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- PDB-6rts: Piperideine-6-carboxylate dehydrogenase from Streptomyces clavuli... -

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Basic information

Entry
Database: PDB / ID: 6rts
TitlePiperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus complexed with NAD+
ComponentsSemialdehyde dehydrogenase Pcd
KeywordsOXIDOREDUCTASE / antibiotic biosynthesis / Streptomyces clavuligerus
Function / homology
Function and homology information


aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / nucleotide binding
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, C-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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / aldehyde dehydrogenase (NAD(+))
Similarity search - Component
Biological speciesStreptomyces clavuligerus ATCC 27064 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)110,91120
Polymers108,1782
Non-polymers2,73318
Water9,782543
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)221,82240
Polymers216,3564
Non-polymers5,46636
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area33440 Å2
ΔGint-303 kcal/mol
Surface area60180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.040, 131.240, 157.710
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-748-

HOH

21B-718-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 561 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 543 / 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: 54.03 %
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: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.25→45.4 Å / Num. obs: 54522 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 21.8 Å2 / Rrim(I) all: 0.159 / Net I/σ(I): 8.32
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.22 / Num. unique obs: 5800 / Rrim(I) all: 0.663 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RTR

6rtr


Resolution: 2.25→45.4 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.961 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20467 2727 5 %RANDOM
Rwork0.16555 ---
obs0.16752 51800 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2---0.33 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.25→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7541 0 170 543 8254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197841
X-RAY DIFFRACTIONr_bond_other_d0.0020.027461
X-RAY DIFFRACTIONr_angle_refined_deg1.471.98310696
X-RAY DIFFRACTIONr_angle_other_deg1.007317054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10651019
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44222.866328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.831151165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8451582
X-RAY DIFFRACTIONr_chiral_restr0.0890.21253
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218983
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021765
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_it1.2332.1514073
X-RAY DIFFRACTIONr_mcbond_other1.2312.1494070
X-RAY DIFFRACTIONr_mcangle_it2.0253.2175085
X-RAY DIFFRACTIONr_mcangle_other2.0253.2185086
X-RAY DIFFRACTIONr_scbond_it1.9752.4593768
X-RAY DIFFRACTIONr_scbond_other1.9752.4593769
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2413.5795610
X-RAY DIFFRACTIONr_long_range_B_refined4.99517.8199029
X-RAY DIFFRACTIONr_long_range_B_other4.91217.6368806
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 200 -
Rwork0.254 3799 -
obs--99.78 %

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