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- PDB-9mpy: Structure of Saro_1862, a UPF0261 domain protein from Novosphingo... -

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Basic information

Entry
Database: PDB / ID: 9mpy
TitleStructure of Saro_1862, a UPF0261 domain protein from Novosphingobium aromaticivorans with bound acetovanillone
ComponentsUPF0261 domain-containing protein
KeywordsHYDROLASE / UPF0261 domain
Function / homologyUncharacterised protein family UPF0261 / UPF0261 domain / : / Uncharacterised protein family (UPF0261) N-terminal domain / Uncharacterised protein family (UPF0261) C-terminal domain / : / CITRIC ACID / 1-(4-hydroxy-3-methoxyphenyl)ethanone / Uncharacterized protein
Function and homology information
Biological speciesNovosphingobium aromaticivorans DSM 12444 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsBingman, C.A. / Hall, B.W. / Fox, B.G. / Donohue, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0018409 United States
Citation
Journal: J.Biol.Chem. / Year: 2025
Title: MarK, a Novosphingobium aromaticivorans kinase required for catabolism of multiple aromatic monomers.
Authors: Hall, B.W. / Neri, J.C. / Bingman, C.A. / Vilbert, A.C. / Eckmann, J.B. / Myers, K.S. / Sibert, B.S. / Wright, E.R. / Fox, B.G. / Kiley, P.J. / Noguera, D.R. / Donohue, T.J.
#1: Journal: To Be Published
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / ...Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / Prisant, M.G. / Read, R.J. / Richardson, J.S. / Richardson, D.C. / Sammito, M.D. / Sobolev, O.V. / Stockwell, D.H. / Terwilliger, T.C. / Urzhumtsev, A.G. / Videau, L.L. / Williams, C.J. / Adams, P.D.
History
DepositionJan 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0261 domain-containing protein
B: UPF0261 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1519
Polymers85,3652
Non-polymers7867
Water15,907883
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-59 kcal/mol
Surface area30340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.911, 96.421, 110.513
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein UPF0261 domain-containing protein


Mass: 42682.516 Da / Num. of mol.: 2 / Mutation: E16K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans DSM 12444 (bacteria)
Gene: Saro_1862 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G771
#2: Chemical ChemComp-I75 / 1-(4-hydroxy-3-methoxyphenyl)ethanone


Mass: 166.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 883 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.0M sodium citrate, 0.1 M sodium cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 1.58→47.94 Å / Num. obs: 124484 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 20.24 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.14 / Net I/σ(I): 8.71
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.58-1.621.49591160.4461.6161
1.62-1.671.2789000.6011.361
1.67-1.711.02986420.6871.1021
1.71-1.770.85884070.7650.9191
1.77-1.820.68881210.8320.7371
1.82-1.890.53379260.90.5721
1.89-1.960.41175870.9310.4411
1.96-2.040.31573670.9560.341
2.04-2.130.25270270.9710.271
2.13-2.230.20867560.9790.2231
2.23-2.360.17964410.9840.1921
2.36-2.50.15360810.9890.1641
2.5-2.670.13457410.9910.1441
2.67-2.880.11253350.9930.121
2.88-3.160.09249580.9940.0991
3.16-3.530.07744770.9960.0831
3.53-4.080.06739890.9960.0721
4.08-50.06234100.9970.0671
5-7.070.06626630.9970.071
7.07-500.05715400.9950.0611

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XSCALEVERSION Jun 30, 2024 BUILT=20241002)data scaling
XDSVERSION Jun 30, 2023 BUILT=20230630data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→47.94 Å / SU ML: 0.2031 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.0016
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1811 2000 1.59 %
Rwork0.1543 123819 -
obs0.1547 124484 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.57 Å2
Refinement stepCycle: LAST / Resolution: 1.58→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5918 0 53 883 6854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166271
X-RAY DIFFRACTIONf_angle_d1.27668534
X-RAY DIFFRACTIONf_chiral_restr0.0854965
X-RAY DIFFRACTIONf_plane_restr0.01331146
X-RAY DIFFRACTIONf_dihedral_angle_d12.78232298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.610.40891000.32198562X-RAY DIFFRACTION97.28
1.61-1.660.28252000.26548691X-RAY DIFFRACTION99.99
1.66-1.70.28291000.23278817X-RAY DIFFRACTION99.99
1.7-1.760.24422000.20318748X-RAY DIFFRACTION100
1.76-1.820.23961000.19138818X-RAY DIFFRACTION100
1.82-1.90.20841000.17418837X-RAY DIFFRACTION99.99
1.9-1.980.20032000.17718764X-RAY DIFFRACTION100
1.98-2.090.21011000.14798861X-RAY DIFFRACTION99.99
2.09-2.220.15032000.13918781X-RAY DIFFRACTION99.99
2.22-2.390.17711000.13748885X-RAY DIFFRACTION100
2.39-2.630.15862000.14468829X-RAY DIFFRACTION99.99
2.63-3.010.18721000.15558965X-RAY DIFFRACTION99.99
3.01-3.790.16521130.13639008X-RAY DIFFRACTION99.99
3.79-47.940.15761870.13329253X-RAY DIFFRACTION99.85
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)
14.5669967428-1.20603439970.03179521556155.079803869250.6140825927815.82355837111-0.02864661050740.0821817191776-0.0134228917756-0.0858961648315-0.04468471207660.388538105031-0.125060744305-0.3342475073620.08641857978040.150062341455-0.000108843380388-0.00848610233790.1248174237020.01658786234880.0544714694144-27.028142268999.157010048311.0237807864
20.75965844972-0.04513206170660.3115932336651.196501948030.05130815210891.53662340987-0.0208148265513-0.00574420094622-0.0762446665855-0.02410424501590.025687779390.1398384194430.0570031729962-0.113833674865-0.004969916508540.15840875868-0.007638471212580.005599713359190.1776413422780.001112090516170.135747678897-24.049771640186.96074349018.62913218283
32.177278765992.57326740426-1.778992943875.45319520879-0.4255920092513.83794722119-0.1207873532570.2512300510670.401678270633-0.02170952790980.08344928439180.887221201989-0.0121681533648-0.7813940016510.05506021418790.2106300536210.009479120917260.001209366531320.29242971674-0.004423251296460.171591035673-32.060919368496.669775489522.0146120885
40.854445397093-0.594433038763-0.05692129135432.386474595150.5896387560790.776642095026-0.0321822053412-0.09960260230190.08786878097310.1536609213180.0703069544494-0.09041778286910.01257057264240.137205347934-0.05196249923990.1287018467690.003164680233160.007677898997110.183435956403-0.01547235735390.135829058108-9.4716213714976.948944318414.3351447591
51.950221027530.5240583331330.4040491174751.136530049070.2478986466190.867471076457-0.04706808114920.141329386229-0.20553922853-0.02625461611840.0720915111693-0.03906131127120.05252835452480.0121946144828-0.02385239641960.1371938258050.01113976630740.01937479452960.149320058054-0.0241856002010.164174496006-12.3617393762.38129521263.54396439443
60.941962804993-0.0447737401214-0.3827253040120.4163555797160.2291345965042.1518398323-0.012970739759-0.0369864397188-0.1153711263860.0695590566924-0.0114124622046-0.02887997943820.1646772975950.08263591483540.04337866547940.1895506165170.00707047147142-0.006832484661480.1498842210590.003479937903550.119993721651-22.138418361188.81444835740.1100075909
71.199111986210.08721279453920.1087916999691.86000016499-0.2220521830450.8434882459180.0359070481602-0.00692409809653-0.108820296055-0.02516733727890.01218118913430.07159066037060.05497131531520.000480189765375-0.05329351829790.1417306598960.00699880925097-0.002804861335090.139788707448-0.002819994176860.161442384413-50.222808646981.608218521643.0601869511
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 37 )AA4 - 371 - 34
22chain 'A' and (resid 38 through 148 )AA38 - 14835 - 145
33chain 'A' and (resid 149 through 176 )AA149 - 176146 - 173
44chain 'A' and (resid 177 through 234 )AA177 - 234174 - 231
55chain 'A' and (resid 235 through 404 )AA235 - 404232 - 401
66chain 'B' and (resid 4 through 176 )BD4 - 1761 - 173
77chain 'B' and (resid 177 through 406 )BD177 - 406174 - 403

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