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- PDB-2z1n: Crystal structure of APE0912 from Aeropyrum pernix K1 -

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Basic information

Entry
Database: PDB / ID: 2z1n
TitleCrystal structure of APE0912 from Aeropyrum pernix K1
Componentsdehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / reductase / SDR
Function / homology: / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Dehydrogenase
Function and homology information
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsIchimura, T. / Yamamura, A. / Mimoto, F. / Ohtsuka, J. / Miyazono, K. / Okai, M. / Kamo, M. / Lee, W.-C. / Nagata, K. / Tanokura, M.
CitationJournal: Proteins / Year: 2008
Title: A unique catalytic triad revealed by the crystal structure of APE0912, a short-chain dehydrogenase/reductase family protein from Aeropyrum pernix K1
Authors: Yamamura, A. / Ichimura, T. / Mimoto, F. / Ohtsuka, J. / Miyazono, K. / Okai, M. / Kamo, M. / Lee, W.-C. / Nagata, K. / Tanokura, M.
History
DepositionMay 10, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dehydrogenase
B: dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7624
Polymers55,7162
Non-polymers462
Water6,449358
1
A: dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9043
Polymers27,8581
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: dehydrogenase


Theoretical massNumber of molelcules
Total (without water)27,8581
Polymers27,8581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: dehydrogenase
B: dehydrogenase
hetero molecules

A: dehydrogenase
B: dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5258
Polymers111,4334
Non-polymers924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area13560 Å2
ΔGint-156.7 kcal/mol
Surface area29790 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-49 kcal/mol
Surface area18250 Å2
MethodPISA
5
A: dehydrogenase
hetero molecules

B: dehydrogenase


Theoretical massNumber of molelcules
Total (without water)55,7624
Polymers55,7162
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3340 Å2
ΔGint-50.8 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.759, 68.869, 69.340
Angle α, β, γ (deg.)90.00, 119.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein dehydrogenase / Short-chain dehydrogenase/reductase


Mass: 27858.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Plasmid: PET26B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YDK1
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 2.5% PEG 8000, 0.05M Tris-HCl, 0.025M MES-NaOH, 0.1M Sodium chloride, 2.5mM NADPH, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 60040 / % possible obs: 95.1 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 33.1
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.1 / % possible all: 79.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O5I

1o5i


Resolution: 1.8→31.19 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.093 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23732 2128 5.1 %RANDOM
Rwork0.18621 ---
obs0.18882 39359 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.218 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3537 0 2 358 3897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223591
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9814865
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1045476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1722.126127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78415594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6661537
X-RAY DIFFRACTIONr_chiral_restr0.1080.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022642
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21799
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22491
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1780.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.2107
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8921.52364
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49223756
X-RAY DIFFRACTIONr_scbond_it2.51531273
X-RAY DIFFRACTIONr_scangle_it3.9964.51109
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 149 -
Rwork0.253 2879 -
obs--97.33 %

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