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

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Basic information

Entry
Database: PDB / ID: 5itv
TitleCrystal structure of Bacillus subtilis BacC Dihydroanticapsin 7-dehydrogenase in complex with NADH
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Dihydroanticapsin 7-dehydrogenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsPerinbam, K. / Balaram, H. / Row, T.N.G. / Gopal, B.
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 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)112,0638
Polymers109,4014
Non-polymers2,6624
Water2,360131
1
A: Dihydroanticapsin 7-dehydrogenase
B: Dihydroanticapsin 7-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0314
Polymers54,7012
Non-polymers1,3312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-38 kcal/mol
Surface area19870 Å2
2
C: Dihydroanticapsin 7-dehydrogenase
D: Dihydroanticapsin 7-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0314
Polymers54,7012
Non-polymers1,3312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-34 kcal/mol
Surface area18950 Å2
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17660 Å2
ΔGint-117 kcal/mol
Surface area31970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.750, 88.080, 78.610
Angle α, β, γ (deg.)90.00, 106.44, 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
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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 291.15 K / Method: microbatch / pH: 6.5
Details: 0.2M Ammonium sulfate, 0.1M BIS-TRIS, pH 6.5, 25% w/v Polyethylene glycol 3350, 10% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 15, 2014
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→38.1 Å / Num. obs: 46073 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 16.3 Å2 / CC1/2: 0.996 / Rsym value: 0.08 / Net I/σ(I): 12.9
Reflection shellResolution: 2.26→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3.8 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLM7.2.0data reduction
SCALA3.3.21data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→38.1 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.622 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.213
RfactorNum. reflection% reflectionSelection details
Rfree0.22097 2205 4.8 %RANDOM
Rwork0.20717 ---
obs0.20783 43846 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.385 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20.1 Å2
2--0.22 Å2-0 Å2
3---0.85 Å2
Refinement stepCycle: 1 / Resolution: 2.26→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7391 0 176 131 7698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197708
X-RAY DIFFRACTIONr_bond_other_d0.0020.027400
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.98310480
X-RAY DIFFRACTIONr_angle_other_deg0.771317016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1295987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55526.408309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.707151295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3311516
X-RAY DIFFRACTIONr_chiral_restr0.060.21238
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028756
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021644
X-RAY DIFFRACTIONr_mcbond_other1.1252.4043962
X-RAY DIFFRACTIONr_mcangle_it1.9763.5994945
X-RAY DIFFRACTIONr_mcangle_other1.9763.5994946
X-RAY DIFFRACTIONr_scbond_it1.3032.7193745
X-RAY DIFFRACTIONr_scbond_other1.3032.7193746
X-RAY DIFFRACTIONr_scangle_other2.273.9985536
X-RAY DIFFRACTIONr_long_range_B_refined4.81222.86632374
X-RAY DIFFRACTIONr_long_range_B_other4.80722.87132328
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A157060.03
12B157060.03
21A157260.02
22C157260.02
31A137150.02
32D137150.02
41B157070.03
42C157070.03
51B136790.03
52D136790.03
61C137090.02
62D137090.02
LS refinement shellResolution: 2.256→2.315 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 174 -
Rwork0.28 3189 -
obs--98.08 %

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