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- PDB-4ns3: Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 4ns3
TitleCrystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis bound with NAD and cobalamin
ComponentsDelta-1-pyrroline-5-carboxylate dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann Fold / dehydrogenase / 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
COBALAMIN / 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: 2.38 Å
AuthorsLagautriere, T. / Bashiri, G. / Baker, E.N.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Use of a "silver bullet" to resolve crystal lattice dislocation disorder: A cobalamin complex of Delta (1)-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis.
Authors: Lagautriere, T. / Bashiri, G. / Baker, E.N.
History
DepositionNov 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Delta-1-pyrroline-5-carboxylate dehydrogenase
B: Delta-1-pyrroline-5-carboxylate dehydrogenase
C: Delta-1-pyrroline-5-carboxylate dehydrogenase
D: Delta-1-pyrroline-5-carboxylate dehydrogenase
E: Delta-1-pyrroline-5-carboxylate dehydrogenase
F: Delta-1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,91212
Polymers367,2646
Non-polymers6,6486
Water47,3972631
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46390 Å2
ΔGint-124 kcal/mol
Surface area99160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.855, 164.855, 260.242
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISMETMETAA0 - 54020 - 560
21HISHISMETMETBB0 - 54020 - 560
12HISHISMETMETAA0 - 54020 - 560
22HISHISMETMETCC0 - 54020 - 560
13HISHISMETMETAA0 - 54020 - 560
23HISHISMETMETDD0 - 54020 - 560
14HISHISALAALAAA0 - 54120 - 561
24HISHISALAALAEE0 - 54120 - 561
15METMETALAALAAA1 - 54121 - 561
25METMETALAALAFF1 - 54121 - 561
16HISHISALAALABB0 - 54120 - 561
26HISHISALAALACC0 - 54120 - 561
17HISHISALAALABB0 - 54120 - 561
27HISHISALAALADD0 - 54120 - 561
18HISHISVALVALBB0 - 54220 - 562
28HISHISVALVALEE0 - 54220 - 562
19METMETALAALABB1 - 54121 - 561
29METMETALAALAFF1 - 54121 - 561
110HISHISASPASPCC0 - 54320 - 563
210HISHISASPASPDD0 - 54320 - 563
111HISHISVALVALCC0 - 54220 - 562
211HISHISVALVALEE0 - 54220 - 562
112METMETALAALACC1 - 54121 - 561
212METMETALAALAFF1 - 54121 - 561
113HISHISVALVALDD0 - 54220 - 562
213HISHISVALVALEE0 - 54220 - 562
114METMETALAALADD1 - 54121 - 561
214METMETALAALAFF1 - 54121 - 561
115METMETALAALAEE1 - 54121 - 561
215METMETALAALAFF1 - 54121 - 561

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.45806, 0.316925, -0.830506), (0.313509, -0.816653, -0.484552), (-0.831801, -0.482325, 0.274717)-63.78868, 11.1266, -37.41512
3given(-0.938306, -0.316321, 0.139723), (-0.315523, 0.617787, -0.720267), (0.141517, -0.719917, -0.679479)-122.70072, -5.61304, 41.45669
4given(0.216491, 0.934548, 0.282404), (-0.109316, -0.26424, 0.958242), (0.970145, -0.238322, 0.044956)-43.81471, -43.20963, 78.49236

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Components

#1: Protein
Delta-1-pyrroline-5-carboxylate dehydrogenase / Pyrroline-5-carboxylate dehydrogenase RocA


Mass: 61210.691 Da / Num. of mol.: 6 / Mutation: G505D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT1224, pruA, rocA, Rv1187 / Production host: Mycobacterium smegmatis (bacteria) / Strain (production host): Mc2 4517
References: UniProt: L7N4Z6, UniProt: O50443*PLUS, EC: 1.5.1.12
#2: Chemical
ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2631 / 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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 0.1 M Bicine/Tris pH 8.1, 12% PEG 1000, 12% PEG 3350, 12% MPD, 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulphate, 0.2% w/v biotin, 0.2% w/v phospho(enol) ...Details: 0.1 M Bicine/Tris pH 8.1, 12% PEG 1000, 12% PEG 3350, 12% MPD, 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulphate, 0.2% w/v biotin, 0.2% w/v phospho(enol)pyruvic acid monosodium salt hydrate, 0.2% w/v D-(+)-Melezitose hydrate, 0.2% w/v cobalamin and 0.02M HEPES sodium pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953691 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953691 Å / Relative weight: 1
ReflectionResolution: 2.38→20.05 Å / Num. obs: 164364 / % possible obs: 99.4 %

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOLREPphasing
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
Blu-IceIcedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→20.049 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU ML: 0.17 / σ(F): 1.34 / Phase error: 19.73 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2051 8211 5.02 %
Rwork0.1566 --
obs0.1591 163475 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.398 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.12 Å20 Å2
2---0.25 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.38→20.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24843 0 418 2631 27892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125914
X-RAY DIFFRACTIONf_angle_d1.34335456
X-RAY DIFFRACTIONf_dihedral_angle_d14.6049250
X-RAY DIFFRACTIONf_chiral_restr0.1153933
X-RAY DIFFRACTIONf_plane_restr0.0064637
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A330340.04
12B330340.04
21A327860.05
22C327860.05
31A327710.05
32D327710.05
41A324560.05
42E324560.05
51A323450.06
52F323450.06
61B327420.05
62C327420.05
71B327440.05
72D327440.05
81B324820.06
82E324820.06
91B323660.06
92F323660.06
101C327230.06
102D327230.06
111C325140.06
112E325140.06
121C325050.06
122F325050.06
131D325600.05
132E325600.05
141D324570.06
142F324570.06
151E323830.05
152F323830.05
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.40430.35932600.27984708X-RAY DIFFRACTION92
2.4043-2.43260.26322690.22065147X-RAY DIFFRACTION100
2.4326-2.46220.26633010.21665130X-RAY DIFFRACTION100
2.4622-2.49330.26962690.20685125X-RAY DIFFRACTION100
2.4933-2.5260.27462680.20215182X-RAY DIFFRACTION100
2.526-2.56060.24482430.19675131X-RAY DIFFRACTION100
2.5606-2.59710.25822640.18445134X-RAY DIFFRACTION100
2.5971-2.63580.25272840.1845146X-RAY DIFFRACTION100
2.6358-2.67690.23853000.18375150X-RAY DIFFRACTION100
2.6769-2.72060.25082810.18655122X-RAY DIFFRACTION100
2.7206-2.76740.25022760.18525131X-RAY DIFFRACTION100
2.7674-2.81760.2452850.17395155X-RAY DIFFRACTION100
2.8176-2.87170.23462490.16765206X-RAY DIFFRACTION100
2.8717-2.93010.25542480.1845170X-RAY DIFFRACTION100
2.9301-2.99360.23952270.17045244X-RAY DIFFRACTION100
2.9936-3.0630.23282570.16715168X-RAY DIFFRACTION100
3.063-3.13930.21122700.16735196X-RAY DIFFRACTION100
3.1393-3.22390.22482700.16175139X-RAY DIFFRACTION100
3.2239-3.31830.21632570.15765191X-RAY DIFFRACTION100
3.3183-3.42490.20193090.15575175X-RAY DIFFRACTION100
3.4249-3.54670.20042980.15095162X-RAY DIFFRACTION100
3.5467-3.68790.18612940.14575168X-RAY DIFFRACTION100
3.6879-3.85460.17862850.14295224X-RAY DIFFRACTION100
3.8546-4.05620.18562670.13285186X-RAY DIFFRACTION100
4.0562-4.3080.17122550.12775230X-RAY DIFFRACTION100
4.308-4.63680.15423000.11445213X-RAY DIFFRACTION100
4.6368-5.09650.14832800.11675250X-RAY DIFFRACTION100
5.0965-5.81820.16192750.13545295X-RAY DIFFRACTION100
5.8182-7.27170.18822940.14455308X-RAY DIFFRACTION100
7.2717-20.04970.14922760.13685478X-RAY DIFFRACTION100

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