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

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Basic information

Entry
Database: PDB / ID: 6rtt
TitlePiperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus complexed with picolinic acid
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
PYRIDINE-2-CARBOXYLIC ACID / aldehyde dehydrogenase (NAD(+))
Similarity search - Component
Biological speciesStreptomyces clavuligerus ATCC 27064 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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

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)109,65016
Polymers108,1782
Non-polymers1,47214
Water13,259736
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)219,30032
Polymers216,3564
Non-polymers2,94428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area27530 Å2
ΔGint-152 kcal/mol
Surface area58990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.820, 130.060, 157.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-906-

HOH

21A-1025-

HOH

31B-1002-

HOH

41B-1054-

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-6PC / PYRIDINE-2-CARBOXYLIC ACID / PICOLINIC ACID


Mass: 123.109 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.64 Å3/Da / Density % sol: 53.39 %
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: BM14 / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.65→45.33 Å / Num. obs: 128777 / % possible obs: 99 % / Redundancy: 7.4 % / Biso Wilson estimate: 17.3 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.088 / Net I/σ(I): 18.65
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 3.29 / Num. unique obs: 5590 / CC1/2: 0.816 / Rrim(I) all: 0.706 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RTR

6rtr


Resolution: 1.65→45.33 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.184 6439 5 %
Rwork0.162 122338 -
obs0.163 128777 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.06 Å2 / Biso mean: 21.0336 Å2 / Biso min: 6.25 Å2
Refinement stepCycle: final / Resolution: 1.65→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7474 0 92 736 8302
Biso mean--28.12 27.71 -
Num. residues----1007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.66870.29461420.2656269263
1.6687-1.68830.28761520.2481289568
1.6883-1.70890.30551600.2364302871
1.7089-1.73060.27121700.2154323876
1.7306-1.75330.20961860.2123352282
1.7533-1.77740.24882030.2121385890
1.7774-1.80280.22482160.1905411797
1.8028-1.82970.21852240.1854425699
1.8297-1.85830.22042260.1814427899
1.8583-1.88870.20622220.1787422099
1.8887-1.92130.2112220.1762422999
1.9213-1.95620.20132240.1683425699
1.9562-1.99390.20262250.1562426799
1.9939-2.03460.19782260.1571428899
2.0346-2.07880.17912230.1511424099
2.0788-2.12720.1812260.148429399
2.1272-2.18030.16832240.15434267100
2.1803-2.23930.17522250.15054266100
2.2393-2.30520.17652260.15374290100
2.3052-2.37960.18372260.15424307100
2.3796-2.46460.19252250.16274273100
2.4646-2.56330.18692260.16094300100
2.5633-2.67990.19772280.16454320100
2.6799-2.82120.17472260.16794307100
2.8212-2.99790.18432280.16524329100
2.9979-3.22940.19692280.16514335100
3.2294-3.55420.17942300.1594354100
3.5542-4.06830.15272300.14334384100
4.0683-5.12440.14672310.13824378100
5.1244-45.330.16832390.16214551100

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