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- PDB-5itw: Crystal structure of Bacillus subtilis BacC Dihydroanticapsin 7-d... -

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Basic information

Entry
Database: PDB / ID: 5itw
TitleCrystal structure of Bacillus subtilis BacC Dihydroanticapsin 7-dehydrogenase
ComponentsDihydroanticapsin 7-dehydrogenase
KeywordsOXIDOREDUCTASE / short-chain dehydrogenases/reductases / Rossmann fold / NAD(P) binding domain
Function / homology
Function and homology information


dihydroanticapsin dehydrogenase / antibiotic biosynthetic process / oxidoreductase activity
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dihydroanticapsin 7-dehydrogenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsPerinbam, K. / Balaram, H. / Row, T.N.G. / Gopal, B.
Funding support India, 2items
OrganizationGrant numberCountry
Council of Scientific and Industrial Research India
Department Of Science & Technology India
CitationJournal: Protein Eng. Des. Sel. / Year: 2017
Title: Probing the influence of non-covalent contact networks identified by charge density analysis on the oxidoreductase BacC.
Authors: Perinbam, K. / Balaram, H. / Guru Row, T.N. / Gopal, B.
History
DepositionMar 17, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroanticapsin 7-dehydrogenase
B: Dihydroanticapsin 7-dehydrogenase
C: Dihydroanticapsin 7-dehydrogenase
D: Dihydroanticapsin 7-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,17012
Polymers109,4014
Non-polymers7698
Water17,781987
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15020 Å2
ΔGint-244 kcal/mol
Surface area33540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.520, 87.200, 78.290
Angle α, β, γ (deg.)90.00, 101.08, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 1 - 255 / Label seq-ID: 1 - 255

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Dihydroanticapsin 7-dehydrogenase / Bacilysin biosynthesis oxidoreductase BacC


Mass: 27350.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: sulfate ions are modelled
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: bacC, ywfD, BSU37720, ipa-82d / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P39640, dihydroanticapsin dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 987 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 291.15 K / Method: microbatch / pH: 6.5
Details: 0.2M Ammonium sulfate, 0.1M BIS-TRIS pH6.5, 25% w/v Polyethylene glycol 3350, 10% glycerol cryoprotectant, 0.05M Tris, 0.25M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 12, 2014
RadiationMonochromator: Band pass 1.9x10-4 for a Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.187→32.95 Å / Num. obs: 305981 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 10.1 Å2 / CC1/2: 0.998 / Rsym value: 0.071 / Net I/σ(I): 9.2
Reflection shellResolution: 1.187→1.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.067 / Mean I/σ(I) obs: 1.5 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLM7.2.0data reduction
SCALA3.3.21data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AWD

3awd


Resolution: 1.19→32.95 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.581 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.034 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.163 15057 4.9 %RANDOM
Rwork0.138 ---
obs0.139 290778 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.258 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20.59 Å2
2--0.55 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.19→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7576 0 40 987 8603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197962
X-RAY DIFFRACTIONr_bond_other_d0.0080.027703
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.96210848
X-RAY DIFFRACTIONr_angle_other_deg1.388317740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76251073
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.82826.571315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61151367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6871515
X-RAY DIFFRACTIONr_chiral_restr0.1010.21287
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029268
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021675
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.131.534212
X-RAY DIFFRACTIONr_mcbond_other2.1091.534211
X-RAY DIFFRACTIONr_mcangle_it2.6192.3055301
X-RAY DIFFRACTIONr_mcangle_other2.6232.3055302
X-RAY DIFFRACTIONr_scbond_it3.8251.8993750
X-RAY DIFFRACTIONr_scbond_other3.7731.8813719
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3462.6875496
X-RAY DIFFRACTIONr_long_range_B_refined5.12514.59610002
X-RAY DIFFRACTIONr_long_range_B_other4.43713.6699442
X-RAY DIFFRACTIONr_rigid_bond_restr3.52315665
X-RAY DIFFRACTIONr_sphericity_free36.5195298
X-RAY DIFFRACTIONr_sphericity_bonded15.65516221
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A159730.1
12B159730.1
21A157390.11
22C157390.11
31A156710.09
32D156710.09
41B156300.09
42C156300.09
51B155310.08
52D155310.08
61C153150.09
62D153150.09
LS refinement shellResolution: 1.187→1.218 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 1097 -
Rwork0.352 20267 -
obs--94.4 %

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