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- PDB-8j1g: Structure of amino acid dehydrogenase in complex with NADPH -

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Basic information

Entry
Database: PDB / ID: 8j1g
TitleStructure of amino acid dehydrogenase in complex with NADPH
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 / nucleotide binding / cytoplasm / ARGININE / Chem-NDP / Ornithine cyclodeaminase family protein
Function and homology information
Biological speciesPseudomonas veronii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)147,95114
Polymers144,1444
Non-polymers3,80710
Water81145
1
A: Ornithine cyclodeaminase family protein
B: Ornithine cyclodeaminase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0378
Polymers72,0722
Non-polymers1,9656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-25 kcal/mol
Surface area23320 Å2
MethodPISA
2
C: Ornithine cyclodeaminase family protein
D: Ornithine cyclodeaminase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9136
Polymers72,0722
Non-polymers1,8414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-33 kcal/mol
Surface area22930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.473, 70.306, 100.137
Angle α, β, γ (deg.)88.65, 72.53, 86.53
Int Tables number1
Space group name H-MP1

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Components

#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
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEG 4000, Na acetate buffer, glycerol, NADPH, arginine

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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 PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2022
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→47.8 Å / Num. obs: 56308 / % possible obs: 98.7 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.068 / Χ2: 0.99 / Net I/σ(I): 18.9
Reflection shellResolution: 2.5→2.57 Å / % possible obs: 98.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 1.2 / Num. measured all: 31137 / Num. unique obs: 4614 / CC1/2: 0.657 / Rpim(I) all: 0.495 / Rrim(I) all: 1.3 / Χ2: 0.96 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.8 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 38.301 / SU ML: 0.349 / Cross valid method: THROUGHOUT / ESU R: 0.452 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27393 2773 4.9 %RANDOM
Rwork0.2252 ---
obs0.22761 53526 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.876 Å2
Baniso -1Baniso -2Baniso -3
1-8.43 Å2-1.17 Å22.39 Å2
2---3.93 Å22.05 Å2
3----2.64 Å2
Refinement stepCycle: 1 / Resolution: 2.5→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9200 0 248 45 9493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0129651
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169224
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.64813204
X-RAY DIFFRACTIONr_angle_other_deg0.4671.56821179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.13251211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.046580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.993101484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.21558
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211274
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022094
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_it3.0862.7274880
X-RAY DIFFRACTIONr_mcbond_other3.0862.7284880
X-RAY DIFFRACTIONr_mcangle_it4.8344.8876079
X-RAY DIFFRACTIONr_mcangle_other4.8354.8876080
X-RAY DIFFRACTIONr_scbond_it3.1183.0214771
X-RAY DIFFRACTIONr_scbond_other3.1183.024770
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0415.4227122
X-RAY DIFFRACTIONr_long_range_B_refined11.08227.8510633
X-RAY DIFFRACTIONr_long_range_B_other11.08127.8210628
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 202 -
Rwork0.341 3957 -
obs--98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.811-0.3573-0.05112.6955-0.24840.5350.1290.255-0.05410.0121-0.1918-0.20530.20610.19310.06290.12540.18270.11330.7902-0.04940.8999-0.9207-0.4037-0.6334
21.8801-0.6169-0.01251.8830.71761.58820.09010.32740.0409-0.0901-0.1290.1517-0.1879-0.18030.03890.06090.1620.09880.75130.00760.9004-34.195622.6006-0.7464
30.5592-0.5983-0.03561.79180.63312.1255-0.36690.2051-0.1770.6980.1817-0.08310.57430.23620.18510.67710.19260.18860.3804-0.06270.6291-5.666627.8596-47.2509
41.193-1.18060.44731.5598-0.66533.0989-0.3302-0.09810.06540.81160.1873-0.0965-0.7387-0.25520.14290.8020.230.06820.2613-0.03980.4589-22.071963.7657-46.7582
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 1101
2X-RAY DIFFRACTION2B4 - 1101
3X-RAY DIFFRACTION3C4 - 1002
4X-RAY DIFFRACTION4D4 - 1002

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