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

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Basic information

Entry
Database: PDB / ID: 6rtu
TitlePiperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus complexed with alpha-aminoadipic acid
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 / 2-AMINOHEXANEDIOIC ACID / aldehyde dehydrogenase (NAD(+))
Similarity search - Component
Biological speciesStreptomyces clavuligerus ATCC 27064 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)109,81919
Polymers108,1782
Non-polymers1,64117
Water13,818767
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)219,63938
Polymers216,3564
Non-polymers3,28334
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area29290 Å2
ΔGint-307 kcal/mol
Surface area59570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.640, 130.480, 157.860
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-989-

HOH

21B-1080-

HOH

31B-1156-

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
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, 784 molecules

#2: Chemical ChemComp-UN1 / 2-AMINOHEXANEDIOIC ACID / Α-Aminoadipate pathway


Type: L-peptide linking / Mass: 161.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 767 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
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: 1.9→45.6 Å / Num. obs: 89138 / % possible obs: 97.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 24 Å2 / Rrim(I) all: 0.086 / Net I/σ(I): 11.9
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.45 / Num. unique obs: 7528 / Rrim(I) all: 0.721 / % possible all: 86.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RTR

6rtr


Resolution: 1.9→45.575 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.87
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 4458 5 %Random selection
Rwork0.165 ---
obs0.1671 89138 97.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→45.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7465 0 95 767 8327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087713
X-RAY DIFFRACTIONf_angle_d0.8610505
X-RAY DIFFRACTIONf_dihedral_angle_d14.2084587
X-RAY DIFFRACTIONf_chiral_restr0.0531221
X-RAY DIFFRACTIONf_plane_restr0.0061387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8974-1.9190.38691260.38462377X-RAY DIFFRACTION83
1.919-1.94150.33411330.29772524X-RAY DIFFRACTION89
1.9415-1.96520.30911380.26172626X-RAY DIFFRACTION92
1.9652-1.99010.27341450.22342767X-RAY DIFFRACTION96
1.9901-2.01630.25021480.21662812X-RAY DIFFRACTION99
2.0163-2.04390.25411530.20752893X-RAY DIFFRACTION100
2.0439-2.07310.2261470.19452795X-RAY DIFFRACTION100
2.0731-2.1040.24871510.1792873X-RAY DIFFRACTION100
2.104-2.13690.20271510.17992871X-RAY DIFFRACTION100
2.1369-2.1720.23161490.18062822X-RAY DIFFRACTION100
2.172-2.20940.25491510.1832874X-RAY DIFFRACTION100
2.2094-2.24960.23191500.18262850X-RAY DIFFRACTION100
2.2496-2.29290.23481490.17842843X-RAY DIFFRACTION100
2.2929-2.33970.2221500.17482851X-RAY DIFFRACTION100
2.3397-2.39050.21971510.16522869X-RAY DIFFRACTION100
2.3905-2.44610.21621510.16642867X-RAY DIFFRACTION100
2.4461-2.50730.21241510.16042867X-RAY DIFFRACTION100
2.5073-2.57510.21371500.15992849X-RAY DIFFRACTION100
2.5751-2.65080.21131510.16482868X-RAY DIFFRACTION100
2.6508-2.73640.21721500.16572854X-RAY DIFFRACTION100
2.7364-2.83420.21261510.1692870X-RAY DIFFRACTION100
2.8342-2.94760.19841530.1662903X-RAY DIFFRACTION99
2.9476-3.08180.20851500.16362852X-RAY DIFFRACTION100
3.0818-3.24420.21510.15932863X-RAY DIFFRACTION99
3.2442-3.44740.20721520.15092894X-RAY DIFFRACTION99
3.4474-3.71350.18221500.14152843X-RAY DIFFRACTION98
3.7135-4.0870.17321520.13552883X-RAY DIFFRACTION98
4.087-4.67780.15951490.12962842X-RAY DIFFRACTION98
4.6778-5.89160.19591510.15542853X-RAY DIFFRACTION97
5.8916-45.58780.17961540.15312925X-RAY DIFFRACTION95

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