 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 / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase-like protein of unknown function
B: Methyltransferase-like protein of unknown function
C: Methyltransferase-like protein of unknown function
D: Methyltransferase-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,68754
Polymers91,3544
Non-polymers3,33450
Water8,935496
1
A: Methyltransferase-like protein of unknown function
B: Methyltransferase-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,42129
Polymers45,6772
Non-polymers1,74427
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-21.1 kcal/mol
Surface area17620 Å2
MethodPISA
2
C: Methyltransferase-like protein of unknown function
D: Methyltransferase-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,26725
Polymers45,6772
Non-polymers1,59023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-21.3 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.391, 61.653, 96.323
Angle α, β, γ (deg.)90.000, 97.450, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEMSETYRTYR6AA9 - 15410 - 155
21MSEMSETYRTYR6BB9 - 15410 - 155
31MSEMSETYRTYR6CC9 - 15410 - 155
41MSEMSETYRTYR6DD9 - 15410 - 155
12GLNGLNPROPRO4AA160 - 201161 - 202
22GLNGLNPROPRO4BB160 - 201161 - 202
32GLNGLNPROPRO4CC160 - 201161 - 202
42GLNGLNPROPRO4DD160 - 201161 - 202

NCS ensembles :
ID
1
2
DetailsCRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Methyltransferase-like protein of unknown function


Mass: 22838.414 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi DSS-3 (bacteria) / Species: Silicibacter pomeroyi / Strain: DSS-3 / DSM 15171 / Gene: YP_167254.1, SPO2022 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LRV1

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Non-polymers , 5 types, 546 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 496 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: NANODROP, 2.1M Ammonium sulfate, 1.5% PEG 400, 15.0% Glycerol, 0.1M HEPES pH 6.9, 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, 0.97914, 0.97932
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 28, 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
20.979141
30.979321
ReflectionResolution: 1.8→29.63 Å / Num. obs: 93599 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 21.483 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.853.20.64812176268830.64899.8
1.85-1.93.20.5031.52114866770.50399.9
1.9-1.953.20.37622081665650.37699.9
1.95-2.013.20.3132.41998863190.31399.9
2.01-2.083.20.2622.81953061460.262100
2.08-2.153.20.2073.61897359760.207100
2.15-2.233.20.1721.81816957190.172100
2.23-2.323.20.1472.71757955270.147100
2.32-2.433.20.1176.11691153210.117100
2.43-2.553.20.1096.71626150980.109100
2.55-2.683.20.0977.21530048130.097100
2.68-2.853.20.0877.81459045790.087100
2.85-3.043.20.0729.21369543130.072100
3.04-3.293.20.0610.71286840490.06100
3.29-3.63.20.04912.81169036880.049100
3.6-4.023.20.043141069433630.043100
4.02-4.653.20.04314.1937029640.043100
4.65-5.693.10.04713794825360.047100
5.69-8.053.10.0512.5607719680.05100
8.05-29.6330.04413.4326610950.04497.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0069refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.63 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.587 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.1
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. SULFATE (SO4) IONS, PEG 400 FRAGMENTS (PG4) AND GLYCEROL (GOL) FROM CRYSTALLIZATION AND ETHYLENE GLYCOL (EDO) FROM CRYO SOLUTION WERE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 4690 5 %RANDOM
Rwork0.168 ---
obs0.17 93597 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.963 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å2-1.37 Å2
2--1.14 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6003 0 213 496 6712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226629
X-RAY DIFFRACTIONr_bond_other_d0.0010.024655
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9689007
X-RAY DIFFRACTIONr_angle_other_deg1.375311228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3475829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34422.279272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87815975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2371562
X-RAY DIFFRACTIONr_chiral_restr0.0910.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217395
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021370
X-RAY DIFFRACTIONr_mcbond_it1.82934069
X-RAY DIFFRACTIONr_mcbond_other0.68431590
X-RAY DIFFRACTIONr_mcangle_it2.93656617
X-RAY DIFFRACTIONr_scbond_it5.04682560
X-RAY DIFFRACTIONr_scangle_it7.224112390
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1732LOOSE POSITIONAL0.315
12B1732LOOSE POSITIONAL0.555
13C1732LOOSE POSITIONAL0.275
14D1732LOOSE POSITIONAL0.35
11A1732LOOSE THERMAL1.9510
12B1732LOOSE THERMAL2.8410
13C1732LOOSE THERMAL4.1410
14D1732LOOSE THERMAL2.710
21A464MEDIUM POSITIONAL0.390.5
22B464MEDIUM POSITIONAL0.350.5
23C464MEDIUM POSITIONAL0.210.5
24D464MEDIUM POSITIONAL0.350.5
21A464MEDIUM THERMAL1.622
22B464MEDIUM THERMAL1.82
23C464MEDIUM THERMAL1.92
24D464MEDIUM THERMAL1.642
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 351 -
Rwork0.244 6523 -
all-6874 -
obs--99.48 %
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)
11.609-0.42130.45721.17370.06280.9003-0.0411-0.03850.18670.12810.0453-0.16570.05870.1654-0.0042-0.09430.0214-0.0127-0.0218-0.0461-0.006367.36550.559157.9464
20.8136-0.09610.00870.96310.27770.9337-0.00160.08830.0381-0.1232-0.00060.10120.0167-0.03510.0022-0.0735-0.0025-0.0073-0.07770.0023-0.016634.357546.959341.6264
30.70010.26290.25811.3650.13823.4611-0.00160.0985-0.0852-0.19120.07720.04360.54060.3098-0.07560.13950.0493-0.0182-0.0288-0.0431-0.104761.84521.7222-3.2007
40.73220.29170.28371.07660.29651.6856-0.04530.08490.0217-0.03740.0052-0.00420.02340.16020.0401-0.0619-0.00640.0074-0.0541-0.0131-0.063265.328120.6328.1604
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 2019 - 202
2X-RAY DIFFRACTION2BB8 - 2019 - 202
3X-RAY DIFFRACTION3CC8 - 2019 - 202
4X-RAY DIFFRACTION4DD8 - 2019 - 202

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