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- PDB-5f13: Structure of Mn bound DUF89 from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 5f13
TitleStructure of Mn bound DUF89 from Saccharomyces cerevisiae
ComponentsProtein-glutamate O-methyltransferase
KeywordsTRANSFERASE / DUF89 / metal-dependent phosphatases
Function / homology
Function and homology information


fructose-1-phosphatase activity / fructose 6-phosphate aldolase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatase activity / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Transcription Elongation Factor S-II; Chain A - #60 / Damage-control phosphatase ARMT1 / Damage-control phosphatase ARMT1-like, metal-binding domain / Damage-control phosphatase ARMT1-like, metal-binding domain superfamily / Damage-control phosphatase ARMT1-like domain / Transcription Elongation Factor S-II; Chain A / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / PHOSPHATE ION / Damage-control phosphatase YMR027W
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.393 Å
AuthorsNocek, B. / Skarina, T. / Joachimiak, A. / Savchenko, A. / Yakunin, A.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: A family of metal-dependent phosphatases implicated in metabolite damage-control.
Authors: Huang, L. / Khusnutdinova, A. / Nocek, B. / Brown, G. / Xu, X. / Cui, H. / Petit, P. / Flick, R. / Zallot, R. / Balmant, K. / Ziemak, M.J. / Shanklin, J. / de Crecy-Lagard, V. / Fiehn, O. / ...Authors: Huang, L. / Khusnutdinova, A. / Nocek, B. / Brown, G. / Xu, X. / Cui, H. / Petit, P. / Flick, R. / Zallot, R. / Balmant, K. / Ziemak, M.J. / Shanklin, J. / de Crecy-Lagard, V. / Fiehn, O. / Gregory, J.F. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F. / Hanson, A.D.
History
DepositionNov 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 1.3Sep 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 / pdbx_struct_oper_list / struct_conn
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_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.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.value / _pdbx_struct_oper_list.symmetry_operation / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-glutamate O-methyltransferase
B: Protein-glutamate O-methyltransferase
C: Protein-glutamate O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,91016
Polymers163,0073
Non-polymers90313
Water2,810156
1
B: Protein-glutamate O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6786
Polymers54,3361
Non-polymers3425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein-glutamate O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6516
Polymers54,3361
Non-polymers3165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein-glutamate O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5814
Polymers54,3361
Non-polymers2453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)223.035, 95.550, 78.097
Angle α, β, γ (deg.)90.00, 105.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Protein-glutamate O-methyltransferase /


Mass: 54335.672 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YMR027W, YM9711.17
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q04371, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 5 types, 169 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% P3350 ,0.1 M NH4 dihydrogen Phosphate, 5mM MnCl2
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.393→30.174 Å / Num. obs: 60334 / % possible obs: 97.1 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.03
Reflection shellResolution: 2.393→2.44 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIXdev_1888refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PT1

3pt1


Resolution: 2.393→30.174 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.86 / Phase error: 25.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 2730 5.08 %
Rwork0.1994 --
obs0.2013 53710 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.393→30.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10600 0 40 156 10796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310877
X-RAY DIFFRACTIONf_angle_d0.63214747
X-RAY DIFFRACTIONf_dihedral_angle_d13.6033866
X-RAY DIFFRACTIONf_chiral_restr0.0251621
X-RAY DIFFRACTIONf_plane_restr0.0031873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3934-2.43470.3267730.26461398X-RAY DIFFRACTION47
2.4347-2.47890.2913900.25111582X-RAY DIFFRACTION54
2.4789-2.52660.30461050.24491714X-RAY DIFFRACTION58
2.5266-2.57810.3018930.24721886X-RAY DIFFRACTION64
2.5781-2.63420.24211240.24912093X-RAY DIFFRACTION72
2.6342-2.69540.27711250.24422344X-RAY DIFFRACTION80
2.6954-2.76280.25971340.24172565X-RAY DIFFRACTION88
2.7628-2.83740.28181510.23812764X-RAY DIFFRACTION94
2.8374-2.92080.25821670.24382826X-RAY DIFFRACTION97
2.9208-3.0150.26571560.24462920X-RAY DIFFRACTION97
3.015-3.12270.26151370.24872880X-RAY DIFFRACTION98
3.1227-3.24760.31241450.23922910X-RAY DIFFRACTION98
3.2476-3.39520.24471640.2142853X-RAY DIFFRACTION98
3.3952-3.57390.2661490.19832880X-RAY DIFFRACTION98
3.5739-3.79740.21731670.18622877X-RAY DIFFRACTION98
3.7974-4.090.20751640.16262900X-RAY DIFFRACTION98
4.09-4.50040.17391410.15062893X-RAY DIFFRACTION98
4.5004-5.14880.1711700.1482900X-RAY DIFFRACTION98
5.1488-6.47630.24351450.18492921X-RAY DIFFRACTION98
6.4763-30.17680.23561300.18922874X-RAY DIFFRACTION93
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)
13.5822-0.59460.58852.8874-0.25791.780.0063-0.12770.67650.0407-0.021-0.1684-0.1130.11720.03930.1768-0.0098-0.05140.2102-0.11430.283319.213764.99285.7163
21.8954-0.0229-0.1212.0602-0.09432.15380.02530.5494-0.4467-0.24120.075-0.22040.27930.0961-0.1130.3540.0712-0.06430.4179-0.18190.244418.0637.6731-15.364
32.36750.07480.21021.37230.17361.69830.04420.0836-0.1543-0.04020.0226-0.17150.12640.079-0.0680.21280.0634-0.05750.223-0.07590.150719.097944.2223-3.4171
42.61720.7106-0.40832.41520.70464.3725-0.2310.2969-0.1354-0.20020.10.64190.1148-0.26210.15110.2966-0.04410.04250.234-0.08720.522127.4752-12.5308-55.6746
51.99920.3336-0.58522.5308-0.01011.8753-0.0841-0.04140.01770.26610.05350.17330.00460.10330.00820.2959-0.00250.09130.2138-0.0420.276934.6244-0.1326-46.0407
64.06340.63410.93460.52070.23322.1161-0.468-0.24110.5080.36170.11950.1554-0.6261-0.19030.10581.048-0.06730.32890.4786-0.23760.425428.996414.7042-27.4982
72.20180.3538-0.6371.6442-0.09731.27090.1351-0.30640.11480.3853-0.12080.2837-0.13220.0883-0.00570.4525-0.01310.13120.2357-0.07070.326535.19793.5483-38.0404
83.98681.2436-0.12833.1710.37043.50740.0240.2741-0.27420.1037-0.1915-0.27890.6076-0.05690.14080.3201-0.04880.11170.3547-0.04230.372471.36285.9511-71.8622
92.73680.8352-0.70362.776-0.25363.0765-0.17650.5956-0.0086-0.15440.08250.20690.2395-0.45290.09070.254-0.03640.06140.4374-0.08810.352558.52596.6894-72.3151
102.55270.51590.30642.1412-0.02465.27860.1529-0.3422-0.73910.2039-0.1635-0.79940.99520.98560.0160.50850.11350.04690.59680.19410.99875.1914-10.8358-45.8027
114.20140.4472-0.19581.84820.40344.0936-0.1029-1.0071-0.54240.4338-0.4846-0.65420.34311.33220.5580.4224-0.0328-0.06561.07390.17720.79985.33141.1343-40.6922
122.6148-0.2701-0.58641.8977-0.84982.8779-0.1164-0.6402-0.51860.1861-0.1663-0.40160.35310.82720.18890.32030.0577-0.01440.56150.08290.549268.7102-2.0878-45.4932
132.8730.5307-1.80511.0834-0.51052.56620.2913-0.5830.14550.1349-0.1599-0.2787-0.29340.6201-0.11650.2732-0.0878-0.02780.4527-0.08810.444772.4511.4041-51.8133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 133 )
2X-RAY DIFFRACTION2chain 'A' and (resid 134 through 273 )
3X-RAY DIFFRACTION3chain 'A' and (resid 274 through 468 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 68 )
5X-RAY DIFFRACTION5chain 'B' and (resid 69 through 190 )
6X-RAY DIFFRACTION6chain 'B' and (resid 191 through 240 )
7X-RAY DIFFRACTION7chain 'B' and (resid 241 through 468 )
8X-RAY DIFFRACTION8chain 'C' and (resid 3 through 41 )
9X-RAY DIFFRACTION9chain 'C' and (resid 42 through 133 )
10X-RAY DIFFRACTION10chain 'C' and (resid 134 through 166 )
11X-RAY DIFFRACTION11chain 'C' and (resid 167 through 227 )
12X-RAY DIFFRACTION12chain 'C' and (resid 228 through 318 )
13X-RAY DIFFRACTION13chain 'C' and (resid 319 through 468 )

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