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- PDB-4mwg: Crystal structure of Burkholderia xenovorans DmrB apo form: A Cub... -

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Basic information

Entry
Database: PDB / ID: 4mwg
TitleCrystal structure of Burkholderia xenovorans DmrB apo form: 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
Dihydromethanopterin reductase (AfpA)
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 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 24, 2013Deposition site: RCSB / 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 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: reflns_shell / software / Item: _reflns_shell.percent_possible_all
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,3914
Polymers22,1031
Non-polymers2883
Water52229
1
A: Putative dihydromethanopterin reductase (AfpA)
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)537,39596
Polymers530,47924
Non-polymers6,91772
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 area70970 Å2
ΔGint-1265 kcal/mol
Surface area151510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.180, 184.180, 184.180
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-304-

HOH

21A-314-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.94 Å3/Da / Density % sol: 58.23 %
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: 2.2→65.2 Å / Num. obs: 14076 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.68 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 57.17
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
2.2-2.260.9660.5987.722285110219810.61296.1
2.26-2.320.9830.4519.52257569719570.45998.6
2.32-2.390.9870.34312.53259669709700.349100
2.39-2.460.9940.24916.44249249469460.254100
2.46-2.540.9950.21719.05234698968960.221100
2.54-2.630.9970.1822.09224428928920.183100
2.63-2.730.9970.15725.46200628608560.16199.5
2.73-2.840.9990.1134.51220508208200.112100
2.84-2.970.9990.07946.36214738068060.081100
2.97-3.1110.0659.01198727527520.061100
3.11-3.2810.04774.41189227397390.048100
3.28-3.4810.0481.84160056896890.041100
3.48-3.7210.032102.97159376546500.03399.4
3.72-4.0210.027113.07152106106080.02899.7
4.02-4.410.023134.48145265765750.02399.8
4.4-4.9210.02138.78123785235240.021100
4.92-5.6810.022131.85105874694650.02399.1
5.68-6.9610.022131.3597514044040.023100
6.96-9.8410.017149.4371683353350.018100
9.84-65.14610.017142.8939272172110.01897.2

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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: 2.2→65.117 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.8231 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 23.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 704 5 %RANDOM
Rwork0.1858 ---
obs0.1874 14073 99.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.49 Å2 / Biso mean: 55.0335 Å2 / Biso min: 23.24 Å2
Refinement stepCycle: LAST / Resolution: 2.2→65.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1347 0 15 29 1391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091407
X-RAY DIFFRACTIONf_angle_d1.0181923
X-RAY DIFFRACTIONf_chiral_restr0.045221
X-RAY DIFFRACTIONf_plane_restr0.005244
X-RAY DIFFRACTIONf_dihedral_angle_d12.653503
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.370.28491340.23392552268698
2.37-2.60850.24751380.189826212759100
2.6085-2.9860.20271390.191226382777100
2.986-3.76190.21941420.193226922834100
3.7619-65.1460.20691510.172928663017100
Refinement TLS params.Method: refined / Origin x: 14.6745 Å / Origin y: 39.4659 Å / Origin z: 64.2539 Å
111213212223313233
T0.2717 Å20.0507 Å20.0172 Å2-0.3915 Å20.0153 Å2--0.2508 Å2
L2.7986 °2-0.2168 °2-0.3567 °2-5.6526 °2-0.311 °2--3.2714 °2
S-0.0167 Å °-0.0425 Å °0.0724 Å °0.0963 Å °-0.0541 Å °0.2962 Å °-0.3909 Å °-0.3519 Å °0.0817 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA12 - 191
2X-RAY DIFFRACTION1allA1 - 203
3X-RAY DIFFRACTION1allA1 - 329

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