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

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Basic information

Entry
Database: PDB / ID: 4ids
TitleCrystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis
ComponentsDelta-1-pyrroline-5-carboxylate dehydrogenase
KeywordsOXIDOREDUCTASE / PruA / delta-pyrroline-5-carboxylic dehydrogenase / aldehyde dehydrogenase / pyrroline-5-carboxylate dehydrogenase / pyrroline-5-carboxylate / dehydrogenation
Function / homology
Function and homology information


L-glutamate gamma-semialdehyde dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase activity / L-proline catabolic process to L-glutamate / 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 ...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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-glutamate gamma-semialdehyde dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 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
DepositionDec 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Delta-1-pyrroline-5-carboxylate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)61,2111
Polymers61,2111
Non-polymers00
Water8,377465
1
A: Delta-1-pyrroline-5-carboxylate dehydrogenase

A: Delta-1-pyrroline-5-carboxylate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)122,4212
Polymers122,4212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556-x+y,y,-z+11
Buried area7950 Å2
ΔGint-14 kcal/mol
Surface area38200 Å2
MethodPISA
2
A: Delta-1-pyrroline-5-carboxylate dehydrogenase
x 6


Theoretical massNumber of molelcules
Total (without water)367,2646
Polymers367,2646
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_666-y+1,-x+1,-z+11
crystal symmetry operation11_556-x+y,y,-z+11
crystal symmetry operation12_566x,x-y+1,-z+11
Buried area39360 Å2
ΔGint-84 kcal/mol
Surface area99060 Å2
MethodPISA
3
A: Delta-1-pyrroline-5-carboxylate dehydrogenase

A: Delta-1-pyrroline-5-carboxylate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)122,4212
Polymers122,4212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+11
Buried area3220 Å2
ΔGint-17 kcal/mol
Surface area42920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.730, 164.730, 195.169
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-918-

HOH

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Components

#1: Protein Delta-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: Rv1187 / Production host: Mycobacterium smegmatis (bacteria) / Strain (production host): Mc2 4517
References: UniProt: I6X0K4, UniProt: O50443*PLUS, EC: 1.5.1.12
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 6.25 Å3/Da / Density % sol: 80.33 %
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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 9, 2011
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→19.95 Å / Num. all: 99327 / Num. obs: 99327 / % possible obs: 99.7 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.04-2.15198.5
6.45-19.95196.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→19.95 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.899 / SU B: 3.139 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE CONSISTS IN AN ARRANGEMENT OF ORDERED AND DISORDERED LAYERS RESULTING IN GAPS BETWEEN ORDERED MOLECULES. ALTHOUGH NO MOLECULES ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE CONSISTS IN AN ARRANGEMENT OF ORDERED AND DISORDERED LAYERS RESULTING IN GAPS BETWEEN ORDERED MOLECULES. ALTHOUGH NO MOLECULES ARE MODELLED WITHIN THIS EMPTY LAYER, MAD DATA FROM SEMET-PRUA CRYSTALS INDICATES THAT PROTEIN ELECTRON DENSITY EXISTS WITHING THESE GAPS AND SUGGESTS A MOTION OF THE ENTIRE LAYER.
RfactorNum. reflection% reflectionSelection details
Rfree0.25971 4973 5 %RANDOM
Rwork0.23695 ---
obs0.23809 94020 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.748 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0.27 Å2-0 Å2
2---0.27 Å2-0 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.04→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4141 0 0 465 4606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194254
X-RAY DIFFRACTIONr_bond_other_d0.0010.023996
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.9455802
X-RAY DIFFRACTIONr_angle_other_deg0.88739143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.615541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4122.99194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12415627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7541536
X-RAY DIFFRACTIONr_chiral_restr0.1160.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214914
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021014
LS refinement shellResolution: 2.038→2.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 339 -
Rwork0.281 6586 -
obs--96.68 %

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