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- PDB-4m7s: Crystal structure of SeMet BtrN in an OPEN conformation -

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Open data


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Basic information

Entry
Database: PDB / ID: 4m7s
TitleCrystal structure of SeMet BtrN in an OPEN conformation
ComponentsBtrN
KeywordsMETAL BINDING PROTEIN / AdoMet radical fold
Function / homology
Function and homology information


2-deoxy-scyllo-inosamine dehydrogenase (AdoMet-dependent) / antibiotic biosynthetic process / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
2-Deoxy-scyllo-inosamine dehydrogenase (BtrN-like) / 4Fe4S-binding SPASM domain / Iron-sulfur cluster-binding domain / Radical SAM superfamily / Radical SAM / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / IRON/SULFUR CLUSTER / S-adenosyl-L-methionine-dependent 2-deoxy-scyllo-inosamine dehydrogenase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.022 Å
AuthorsGoldman, P.J. / Drennan, C.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: X-ray analysis of butirosin biosynthetic enzyme BtrN redefines structural motifs for AdoMet radical chemistry.
Authors: Goldman, P.J. / Grove, T.L. / Booker, S.J. / Drennan, C.L.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BtrN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0326
Polymers31,0761
Non-polymers9575
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.408, 42.058, 50.925
Angle α, β, γ (deg.)90.000, 105.400, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-654-

HOH

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Components

#1: Protein BtrN / BtrN protein


Mass: 31075.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Gene: btrN / Production host: Escherichia coli (E. coli) / References: UniProt: Q8G907
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 1.65 Å3/Da / Density meas: 25.51 Mg/m3
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 13-18 % Jeffamine ED-2001 pH 7.0 (Hampton Research) and 100 mM imidazole pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 25638 / Biso Wilson estimate: 26.51 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.02-2.09174
2.09-2.18198.6
2.18-2.27199.9
2.27-2.391100
2.39-2.541100
2.54-2.741100
2.74-3.021100
3.02-3.451100
3.45-4.35199.8
4.35-501100

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
APEXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.022→38.513 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.8353 / SU ML: 0.2 / σ(F): 1.38 / Phase error: 23.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 1291 5.03 %
Rwork0.1706 --
obs0.173 13343 98.5 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.66 Å2 / Biso mean: 39.3754 Å2 / Biso min: 14.89 Å2
Refinement stepCycle: LAST / Resolution: 2.022→38.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 0 33 57 1775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071777
X-RAY DIFFRACTIONf_angle_d1.1292410
X-RAY DIFFRACTIONf_chiral_restr0.084268
X-RAY DIFFRACTIONf_plane_restr0.004304
X-RAY DIFFRACTIONf_dihedral_angle_d17.208657
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0216-2.10250.2961270.23132436256388
2.1025-2.19820.26461450.20462730287599
2.1982-2.31410.24821480.17627272875100
2.3141-2.45910.21611450.16627572902100
2.4591-2.64890.20241430.166127402883100
2.6489-2.91540.21151450.165327362881100
2.9154-3.3370.23311470.168427462893100
3.337-4.20350.20071420.152627582900100
4.2035-38.51970.20441490.172927282877100
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)
12.56971.2777-0.60794.0611-0.22591.04370.04570.0539-0.2294-0.05070.0186-0.16640.28410.0511-0.05640.35530.048-0.04160.2477-0.04750.2313114.7691-20.851310.8999
21.83032.0284-0.75854.6268-2.80844.16280.0632-0.10130.05580.12260.00730.1179-0.1957-0.0539-0.08350.16070.0329-0.02740.1565-0.02470.151110.2061-13.167619.25
38.2012-5.78570.27817.66321.12816.2910.32180.3171-0.9409-0.4571-0.34930.6950.3841-0.61830.07990.2203-0.0636-0.0410.2707-0.00320.3261103.5411-24.722617.376
43.98771.5369-3.63794.5833-2.42883.6293-0.37160.2305-0.261-0.12030.2290.06140.5725-0.90010.41060.3301-0.1431-0.12750.4858-0.06950.3886101.4104-23.61894.9544
52.82970.08441.49914.14940.74435.3141-0.14760.4940.0104-0.68140.175-0.0604-0.24910.414-0.02330.269-0.03970.01450.28490.01640.1714116.1808-12.3211-0.8513
65.47670.5048-3.69594.6004-1.75618.0651-0.21630.2497-0.7085-0.01430.16911.03830.1015-0.7190.04120.3948-0.0463-0.08080.3212-0.08360.4995104.6389-21.8535-6.3811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:37)A1 - 37
2X-RAY DIFFRACTION2chain 'A' and (resseq 38:107)A38 - 107
3X-RAY DIFFRACTION3chain 'A' and (resseq 108:120)A108 - 120
4X-RAY DIFFRACTION4chain 'A' and (resseq 135:170)A135 - 170
5X-RAY DIFFRACTION5chain 'A' and (resseq 171:228)A171 - 228
6X-RAY DIFFRACTION6chain 'A' and (resseq 229:249)A229 - 249

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