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- PDB-4m7t: Crystal structure of BtrN in complex with AdoMet and 2-DOIA -

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Basic information

Entry
Database: PDB / ID: 4m7t
TitleCrystal structure of BtrN in complex with AdoMet and 2-DOIA
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
Chem-25W / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / S-adenosyl-L-methionine-dependent 2-deoxy-scyllo-inosamine dehydrogenase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.56 Å
AuthorsDrennan, C.L. / Goldman, P.J.
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
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: BtrN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0196
Polymers30,6621
Non-polymers1,3575
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.664, 55.175, 116.853
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein BtrN / BtrN protein


Mass: 30662.014 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

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Non-polymers , 5 types, 292 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-25W / (1R,2S,3S,4R,5S)-5-aminocyclohexane-1,2,3,4-tetrol


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 30 mM citric acid / 70 mM Bis-TRIS propane pH 7.6 and 25-31% PEG 4000, 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: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.56→100 Å / Num. obs: 40313 / % possible obs: 96 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.127 / Χ2: 1.009 / Net I/σ(I): 5.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.56-1.622.70.47431490.863176
1.62-1.683.30.44737090.901190.4
1.68-1.763.80.42640560.929198.1
1.76-1.854.20.37341250.988199.2
1.85-1.974.80.31741351.025199.5
1.97-2.124.80.24841591.051199.6
2.12-2.334.90.18841611.059199.7
2.33-2.675.10.15241911.047199.6
2.67-3.364.90.10842311.064199.5
3.36-1004.80.07843970.983198.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å40.17 Å
Translation4 Å40.17 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.2phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
APEXdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→40.115 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.8654 / SU ML: 0.14 / σ(F): 0 / Phase error: 19.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1825 2021 5.04 %
Rwork0.1641 --
obs0.1651 40094 95.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.28 Å2 / Biso mean: 24.1774 Å2 / Biso min: 14.19 Å2
Refinement stepCycle: LAST / Resolution: 1.56→40.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 60 287 2292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082060
X-RAY DIFFRACTIONf_angle_d1.2272801
X-RAY DIFFRACTIONf_chiral_restr0.08310
X-RAY DIFFRACTIONf_plane_restr0.005349
X-RAY DIFFRACTIONf_dihedral_angle_d22.212771
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5604-1.59950.26961110.25312042215373
1.5995-1.64270.28241330.24032382251585
1.6427-1.69110.24811380.22582593273192
1.6911-1.74560.23671440.20212722286698
1.7456-1.8080.22261470.17992771291898
1.808-1.88040.21881460.170127882934100
1.8804-1.9660.19051470.166228182965100
1.966-2.06960.1741520.1552808296099
2.0696-2.19930.18541480.14762824297299
2.1993-2.36910.18081490.150728282977100
2.3691-2.60750.17721490.16392841299099
2.6075-2.98470.16081500.16722850300099
2.9847-3.75990.17521500.152882303299
3.7599-40.12810.15341570.15252924308196

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