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- PDB-4oa8: X-ray crystal structure of O-methyltransferase from Anaplasma pha... -

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Basic information

Entry
Database: PDB / ID: 4oa8
TitleX-ray crystal structure of O-methyltransferase from Anaplasma phagocytophilum in apo form
ComponentsO-methyltransferase family protein
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / O-methyltransferase
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation
Similarity search - Function
: / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
O-methyltransferase family protein
Similarity search - Component
Biological speciesAnaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos Pathog. / Year: 2015
Title: An O-Methyltransferase Is Required for Infection of Tick Cells by Anaplasma phagocytophilum.
Authors: Oliva Chavez, A.S. / Fairman, J.W. / Felsheim, R.F. / Nelson, C.M. / Herron, M.J. / Higgins, L. / Burkhardt, N.Y. / Oliver, J.D. / Markowski, T.W. / Kurtti, T.J. / Edwards, T.E. / Munderloh, U.G.
History
DepositionJan 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_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 / _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: O-methyltransferase family protein
B: O-methyltransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7275
Polymers50,6182
Non-polymers1083
Water3,189177
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-51 kcal/mol
Surface area17080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.150, 76.400, 79.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 6 - 217 / Label seq-ID: 15 - 226

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein O-methyltransferase family protein


Mass: 25309.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
Strain: HZ / Gene: APH_0584 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2GKC7, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.4 uL protein @ 20 mg/mL + 0.4 uL JCSG+ well D6 - 0.2 M magnesium chloride, 0.1 M TRIS pH 8.50, 20% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 24924 / Num. obs: 24484 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 4.71 % / Biso Wilson estimate: 39.954 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 27.49
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.15-2.210.4913.398041179898.1
2.21-2.270.4174.268398169397.7
2.27-2.330.364.98390168498.2
2.33-2.40.2716.528221166698.1
2.4-2.480.2128.147707156398.1
2.48-2.570.1819.517681157198.7
2.57-2.670.14311.667194147698.9
2.67-2.780.11813.957073145198.3
2.78-2.90.08518.326623138599.2
2.9-3.040.06224.26204133098.6
3.04-3.210.04631.375927127898.5
3.21-3.40.03539.025534120899.2
3.4-3.630.02749.655165113798.8
3.63-3.930.02257.964689105598.5
3.93-4.30.01868.27442298097.8
4.3-4.810.01774.49391689498.1
4.81-5.550.01774.23354279398.3
5.55-6.80.01869.56301567998.1
6.8-9.620.01585.48232454297.1
9.620.01290.81117230188.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4OA5

4oa5


Resolution: 2.15→44.05 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.334 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 1244 5.1 %RANDOM
Rwork0.1848 ---
obs0.1872 24468 98.3 %-
all-24924 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.74 Å2 / Biso mean: 38.35 Å2 / Biso min: 9.72 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å20 Å2
2--1.34 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.15→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3168 0 6 177 3351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193233
X-RAY DIFFRACTIONr_bond_other_d0.0050.023051
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9544393
X-RAY DIFFRACTIONr_angle_other_deg1.08236982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2515427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77425.403124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80315522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.423156
X-RAY DIFFRACTIONr_chiral_restr0.0870.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023716
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02712
X-RAY DIFFRACTIONr_mcbond_it1.6962.1831708
X-RAY DIFFRACTIONr_mcbond_other1.6962.1831707
X-RAY DIFFRACTIONr_mcangle_it2.5953.2692132
Refine LS restraints NCS

Ens-ID: 1 / Number: 11925 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 87 -
Rwork0.297 1711 -
all-1798 -
obs--98.09 %
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)
16.5808-0.58761.76541.49811.39112.13350.1499-0.2168-0.60030.4260.1668-0.10680.50470.094-0.31680.24410.0106-0.08380.0530.04550.134613.254882.4004107.9973
23.47922.45950.695516.353-0.16022.804-0.13020.0854-0.2219-0.37830.3951-0.120.3017-0.1299-0.26490.146-0.0077-0.03610.171-0.01240.06210.372390.1267102.8959
31.21840.71090.20242.06840.79142.06210.01920.06660.04020.13140.02310.02920.1612-0.2733-0.04230.0845-0.0251-0.01830.18430.00650.0415-2.20192.197397.988
44.4475-1.164-0.620217.29779.16658.814-0.34410.39640.0803-1.19710.7352-0.1097-0.57990.2294-0.39120.1745-0.0593-0.03410.23110.00810.04982.635197.374983.5566
53.20950.07370.0362.6940.80921.398-0.13010.5898-0.3047-0.12090.2715-0.16170.07030.1067-0.14140.1037-0.0619-0.01520.265-0.09820.062913.794893.209586.3101
64.19684.03871.04794.11670.70070.8007-0.1920.6005-0.572-0.25450.5032-0.54690.02550.1863-0.31120.06330.00360.08330.3144-0.18130.340832.043198.471587.628
72.72421.07310.66491.72950.84612.44020.01720.1003-0.0116-0.06430.187-0.25930.02410.0609-0.20420.054-0.0072-0.01840.1477-0.03330.162427.8571108.617498.294
81.42420.37440.52461.80130.06016.4281-0.09460.05210.01390.00190.1048-0.4644-0.08880.2092-0.01020.0193-0.0434-0.00920.2-0.11380.277237.523115.0765101.6954
91.5209-0.6975-0.44622.983-0.60920.77450.12740.01570.12880.31170.0256-0.45070.00980.1491-0.1530.13990.0327-0.15030.1788-0.06960.21929.1367100.4679110.6491
102.7119-1.3852-0.30022.37250.19851.73010.0572-0.0570.10240.30180.1702-0.28670.16740.049-0.22740.1512-0.001-0.12890.1397-0.05540.153724.639995.0303111.3261
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 34
2X-RAY DIFFRACTION2A35 - 53
3X-RAY DIFFRACTION3A54 - 142
4X-RAY DIFFRACTION4A143 - 151
5X-RAY DIFFRACTION5A152 - 218
6X-RAY DIFFRACTION6B6 - 37
7X-RAY DIFFRACTION7B38 - 90
8X-RAY DIFFRACTION8B91 - 125
9X-RAY DIFFRACTION9B126 - 178
10X-RAY DIFFRACTION10B179 - 218

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