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- PDB-5yu3: Structural basis for recognition of L-lysine, L-ornithine, and L-... -

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Basic information

Entry
Database: PDB / ID: 5yu3
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 / PROLINE / Lysine cyclodeaminase
Similarity search - Component
Biological speciesStreptomyces pristinaespiralis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.79 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)149,55616
Polymers146,3494
Non-polymers3,20612
Water24,9511385
1
A: Lysine cyclodeaminase
B: Lysine cyclodeaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7788
Polymers73,1752
Non-polymers1,6036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-94 kcal/mol
Surface area22330 Å2
MethodPISA
2
C: Lysine cyclodeaminase
D: Lysine cyclodeaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7788
Polymers73,1752
Non-polymers1,6036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9160 Å2
ΔGint-94 kcal/mol
Surface area22490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)271.529, 64.783, 106.858
Angle α, β, γ (deg.)90.00, 104.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-679-

HOH

21B-794-

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-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1385 / 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: 3.11 Å3/Da / Density % sol: 60.49 %
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: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 169178 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 42.2
Reflection shellResolution: 1.79→1.82 Å / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 4.7 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.79→37.251 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 19.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 8337 4.93 %
Rwork0.1658 --
obs0.1672 169118 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→37.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10292 0 212 1385 11889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610716
X-RAY DIFFRACTIONf_angle_d1.13714636
X-RAY DIFFRACTIONf_dihedral_angle_d7.5846392
X-RAY DIFFRACTIONf_chiral_restr0.0661700
X-RAY DIFFRACTIONf_plane_restr0.0061920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.81040.27472470.23594794X-RAY DIFFRACTION89
1.8104-1.83170.25862660.225305X-RAY DIFFRACTION100
1.8317-1.8540.24892460.20595367X-RAY DIFFRACTION100
1.854-1.87750.2362840.20195340X-RAY DIFFRACTION100
1.8775-1.90220.2552800.20065361X-RAY DIFFRACTION100
1.9022-1.92820.242710.19575330X-RAY DIFFRACTION100
1.9282-1.95580.23022630.18345383X-RAY DIFFRACTION100
1.9558-1.9850.232700.17925345X-RAY DIFFRACTION100
1.985-2.0160.20812860.17585385X-RAY DIFFRACTION100
2.016-2.0490.21652630.17955372X-RAY DIFFRACTION100
2.049-2.08440.21952860.18545328X-RAY DIFFRACTION100
2.0844-2.12230.21722700.17945322X-RAY DIFFRACTION100
2.1223-2.16310.21212940.17465356X-RAY DIFFRACTION100
2.1631-2.20720.21992780.16795346X-RAY DIFFRACTION100
2.2072-2.25520.21162840.17065355X-RAY DIFFRACTION100
2.2552-2.30770.21352730.1655384X-RAY DIFFRACTION100
2.3077-2.36540.20062720.16475366X-RAY DIFFRACTION100
2.3654-2.42930.21972750.17065389X-RAY DIFFRACTION100
2.4293-2.50080.18512910.16645354X-RAY DIFFRACTION100
2.5008-2.58150.21282840.17165360X-RAY DIFFRACTION100
2.5815-2.67370.20922880.16995393X-RAY DIFFRACTION100
2.6737-2.78070.19362640.17115363X-RAY DIFFRACTION100
2.7807-2.90720.20032840.17135414X-RAY DIFFRACTION100
2.9072-3.06040.16772740.16865388X-RAY DIFFRACTION100
3.0604-3.25210.20192890.16125397X-RAY DIFFRACTION100
3.2521-3.5030.16972870.16235387X-RAY DIFFRACTION100
3.503-3.85520.15943080.14115398X-RAY DIFFRACTION100
3.8552-4.41230.15142780.13655447X-RAY DIFFRACTION100
4.4123-5.55610.15732760.14365478X-RAY DIFFRACTION100
5.5561-37.25940.19253060.17095574X-RAY DIFFRACTION100

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