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- PDB-5gzj: Cyclodeaminase_PA -

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Basic information

Entry
Database: PDB / ID: 5gzj
TitleCyclodeaminase_PA
ComponentsLysine cyclodeaminase
KeywordsLYASE / dimer / complexes / cyclization / deamination
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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Lysine cyclodeaminase
Similarity search - Component
Biological speciesStreptomyces pristinaespiralis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.87 Å
AuthorsYing, H. / Chen, K.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: To Be Published
Title: Cyclodeaminase_PA
Authors: Ying, H. / Chen, K.
History
DepositionSep 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5394
Polymers76,2122
Non-polymers1,3272
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9240 Å2
ΔGint-74 kcal/mol
Surface area24210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.604, 93.250, 118.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysine cyclodeaminase


Mass: 38106.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces pristinaespiralis (bacteria)
Gene: pipA, SPRI_0308, SPRI_7045 / Plasmid: pET-28a / Production host: Eschirchia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D9UBW0, ornithine cyclodeaminase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2%(v/v) polyethylene glycol 400, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5417 Å
DetectorType: RIGAKU SATURN 944 / Detector: IMAGE PLATE / Date: Aug 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 59165 / % possible obs: 100 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.48
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.31 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementResolution: 1.87→29.63 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.32 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19396 2987 5.1 %RANDOM
Rwork0.15285 ---
obs0.15494 56102 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.937 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.87→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5238 0 88 468 5794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195511
X-RAY DIFFRACTIONr_bond_other_d0.0010.025271
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.9927541
X-RAY DIFFRACTIONr_angle_other_deg2.004312088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3875713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04322.704233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6415829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6451558
X-RAY DIFFRACTIONr_chiral_restr0.1170.2873
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216280
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021224
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.662.3372837
X-RAY DIFFRACTIONr_mcbond_other2.6582.3362836
X-RAY DIFFRACTIONr_mcangle_it3.2493.4893555
X-RAY DIFFRACTIONr_mcangle_other3.253.4913556
X-RAY DIFFRACTIONr_scbond_it3.5132.6942674
X-RAY DIFFRACTIONr_scbond_other3.5122.6942675
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8593.9063987
X-RAY DIFFRACTIONr_long_range_B_refined7.72419.9236272
X-RAY DIFFRACTIONr_long_range_B_other7.18519.5946129
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.868→1.916 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.187 216 -
Rwork0.15 4038 -
obs--98.43 %

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