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- PDB-5gzm: Cyclodeaminase_PA -

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Basic information

Entry
Database: PDB / ID: 5gzm
TitleCyclodeaminase_PA
ComponentsLysine cyclodeaminase
KeywordsLYASE / dimer / complex / 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 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 / Resolution: 1.8 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 29, 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

Downloads & links

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Assembly

Deposited unit
A: Lysine cyclodeaminase
B: Lysine cyclodeaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7976
Polymers76,2122
Non-polymers1,5854
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-65 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.779, 74.131, 95.761
Angle α, β, γ (deg.)90.00, 132.84, 90.00
Int Tables number5
Space group name H-MC121

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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: Escherichia coli (E. coli) / 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: Chemical ChemComp-YCP / (2S)-piperidine-2-carboxylic acid


Type: L-peptide linking / Mass: 129.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
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: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 63049 / % possible obs: 96.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 26.02
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.01

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementResolution: 1.8→37.79 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.644 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3188 5.1 %RANDOM
Rwork0.166 ---
obs0.168 59857 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5236 0 106 324 5666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195454
X-RAY DIFFRACTIONr_bond_other_d0.0060.025234
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.9977451
X-RAY DIFFRACTIONr_angle_other_deg1.0673.00211998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8985699
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62322.599227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97415818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2371557
X-RAY DIFFRACTIONr_chiral_restr0.1090.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021207
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_it3.0333.182807
X-RAY DIFFRACTIONr_mcbond_other3.0333.1792807
X-RAY DIFFRACTIONr_mcangle_it3.7174.7553501
X-RAY DIFFRACTIONr_mcangle_other3.7174.7553502
X-RAY DIFFRACTIONr_scbond_it3.983.5992647
X-RAY DIFFRACTIONr_scbond_other3.983.5992648
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5965.2443951
X-RAY DIFFRACTIONr_long_range_B_refined6.89626.4676135
X-RAY DIFFRACTIONr_long_range_B_other6.87426.2236036
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 135 -
Rwork0.195 2862 -
obs--62.28 %

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