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- PDB-5yu1: Structural basis for recognition of L-lysine, L-ornithine, and L-... -

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Basic information

Entry
Database: PDB / ID: 5yu1
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 / homology
Function and homology information


ornithine cyclodeaminase activity / ornithine cyclodeaminase / nucleotide binding / cytoplasm
Similarity search - Function
Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / (2S)-piperidine-2-carboxylic acid / Lysine cyclodeaminase
Similarity search - Component
Biological speciesStreptomyces pristinaespiralis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.923 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

Downloads & links

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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)149,61216
Polymers146,3494
Non-polymers3,26212
Water22,2311234
1
A: Lysine cyclodeaminase
B: Lysine cyclodeaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8068
Polymers73,1752
Non-polymers1,6316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-95 kcal/mol
Surface area22160 Å2
MethodPISA
2
C: Lysine cyclodeaminase
D: Lysine cyclodeaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8068
Polymers73,1752
Non-polymers1,6316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9190 Å2
ΔGint-94 kcal/mol
Surface area22510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)271.362, 64.537, 106.308
Angle α, β, γ (deg.)90.00, 104.17, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-778-

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


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-YCP / (2S)-piperidine-2-carboxylic acid


Type: L-peptide linking / Mass: 129.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1234 / 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: 3.08 Å3/Da / Density % sol: 60.11 %
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: 134717 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 39.6
Reflection shellResolution: 1.92→1.95 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 12 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.923→31.416 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1991 6783 5.04 %
Rwork0.1661 --
obs0.1677 134631 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.923→31.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10292 0 216 1234 11742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610720
X-RAY DIFFRACTIONf_angle_d0.97314640
X-RAY DIFFRACTIONf_dihedral_angle_d7.5266388
X-RAY DIFFRACTIONf_chiral_restr0.0541700
X-RAY DIFFRACTIONf_plane_restr0.0061920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9229-1.94480.28692000.26084017X-RAY DIFFRACTION93
1.9448-1.96770.23182240.19784222X-RAY DIFFRACTION99
1.9677-1.99160.22652450.1794179X-RAY DIFFRACTION99
1.9916-2.01690.22842360.1684231X-RAY DIFFRACTION99
2.0169-2.04340.2112110.17264282X-RAY DIFFRACTION99
2.0434-2.07140.22382280.18544223X-RAY DIFFRACTION99
2.0714-2.1010.2132190.16544218X-RAY DIFFRACTION99
2.101-2.13230.18032350.16394246X-RAY DIFFRACTION100
2.1323-2.16560.19132140.15734313X-RAY DIFFRACTION100
2.1656-2.20110.21412200.16394247X-RAY DIFFRACTION100
2.2011-2.23910.23092120.17974268X-RAY DIFFRACTION99
2.2391-2.27980.28642190.2394277X-RAY DIFFRACTION100
2.2798-2.32360.20672480.1684269X-RAY DIFFRACTION100
2.3236-2.3710.20212210.16444291X-RAY DIFFRACTION100
2.371-2.42260.21722410.16654269X-RAY DIFFRACTION100
2.4226-2.47890.19262300.16334292X-RAY DIFFRACTION100
2.4789-2.54080.20742270.16674251X-RAY DIFFRACTION100
2.5408-2.60950.19272330.1724297X-RAY DIFFRACTION100
2.6095-2.68630.21022290.16744303X-RAY DIFFRACTION100
2.6863-2.77290.20752460.16934250X-RAY DIFFRACTION100
2.7729-2.8720.22342590.16414255X-RAY DIFFRACTION100
2.872-2.98690.20572500.16984280X-RAY DIFFRACTION100
2.9869-3.12270.17612290.16374302X-RAY DIFFRACTION100
3.1227-3.28720.19792090.15894325X-RAY DIFFRACTION100
3.2872-3.49290.19382050.15624346X-RAY DIFFRACTION100
3.4929-3.76210.16722190.14714344X-RAY DIFFRACTION100
3.7621-4.140.17522400.14264288X-RAY DIFFRACTION100
4.14-4.73730.16172500.13774262X-RAY DIFFRACTION99
4.7373-5.96180.19361970.16814377X-RAY DIFFRACTION99
5.9618-31.42030.20331870.18914124X-RAY DIFFRACTION91

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