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- PDB-8j1c: Structure of amino acid dehydrogenase in complex with NADP -

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Basic information

Entry
Database: PDB / ID: 8j1c
TitleStructure of amino acid dehydrogenase in complex with NADP
ComponentsOrnithine cyclodeaminase family protein
KeywordsOXIDOREDUCTASE / dehydrogenase
Function / homologyOrnithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding domain superfamily / IMIDAZOLE / LYSINE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ornithine cyclodeaminase family protein
Function and homology information
Biological speciesPseudomonas veronii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSakuraba, H. / Ohshima, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K05658 Japan
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: First crystal structure of an NADP + -dependent l-arginine dehydrogenase belonging to the mu-crystallin family.
Authors: Kawakami, R. / Takami, N. / Hayashi, J. / Yoneda, K. / Ohmori, T. / Ohshima, T. / Sakuraba, H.
History
DepositionApr 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ornithine cyclodeaminase family protein
B: Ornithine cyclodeaminase family protein
C: Ornithine cyclodeaminase family protein
D: Ornithine cyclodeaminase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,79112
Polymers144,1444
Non-polymers2,6478
Water4,197233
1
A: Ornithine cyclodeaminase family protein
B: Ornithine cyclodeaminase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8377
Polymers72,0722
Non-polymers1,7655
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-28 kcal/mol
Surface area23260 Å2
MethodPISA
2
C: Ornithine cyclodeaminase family protein
D: Ornithine cyclodeaminase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9545
Polymers72,0722
Non-polymers8823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-22 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.965, 92.617, 162.475
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Ornithine cyclodeaminase family protein


Mass: 36036.043 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas veronii (bacteria) / Gene: HBO43_18005 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7Y0ZV07

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Non-polymers , 5 types, 241 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 8000, imidazole buffer, NaCl, NADP, lysine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2022
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→46.8 Å / Num. obs: 70419 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Χ2: 0.97 / Net I/σ(I): 16.8
Reflection shellResolution: 2.2→2.25 Å / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 1.192 / Num. measured all: 30922 / Num. unique obs: 4445 / CC1/2: 0.73 / Rpim(I) all: 0.487 / Rrim(I) all: 1.288 / Χ2: 0.98 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.8 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.56 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.275 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25957 3563 5.1 %RANDOM
Rwork0.21296 ---
obs0.21534 66780 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.631 Å2
Baniso -1Baniso -2Baniso -3
1--2.32 Å2-0 Å2-0 Å2
2--0.06 Å2-0 Å2
3---2.26 Å2
Refinement stepCycle: 1 / Resolution: 2.2→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9119 0 173 233 9525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0129488
X-RAY DIFFRACTIONr_bond_other_d0.0020.0168784
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.64312968
X-RAY DIFFRACTIONr_angle_other_deg0.4581.55820421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.11951201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.891553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.379101460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.21543
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210684
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021725
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_it3.8054.9424846
X-RAY DIFFRACTIONr_mcbond_other3.84.9424846
X-RAY DIFFRACTIONr_mcangle_it5.4717.3886033
X-RAY DIFFRACTIONr_mcangle_other5.477.3896034
X-RAY DIFFRACTIONr_scbond_it4.1475.3284642
X-RAY DIFFRACTIONr_scbond_other4.1465.3284643
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1747.8546936
X-RAY DIFFRACTIONr_long_range_B_refined8.43962.8199841
X-RAY DIFFRACTIONr_long_range_B_other8.44262.8239818
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 244 -
Rwork0.307 4865 -
obs--100 %

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