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- PDB-5yu0: Structural basis for recognition of L-lysine, L-ornithine, and L-... -

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Basic information

Entry
Database: PDB / ID: 5yu0
TitleStructural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase
ComponentsLysine cyclodeaminase
KeywordsLYASE / L-lysine cyclodeaminase / Streptomyces pristinaespiralis
Function / homologyornithine cyclodeaminase / ornithine cyclodeaminase activity / Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Lysine cyclodeaminase
Function and homology information
Biological speciesStreptomyces pristinaespiralis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.92 Å
AuthorsMin, K.J. / Yoon, H.J. / Matsuura, A. / Kim, Y.H. / Lee, H.H.
CitationJournal: Mol. Cells / Year: 2018
Title: Structural Basis for Recognition of L-lysine, L-ornithine, and L-2,4-diamino Butyric Acid by Lysine Cyclodeaminase.
Authors: Min, K. / Yoon, H.J. / Matsuura, A. / Kim, Y.H. / Lee, H.H.
History
DepositionNov 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Lysine cyclodeaminase
B: Lysine cyclodeaminase
C: Lysine cyclodeaminase
D: Lysine cyclodeaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,09512
Polymers146,3494
Non-polymers2,7468
Water22,1401229
1
A: Lysine cyclodeaminase
B: Lysine cyclodeaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5486
Polymers73,1752
Non-polymers1,3734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-94 kcal/mol
Surface area22210 Å2
MethodPISA
2
C: Lysine cyclodeaminase
D: Lysine cyclodeaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5486
Polymers73,1752
Non-polymers1,3734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-92 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)270.511, 64.388, 106.403
Angle α, β, γ (deg.)90.00, 104.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-765-

HOH

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Components

#1: Protein
Lysine cyclodeaminase


Mass: 36587.363 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces pristinaespiralis (bacteria)
Gene: pipA, SPRI_0308, SPRI_7045 / Production host: Escherichia coli (E. coli) / References: UniProt: D9UBW0, ornithine cyclodeaminase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


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


Mass: 18.015 Da / Num. of mol.: 1229 / 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: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 100mM CAPSO buffer (pH 9.6), 0.2M Li2SO4, 0.9M Na-K tartrate, 2% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 136288 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 28.6
Reflection shellResolution: 1.92→1.95 Å / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 4.1 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.92→44.471 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1945 6816 5.03 %
Rwork0.1643 --
obs0.1658 135452 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→44.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10292 0 180 1229 11701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710684
X-RAY DIFFRACTIONf_angle_d0.98514596
X-RAY DIFFRACTIONf_dihedral_angle_d7.5996372
X-RAY DIFFRACTIONf_chiral_restr0.0551696
X-RAY DIFFRACTIONf_plane_restr0.0061916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.94180.27052270.22714252X-RAY DIFFRACTION99
1.9418-1.96470.24722270.20374215X-RAY DIFFRACTION99
1.9647-1.98860.23792320.20264179X-RAY DIFFRACTION99
1.9886-2.01380.2392170.1954285X-RAY DIFFRACTION99
2.0138-2.04030.22762420.19054211X-RAY DIFFRACTION99
2.0403-2.06820.22092310.18784241X-RAY DIFFRACTION99
2.0682-2.09780.22262450.17754206X-RAY DIFFRACTION99
2.0978-2.12910.21682010.17934300X-RAY DIFFRACTION100
2.1291-2.16240.20712240.17224262X-RAY DIFFRACTION100
2.1624-2.19780.21222060.1674258X-RAY DIFFRACTION99
2.1978-2.23570.19212500.16424258X-RAY DIFFRACTION100
2.2357-2.27640.20282370.16944224X-RAY DIFFRACTION99
2.2764-2.32020.20432420.16384286X-RAY DIFFRACTION100
2.3202-2.36750.21162190.16434264X-RAY DIFFRACTION100
2.3675-2.4190.19142350.16784280X-RAY DIFFRACTION100
2.419-2.47530.21442410.16494316X-RAY DIFFRACTION100
2.4753-2.53720.22672420.1694195X-RAY DIFFRACTION100
2.5372-2.60570.21712110.16584327X-RAY DIFFRACTION100
2.6057-2.68240.18672240.16364314X-RAY DIFFRACTION100
2.6824-2.7690.22372240.16214266X-RAY DIFFRACTION100
2.769-2.86790.19542230.16264294X-RAY DIFFRACTION100
2.8679-2.98270.20032240.17584315X-RAY DIFFRACTION100
2.9827-3.11840.21452390.17164296X-RAY DIFFRACTION100
3.1184-3.28280.17992270.15994320X-RAY DIFFRACTION100
3.2828-3.48840.18372150.16074333X-RAY DIFFRACTION100
3.4884-3.75760.17092200.14344357X-RAY DIFFRACTION100
3.7576-4.13550.16932460.14274301X-RAY DIFFRACTION100
4.1355-4.73340.14482350.13594351X-RAY DIFFRACTION100
4.7334-5.96130.1772180.16614418X-RAY DIFFRACTION100
5.9613-44.48290.18881920.17174512X-RAY DIFFRACTION100

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