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- PDB-4pca: X-ray crystal structure of an O-methyltransferase from Anaplasma ... -

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Basic information

Entry
Database: PDB / ID: 4pca
TitleX-ray crystal structure of an O-methyltransferase from Anaplasma phagocytophilum bound to SAH and Manganese
ComponentsO-methyltransferase family protein
KeywordsTRANSFERASE / methyltransferase SAH / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyVaccinia Virus protein VP39 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : / S-ADENOSYL-L-HOMOCYSTEINE / :
Function and homology information
Biological speciesAnaplasma phagocytophilum str. HGE1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFairman, J.W. / Abendroth, J. / Lorimer, D. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
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
DepositionApr 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _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: O-methyltransferase family protein
B: O-methyltransferase family protein
C: O-methyltransferase family protein
D: O-methyltransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,97018
Polymers100,8404
Non-polymers2,13014
Water17,691982
1
A: O-methyltransferase family protein
B: O-methyltransferase family protein
hetero molecules

D: O-methyltransferase family protein
hetero molecules

C: O-methyltransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,97018
Polymers100,8404
Non-polymers2,13014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area13530 Å2
ΔGint-84 kcal/mol
Surface area31650 Å2
MethodPISA
2
A: O-methyltransferase family protein
B: O-methyltransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4238
Polymers50,4202
Non-polymers1,0036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-36 kcal/mol
Surface area18520 Å2
MethodPISA
3
C: O-methyltransferase family protein
hetero molecules

D: O-methyltransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,54710
Polymers50,4202
Non-polymers1,1278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y+1/2,-z-1/21
Buried area4570 Å2
ΔGint-30 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.210, 102.760, 103.320
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
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: THR / End label comp-ID: THR

Dom-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1chain AAA-2 - 2186 - 226
2chain BBB0 - 2188 - 226
3chain CCC0 - 2188 - 226
4chain DDD-2 - 2186 - 226

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Components

#1: Protein
O-methyltransferase family protein


Mass: 25210.098 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma phagocytophilum str. HGE1 (bacteria)
Gene: HGE1_02637 / Production host: Escherichia coli (E. coli) / References: UniProt: S6G476
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 982 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 400 nl of protein solution plus 400 nl of precipitant. Precipitant was MCSG2 well H5 - 0.1 M succinic acid pH 7.0, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 12, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 145193 / Num. obs: 144437 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.18 % / Biso Wilson estimate: 12.02 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.08 / Χ2: 0.976 / Net I/σ(I): 16.27 / Num. measured all: 892627
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.5-1.546.180.850.5733.146505810619105230.62699.1
1.54-1.580.8970.453.996372210379102910.49299.2
1.58-1.630.9330.3674.91617871005599780.40199.2
1.63-1.680.9520.3085.7860481981897570.33799.4
1.68-1.730.9670.2457.1858668952294700.26899.5
1.73-1.790.9740.2098.4656835920491650.22899.6
1.79-1.860.9820.16610.3754960890188710.18299.7
1.86-1.940.9890.12813.0452855858285580.14199.7
1.94-2.020.9920.10515.6450686821481880.11599.7
2.02-2.120.9940.08818.2648470786278520.09699.9
2.12-2.240.9950.07321.646299750074950.0899.9
2.24-2.370.9960.06623.3843933710370980.07299.9
2.37-2.540.9970.05825.7341304667166670.06399.9
2.54-2.740.9970.05428.0838763625362510.059100
2.74-30.9970.04830.8235680575857510.05399.9
3-3.350.9980.04334.4832239522052110.04799.8
3.35-3.870.9980.0437.7628517465946430.04499.7
3.87-4.740.9980.03839.824153396839570.04199.7
4.74-6.710.9980.03838.7518444309830470.04298.4
6.710.9980.03840.089773180716640.04292.1

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9pre_1665)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OA5

4oa5


Resolution: 1.5→40.584 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1721 7142 4.95 %RANDOM
Rwork0.1469 137271 --
obs0.1482 144413 99.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.99 Å2 / Biso mean: 17.7413 Å2 / Biso min: 5.83 Å2
Refinement stepCycle: final / Resolution: 1.5→40.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6694 0 132 982 7808
Biso mean--15.82 30.37 -
Num. residues----878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157271
X-RAY DIFFRACTIONf_angle_d1.5869916
X-RAY DIFFRACTIONf_chiral_restr0.0751171
X-RAY DIFFRACTIONf_plane_restr0.0081253
X-RAY DIFFRACTIONf_dihedral_angle_d14.242744
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3720X-RAY DIFFRACTION9.692TORSIONAL
12B3720X-RAY DIFFRACTION9.692TORSIONAL
13C3720X-RAY DIFFRACTION9.692TORSIONAL
14D3720X-RAY DIFFRACTION9.692TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5001-1.51710.24252210.20074503472499
1.5171-1.53490.21532320.19714545477799
1.5349-1.55370.222400.18454474471499
1.5537-1.57330.22562420.17544502474499
1.5733-1.5940.21012340.16884512474699
1.594-1.61590.19782330.16464533476699
1.6159-1.6390.2032470.16044537478499
1.639-1.66340.18322110.1644536474799
1.6634-1.68940.18952220.156445624784100
1.6894-1.71710.18232340.15624529476399
1.7171-1.74670.18782250.1514562478799
1.7467-1.77850.18132440.147845594803100
1.7785-1.81270.19832510.14914525477699
1.8127-1.84970.1782440.149745324776100
1.8497-1.88990.17032540.144245444798100
1.8899-1.93390.18022370.148945834820100
1.9339-1.98220.18462280.154745704798100
1.9822-2.03580.192180.148345964814100
2.0358-2.09570.16362590.144745674826100
2.0957-2.16340.15412390.140645824821100
2.1634-2.24070.15742530.138845894842100
2.2407-2.33040.16812430.143645584801100
2.3304-2.43640.16872280.144646494877100
2.4364-2.56490.17232070.142346394846100
2.5649-2.72550.15592330.142546454878100
2.7255-2.93590.17252450.147446154860100
2.9359-3.23130.17882380.14646624900100
3.2313-3.69860.16212510.139246544905100
3.6986-4.65870.14242740.123646844958100
4.6587-40.59910.16852550.14974723497896
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)
13.48740.39880.88020.45690.66621.0017-0.08340.33860.2709-0.06920.02520.0828-0.0893-0.01190.02210.1034-0.01380.00050.14470.04150.1428-12.9039-47.2872-9.9394
20.45230.0925-0.04671.41070.14780.5440.0041-0.00480.0318-0.019-0.0048-0.0367-0.03110.00670.0010.0561-0.0071-0.0020.06620.00890.06721.2434-29.8957-12.1414
31.6097-2.0287-1.02143.01560.88681.44180.11420.144-0.0782-0.3085-0.09950.07630.0242-0.0668-0.00150.1681-0.0018-0.02470.1184-0.01070.08141.9619-50.3177-29.9906
41.3702-0.18750.42042.86050.50531.63710.06680.0223-0.0144-0.1548-0.0077-0.03-0.0172-0.0131-0.04680.0628-0.0010.00920.06010.00980.05938.0251-53.153-23.499
51.50220.2270.90321.24810.39911.68750.05190.0687-0.0099-0.0703-0.0356-0.2659-0.01860.1131-0.05820.0562-0.00030.00740.0798-0.00550.131118.6062-56.1302-20.5417
62.17030.19050.07993.585-0.85233.77580.05910.1697-0.1089-0.3529-0.0062-0.20830.10820.2053-0.030.09780.03610.03060.1019-0.03660.137820.3806-63.2414-27.4577
71.3068-0.27610.29641.0424-0.07970.7585-0.0008-0.0785-0.10060.08510.0056-0.01840.026-0.01060.0020.0715-0.0082-0.01980.06670.0140.08037.2563-58.3964-8.0821
85.28520.8694-0.26622.8409-0.66193.9946-0.0760.38090.0155-0.34290.14480.1604-0.045-0.2129-0.05340.1113-0.0083-0.02830.1159-0.00190.094522.0111-6.0709-51.8386
92.15482.53310.30786.97712.35271.5746-0.2770.2461-0.2443-0.6730.2365-0.2113-0.07620.12370.05430.1477-0.01770.01790.1231-0.01590.100628.116-19.5318-55.2008
100.91450.4388-0.39122.31110.02331.6877-0.1122-0.0322-0.1301-0.0161-0.0049-0.01620.0820.07180.07540.06940.01660.03370.10070.01060.089729.9919-21.6627-43.6287
110.18940.00630.11451.58910.44643.2458-0.1689-0.0523-0.20320.09630.00540.02930.34490.13550.12890.15670.01820.07260.09360.00160.163629.1424-33.2539-46.7881
121.6657-0.08010.90261.5825-0.18481.26930.055-0.1418-0.33560.2568-0.0955-0.0560.3720.19290.00140.20720.0390.030.1660.06480.155629.9566-27.8948-31.3336
131.0297-0.31450.31981.31530.05470.678-0.0924-0.2048-0.21440.2963-0.01420.08140.0760.08280.02820.12880.01730.03140.15940.05710.101225.3803-19.3444-29.8793
144.5626-0.8261-1.70052.9778-1.90063.8213-0.0039-0.2482-0.30740.04360.00040.72740.2033-0.7465-0.08230.1403-0.04220.02330.2917-0.0110.24157.4476-13.2103-28.1112
151.4697-0.0180.43481.55770.03361.3624-0.0125-0.2271-0.07460.2686-0.05780.00820.01850.11890.04250.0961-0.00080.00930.1310.030.070525.2438-11.6386-28.9019
163.832-0.23140.89290.68-0.04770.41410.14750.044-0.011-0.1651-0.0446-0.1136-0.0876-0.1115-0.06450.14430.00830.01670.13210.02540.088163.8594-46.6483-21.5017
171.8898-0.1346-0.40573.4232-0.43041.43130.04710.13520.07520.0408-0.0548-0.0767-0.0263-0.00070.03910.12110.0254-0.00770.12810.00470.048453.0958-47.3221-18.7352
181.2005-0.3326-0.1151.4328-0.03230.82970.04540.1696-0.0226-0.1282-0.07680.1119-0.1105-0.14610.01740.09860.0301-0.0220.1436-0.01720.07841.6803-42.9681-14.9638
191.8642-0.7828-0.19252.39783.57675.9807-0.0344-0.41450.52030.42630.3213-0.4082-0.18060.41970.00890.20020.0191-0.03860.2277-0.10560.27460.1779-42.13012.6409
201.7253-0.2941-0.29511.7720.01551.1193-0.0369-0.09490.09290.24130.05750.0648-0.0728-0.06850.04940.08830.02370.00520.1122-0.00140.09449.43-51.7593-1.4642
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 16 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 218 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 30 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 31 through 55 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 56 through 90 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 91 through 116 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 117 through 218 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 0 through 16 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 17 through 30 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 31 through 90 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 91 through 116 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 117 through 138 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 139 through 168 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 169 through 182 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 183 through 218 )C0
16X-RAY DIFFRACTION16chain 'D' and (resid -2 through 30 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 31 through 55 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 56 through 165 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 166 through 180 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 181 through 218 )D0

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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