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- PDB-3wis: Crystal structure of Burkholderia xenovorans DmrB in complex with... -

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Basic information

Entry
Database: PDB / ID: 3wis
TitleCrystal structure of Burkholderia xenovorans DmrB in complex with FMN: A Cubic Protein Cage for Redox Transfer
ComponentsPutative dihydromethanopterin reductase (AfpA)
KeywordsOXIDOREDUCTASE / methanopterin / dihydromethanopterin reductase / flavin / protein cage
Function / homology
Function and homology information


catalytic activity / nucleotide binding
Similarity search - Function
Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Dihydromethanopterin reductase (AfpA)
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.901 Å
AuthorsBobik, T.A. / Cascio, D. / Jorda, J. / McNamara, D.E. / Bustos, C. / Wang, T.C. / Rasche, M.E. / Yeates, T.O.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure of dihydromethanopterin reductase, a cubic protein cage for redox transfer
Authors: Mcnamara, D.E. / Cascio, D. / Jorda, J. / Bustos, C. / Wang, T.C. / Rasche, M.E. / Yeates, T.O. / Bobik, T.A.
History
DepositionSep 25, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Apr 23, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Mar 20, 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

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Assembly

Deposited unit
A: Putative dihydromethanopterin reductase (AfpA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4007
Polymers22,1031
Non-polymers1,2976
Water1,06359
1
A: Putative dihydromethanopterin reductase (AfpA)
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)561,605168
Polymers530,47924
Non-polymers31,127144
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_556-y,-x,-z+11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation33_545y,z-1/2,x+1/21
crystal symmetry operation34_545-y,z-1/2,-x+1/21
crystal symmetry operation35_555y,-z+1/2,-x+1/21
crystal symmetry operation36_555-y,-z+1/2,x+1/21
crystal symmetry operation41_545x,z-1/2,-y+1/21
crystal symmetry operation42_545-x,z-1/2,y+1/21
crystal symmetry operation43_555-x,-z+1/2,-y+1/21
crystal symmetry operation44_555x,-z+1/2,y+1/21
crystal symmetry operation53_455z-1/2,x,y+1/21
crystal symmetry operation54_455z-1/2,-x,-y+1/21
crystal symmetry operation55_555-z+1/2,-x,y+1/21
crystal symmetry operation56_555-z+1/2,x,-y+1/21
crystal symmetry operation69_455z-1/2,y,-x+1/21
crystal symmetry operation70_455z-1/2,-y,x+1/21
crystal symmetry operation71_555-z+1/2,y,x+1/21
crystal symmetry operation72_555-z+1/2,-y,-x+1/21
Buried area121320 Å2
ΔGint-1798 kcal/mol
Surface area145360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.840, 183.840, 183.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

21A-309-

HOH

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Components

#1: Protein Putative dihydromethanopterin reductase (AfpA)


Mass: 22103.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: Bxeno_B0583, Bxe_B2440, DmrB / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13QT8
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.0M (NH4)2SO4, 20mM Tris HCl pH 8, 100mM NaCl, 5% glycerol, 4mM DTT, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.9→91.92 Å / Num. obs: 21516 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 24.9 % / Biso Wilson estimate: 28.75 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 36.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-1.950.9310.9545.0438593156115550.97499.6
1.95-20.9680.7566.8338376151115100.77299.9
2-2.060.9750.6028.5634864148214820.615100
2.06-2.130.9840.46110.8437400141514150.47100
2.13-2.20.9890.35913.5837103139413940.366100
2.2-2.270.9930.28416.9935359135613550.28999.9
2.27-2.360.9960.22620.3633440129512950.23100
2.36-2.450.9970.18624.1931237127212710.1999.9
2.45-2.560.9980.16526.2429219120412020.16999.8
2.56-2.690.9980.12532.7830986116711670.127100
2.69-2.830.9990.09838.5328823110111010.1100
2.83-3.010.9990.07248.326783104810470.07499.9
3.01-3.210.9990.05756.7323800100910090.059100
3.21-3.4710.04470.96229749209200.045100
3.47-3.810.03584.2222658728710.03699.9
3.8-4.2510.03292.03191347897890.032100
4.25-4.9110.02994.75151657117100.0399.9
4.91-6.0110.0395.62147556126120.031100
6.01-8.510.02994.91107504934930.03100
8.5-91.9210.02395.4857623203180.02499.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1457refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SIRAS / Resolution: 1.901→91.92 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.8824 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 17.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1878 1075 5 %RANDOM
Rwork0.1612 ---
obs0.1626 21514 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.25 Å2 / Biso mean: 35.0006 Å2 / Biso min: 16.55 Å2
Refinement stepCycle: LAST / Resolution: 1.901→91.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 82 59 1531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081533
X-RAY DIFFRACTIONf_angle_d1.1082109
X-RAY DIFFRACTIONf_chiral_restr0.052236
X-RAY DIFFRACTIONf_plane_restr0.006261
X-RAY DIFFRACTIONf_dihedral_angle_d11.683545
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.901-1.9880.23241310.17824982629
1.988-2.09280.20681310.169924842615
2.0928-2.22390.20161320.160525012633
2.2239-2.39560.20391320.163425222654
2.3956-2.63670.18411320.170925092641
2.6367-3.01830.20941350.16725582693
3.0183-3.80280.18271360.154125932729
3.8028-92.02750.16981460.157327742920
Refinement TLS params.Method: refined / Origin x: 15.1484 Å / Origin y: 39.2289 Å / Origin z: 63.8459 Å
111213212223313233
T0.1659 Å20.0142 Å20.0145 Å2-0.1921 Å20.0106 Å2--0.188 Å2
L1.6317 °2-0.1762 °2-0.0188 °2-2.143 °20.4232 °2--1.6702 °2
S-0.0002 Å °-0.0362 Å °0.1158 Å °-0.0865 Å °-0.0337 Å °0.1545 Å °-0.151 Å °-0.2374 Å °0.0357 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA12 - 191
2X-RAY DIFFRACTION1allA2 - 202
3X-RAY DIFFRACTION1allA1 - 359
4X-RAY DIFFRACTION1allA2 - 206

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