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- PDB-6rtr: Piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus -

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Basic information

Entry
Database: PDB / ID: 6rtr
TitlePiperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus
ComponentsSemialdehyde dehydrogenase Pcd
KeywordsOXIDOREDUCTASE / antibiotic biosynthesis / Streptomyces clavuligerus
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity
Similarity search - Function
Aldehyde dehydrogenase family 7 member A1-like / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal ...Aldehyde dehydrogenase family 7 member A1-like / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / aldehyde dehydrogenase (NAD(+))
Similarity search - Component
Biological speciesStreptomyces clavuligerus ATCC 27064 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsHasse, D. / Huelsemann, J. / Carlsson, G. / Andersson, I.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structure and mechanism of piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus.
Authors: Hasse, D. / Hulsemann, J. / Carlsson, G.H. / Valegard, K. / Andersson, I.
History
DepositionMay 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Semialdehyde dehydrogenase Pcd
B: Semialdehyde dehydrogenase Pcd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,49217
Polymers108,1782
Non-polymers1,31415
Water12,755708
1
A: Semialdehyde dehydrogenase Pcd
B: Semialdehyde dehydrogenase Pcd
hetero molecules

A: Semialdehyde dehydrogenase Pcd
B: Semialdehyde dehydrogenase Pcd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,98434
Polymers216,3564
Non-polymers2,62830
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area26230 Å2
ΔGint-233 kcal/mol
Surface area60120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.720, 130.370, 157.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1013-

HOH

21A-1062-

HOH

31B-843-

HOH

41B-1034-

HOH

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Components

#1: Protein Semialdehyde dehydrogenase Pcd


Mass: 54088.996 Da / Num. of mol.: 2 / Mutation: S140T A503T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus ATCC 27064 (bacteria)
Gene: pcd / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: O85725
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate pH 5, 2.2 M ammonium sulphate, 0.2 M lithium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9764 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 1.55→45.25 Å / Num. obs: 161305 / % possible obs: 98.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.5 Å2 / Rrim(I) all: 0.071 / Net I/σ(I): 17.72
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.89 / Num. unique obs: 49255 / Rrim(I) all: 0.764 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JG7

2jg7


Resolution: 1.55→45.25 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.529 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18627 8067 5 %RANDOM
Rwork0.16359 ---
obs0.16472 153270 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.55→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7426 0 76 708 8210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197695
X-RAY DIFFRACTIONr_bond_other_d0.0020.027409
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.97110490
X-RAY DIFFRACTIONr_angle_other_deg1.012316937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95351007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69622.84331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.562151174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8631584
X-RAY DIFFRACTIONr_chiral_restr0.1010.21238
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218833
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021723
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_it1.8152.2264013
X-RAY DIFFRACTIONr_mcbond_other1.8042.2244010
X-RAY DIFFRACTIONr_mcangle_it2.5943.3265008
X-RAY DIFFRACTIONr_mcangle_other2.5943.3275009
X-RAY DIFFRACTIONr_scbond_it3.1242.6523682
X-RAY DIFFRACTIONr_scbond_other3.1242.6523683
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8013.8235478
X-RAY DIFFRACTIONr_long_range_B_refined6.32719.3249132
X-RAY DIFFRACTIONr_long_range_B_other6.17918.7588781
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 585 -
Rwork0.392 11120 -
obs--97.39 %

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