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- PDB-4f3n: High resolution native crystal structure of an uncharacterized AC... -

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Basic information

Entry
Database: PDB / ID: 4f3n
TitleHigh resolution native crystal structure of an uncharacterized ACR, COG1565 superfamily protein from Burkholderia thailandensis, solved by iodide ion SAD
ComponentsUncharacterized ACR, COG1565 superfamily
KeywordsUNKNOWN FUNCTION / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / iodide ion phasing / SAD / methyltransferase superfamily / putative uncharacterize protein / transferase / similar fold to 1zkd
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / methylation
Similarity search - Function
Rossmann fold - #12710 / Protein arginine methyltransferase NDUFAF7 / Protein arginine methyltransferase NDUFAF7 superfamily / Putative S-adenosyl-L-methionine-dependent methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized ACR, COG1565 superfamily
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized ACR, COG1565 superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3614
Polymers46,1071
Non-polymers2543
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.860, 50.130, 142.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized ACR, COG1565 superfamily


Mass: 46106.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_I0294 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2T1U7
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


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


Mass: 18.015 Da / Num. of mol.: 270 / 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: 1.94 Å3/Da / Density % sol: 36.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: ButhA.17973.a.A1 PS01383 at 21.5 mg/mL against JCSG+ H7 0.2 M ammonium sulfate, 0.1 M BisTris pH 5.5, 25% PEG 3350 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 231359h7, ...Details: ButhA.17973.a.A1 PS01383 at 21.5 mg/mL against JCSG+ H7 0.2 M ammonium sulfate, 0.1 M BisTris pH 5.5, 25% PEG 3350 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 231359h7, PEGasIS iodide soak 1M NaI/20EG, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT11.5418
SYNCHROTRONSSRL BL7-121.377552
Detector
TypeIDDetectorDate
RIGAKU SATURN 944+1CCDMar 22, 2012
ADSC QUANTUM 315r2CCDApr 27, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.3775521
ReflectionResolution: 1.75→50 Å / Num. all: 37042 / Num. obs: 36871 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 22.921 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 26.89
Reflection shell

Diffraction-ID: 1,3

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.80.343.287148260796
1.8-1.840.2844.228024260599.6
1.84-1.90.2265.388272255199.6
1.9-1.960.1876.868340246899.5
1.96-2.020.1389.148543241199.8
2.02-2.090.12110.928513232399.5
2.09-2.170.09914.299276225299.9
2.17-2.260.08619.77105722177100
2.26-2.360.07821.99109092090100
2.36-2.470.06725.22109982000100
2.47-2.610.06427.3411236191699.9
2.61-2.770.05433.1511694181799.9
2.77-2.960.04641.97130321717100
2.96-3.20.03848.56125561586100
3.2-3.50.02962.07116321475100
3.5-3.910.02473.31104131346100
3.91-4.520.02182.1893311206100
4.52-5.530.02175.527871102699.9
5.53-7.830.02663.436075809100
7.830.01986.75321448999

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.1779 / WRfactor Rwork: 0.1503 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8973 / SU B: 4.074 / SU ML: 0.066 / SU R Cruickshank DPI: 0.1093 / SU Rfree: 0.1049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1988 1842 5 %RANDOM
Rwork0.1671 ---
obs0.1687 36871 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.14 Å2 / Biso mean: 18.1606 Å2 / Biso min: 6.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2746 0 14 270 3030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192861
X-RAY DIFFRACTIONr_bond_other_d0.0010.021857
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9613907
X-RAY DIFFRACTIONr_angle_other_deg0.93834499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9685386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.72523.065124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74515397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.881522
X-RAY DIFFRACTIONr_chiral_restr0.0920.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213338
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02628
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 110 -
Rwork0.217 2304 -
all-2414 -
obs--95.68 %
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)
11.12670.1214-0.03870.4488-0.37070.78190.0735-0.11070.03990.1248-0.01370.0042-0.110.0606-0.05980.0382-0.01230.00620.0239-0.01570.013227.29781.4035-23.2578
20.92210.07930.08410.47040.15620.3984-0.0667-0.03580.0472-0.00810.07110.0019-0.03070.0243-0.00440.0286-0.00710.0090.021-0.01250.01635.52017.7539-4.8443
31.5242-0.3745-0.72950.40840.05730.3967-0.06620.0306-0.17710.0223-0.02920.02180.0264-0.0080.09540.02360.00250.00410.0162-0.01940.043721.3434-16.1347-25.5295
40.6737-0.2373-0.08970.19380.09190.0455-0.00980.0617-0.05250.0075-0.01350.04960.0068-0.00650.02330.0199-0.0131-0.00690.0186-0.00080.02062.5541-4.6116-16.8446
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 89
2X-RAY DIFFRACTION2A90 - 192
3X-RAY DIFFRACTION3A193 - 250
4X-RAY DIFFRACTION4A251 - 410

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