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- PDB-6t3e: Structure of Thermococcus litoralis Delta(1)-pyrroline-2-carboxyl... -

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Basic information

Entry
Database: PDB / ID: 6t3e
TitleStructure of Thermococcus litoralis Delta(1)-pyrroline-2-carboxylate reductase in complex with NADH and L-proline
ComponentsDELTA1-pyrroline-2-carboxylate reductase
KeywordsOXIDOREDUCTASE / Reductase / L-Hydroxyproline metabolism / Delta(1)-pyrroline-2-carboxylate / Thermococcus litoralis
Function / homology
Function and homology information


nucleotide binding / cytoplasm
Similarity search - Function
ornithine cyclodeaminase, domain 1 / ornithine cyclodeaminase, domain 1 / Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / PROLINE / Ornithine cyclodeaminase family protein
Similarity search - Component
Biological speciesThermococcus litoralis DSM 5473 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFerraris, D.M. / Miggiano, R. / Ferrario, E. / Rizzi, M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Structure of Thermococcus litoralis Delta1-pyrroline-2-carboxylate reductase in complex with NADH and L-proline.
Authors: Ferrario, E. / Miggiano, R. / Rizzi, M. / Ferraris, D.M.
History
DepositionOct 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: 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

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Assembly

Deposited unit
A: DELTA1-pyrroline-2-carboxylate reductase
B: DELTA1-pyrroline-2-carboxylate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1056
Polymers76,5442
Non-polymers1,5614
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-42 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.688, 51.509, 92.290
Angle α, β, γ (deg.)90.000, 115.906, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A'A5 - 326
221(chain 'B' and resid 5 through 327)B5 - 326
132chain 'C'C1
242chain 'D'D1
153chain 'E'E1
263chain 'F'F1

NCS ensembles :
ID
1
2
3

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Components

#1: Protein DELTA1-pyrroline-2-carboxylate reductase


Mass: 38272.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus litoralis DSM 5473 (archaea)
Production host: Escherichia coli (E. coli)
References: UniProt: H3ZMH3*PLUS, 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH)
#2: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.8
Details: 0.2 M Potassium nitrate pH=6.8, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.6→43.8 Å / Num. all: 93981 / Num. obs: 20334 / % possible obs: 94.3 % / Redundancy: 4.6 % / Biso Wilson estimate: 45.13 Å2 / CC1/2: 0.93 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.12 / Net I/σ(I): 11.05
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.64 / Num. unique all: 9154 / Num. unique obs: 2015 / CC1/2: 0.6 / Rpim(I) all: 0.44 / % possible all: 95.8

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Processing

Software
NameVersionClassification
EDNAdata collection
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OMO

1omo


Resolution: 2.6→43.77 Å / SU ML: 0.3294 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.1516
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1012 5.01 %RANDOM
Rwork0.1888 ---
obs0.1913 20298 94.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.87 Å2
Refinement stepCycle: LAST / Resolution: 2.6→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4963 0 104 19 5086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715137
X-RAY DIFFRACTIONf_angle_d0.90936941
X-RAY DIFFRACTIONf_chiral_restr0.0517825
X-RAY DIFFRACTIONf_plane_restr0.0063863
X-RAY DIFFRACTIONf_dihedral_angle_d6.95953139
LS refinement shellResolution: 2.6→2.733 Å
RfactorNum. reflection% reflection
Rfree0.3009 83 -
Rwork0.2404 3001 -
obs-1961 91.8 %
Refinement TLS params.Method: refined / Origin x: 21.9355010513 Å / Origin y: -1.31258423856 Å / Origin z: -2.04954543162 Å
111213212223313233
T0.24992036251 Å20.0025618615467 Å2-0.0231519431032 Å2-0.218310793384 Å20.0491192291422 Å2--0.319692434737 Å2
L0.894915502292 °2-0.0280215440962 °2-0.197561585188 °2-0.466575284649 °20.454250424684 °2--1.76375111287 °2
S0.00412658447346 Å °0.138312846889 Å °0.0299800380084 Å °-0.0353373236859 Å °-0.0196600598916 Å °0.0932005059133 Å °-0.0578510528574 Å °0.00229783608832 Å °0.0189794371383 Å °
Refinement TLS groupSelection details: all

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