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- PDB-4jdc: Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 4jdc
TitleCrystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis
Components1-pyrroline-5-carboxylate dehydrogenase
KeywordsOXIDOREDUCTASE / pyrroline-5-carboxylate dehydrogenase / Aldehyde dehydrogenase / oxydoreduction
Function / homology
Function and homology information


1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / L-glutamate gamma-semialdehyde dehydrogenase / cytoplasmic side of plasma membrane / nucleotide binding / metal ion binding
Similarity search - Function
Delta-1-pyrroline-5-carboxylate dehydrogenase / 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, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal ...Delta-1-pyrroline-5-carboxylate dehydrogenase / 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, cysteine active site / Aldehyde dehydrogenases cysteine 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-glutamate gamma-semialdehyde dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLagautriere, T. / Bashiri, G. / Baker, E.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Characterization of the proline-utilization pathway in Mycobacterium tuberculosis through structural and functional studies.
Authors: Lagautriere, T. / Bashiri, G. / Paterson, N.G. / Berney, M. / Cook, G.M. / Baker, E.N.
History
DepositionFeb 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8742
Polymers61,2111
Non-polymers6631
Water7,008389
1
A: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules

A: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,7484
Polymers122,4212
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556x,x-y,-z+11
Buried area9940 Å2
ΔGint-14 kcal/mol
Surface area37560 Å2
MethodPISA
2
A: 1-pyrroline-5-carboxylate dehydrogenase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)371,24512
Polymers367,2646
Non-polymers3,9816
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_666-y+1,-x+1,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
crystal symmetry operation12_556x,x-y,-z+11
Buried area44630 Å2
ΔGint-80 kcal/mol
Surface area97850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.133, 163.133, 96.181
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-898-

HOH

21A-1006-

HOH

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Components

#1: Protein 1-pyrroline-5-carboxylate dehydrogenase /


Mass: 61210.691 Da / Num. of mol.: 1 / Mutation: G505D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: RVBD_1187 / Production host: Mycobacterium smegmatis (bacteria) / Strain (production host): Mc2 4517
References: UniProt: I6X0K4, UniProt: O50443*PLUS, EC: 1.5.1.12
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 0.1 M Bicine/Tris pH 8.1, 12% polyethylene glycol (PEG) 1000, 12% PEG 3350, 12% 2-methyl-2,4-pentandiol (MPD), 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate and 0.03 M ammonium ...Details: 0.1 M Bicine/Tris pH 8.1, 12% polyethylene glycol (PEG) 1000, 12% PEG 3350, 12% 2-methyl-2,4-pentandiol (MPD), 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate and 0.03 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953688 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953688 Å / Relative weight: 1
ReflectionResolution: 1.6→29.8 Å / Num. obs: 93414 / % possible obs: 99.8 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.6-1.69198.7
5.07-29.84199.3

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Processing

Software
NameVersionClassification
Blu-Iceicedata collection
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→29.8 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.434 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20203 4908 5 %RANDOM
Rwork0.17025 ---
obs0.17183 93414 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.008 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 27 389 4524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0194242
X-RAY DIFFRACTIONr_angle_refined_deg2.6441.9545791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6425536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72522.969192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20315622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5581536
X-RAY DIFFRACTIONr_chiral_restr0.2070.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0213298
LS refinement shellResolution: 1.602→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 334 -
Rwork0.316 6205 -
obs--97.09 %

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