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- PDB-4tmc: CRYSTAL STRUCTURE of OLD YELLOW ENZYME from CANDIDA MACEDONIENSIS... -

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Basic information

Entry
Database: PDB / ID: 4tmc
TitleCRYSTAL STRUCTURE of OLD YELLOW ENZYME from CANDIDA MACEDONIENSIS AKU4588 COMPLEXED with P-HYDROXYBENZALDEHYDE
ComponentsOld yellow enzyme
KeywordsFLAVOPROTEIN / TIM BARREL MOTIF / DEHYDROGENASE
Function / homology
Function and homology information


NADPH dehydrogenase activity / FMN binding
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / P-HYDROXYBENZALDEHYDE / Old yellow enzyme
Similarity search - Component
Biological speciesKluyveromyces marxianus (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHorita, S. / Kataoka, M. / Kitamura, N. / Nakagawa, T. / Miyakawa, T. / Ohtsuka, J. / Nagata, K. / Shimizu, S. / Tanokura, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
the National Project on Protein Structural and Functional Analyses Japan
the Targeted Proteins Research Program Japan
the Platform for Drug Discovery, Informatics, and Structural Life Sciences Japan
Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan Japan
CitationJournal: Chembiochem / Year: 2015
Title: An Engineered Old Yellow Enzyme that Enables Efficient Synthesis of (4R,6R)-Actinol in a One-Pot Reduction System
Authors: Horita, S. / Kataoka, M. / Kitamura, N. / Nakagawa, T. / Miyakawa, T. / Ohtsuka, J. / Nagata, K. / Shimizu, S. / Tanokura, M.
History
DepositionMay 31, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
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: Old yellow enzyme
B: Old yellow enzyme
C: Old yellow enzyme
D: Old yellow enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,10412
Polymers183,7914
Non-polymers2,3148
Water18,9161050
1
A: Old yellow enzyme
C: Old yellow enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0526
Polymers91,8952
Non-polymers1,1574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-0 kcal/mol
Surface area28640 Å2
MethodPISA
2
B: Old yellow enzyme
D: Old yellow enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0526
Polymers91,8952
Non-polymers1,1574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-3 kcal/mol
Surface area28460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.394, 151.027, 199.893
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
Old yellow enzyme


Mass: 45947.645 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces marxianus (yeast) / Strain: AKU4588 / Gene: oye / Production host: Escherichia coli (E. coli) / References: UniProt: Q6I7B7
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-HBA / P-HYDROXYBENZALDEHYDE


Mass: 122.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1050 / 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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25%(V/V) PEG 3350, 100MM TRIS-HCL, 200MM AMMONIUM SULFATE, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
PH range: 8

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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 / Date: Dec 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 147656 / % possible obs: 99.9 % / Redundancy: 7.3 % / Net I/σ(I): 23

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Processing

Software
NameVersionClassification
PHASERmodel building
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OYA

1oya


Resolution: 1.8→19.95 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.952 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.205 7378 5 %RANDOM
Rwork0.167 ---
obs0.169 147411 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.09 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12800 0 160 1050 14010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0213304
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212362
X-RAY DIFFRACTIONr_angle_refined_deg1.8921.97118050
X-RAY DIFFRACTIONr_angle_other_deg0.947328496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49551588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51824.154650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.586152204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.611584
X-RAY DIFFRACTIONr_chiral_restr0.1240.21852
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02115108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023124
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 524 -
Rwork0.22 10001 -
obs--98.59 %
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)
10.1979-0.1926-0.0190.7003-0.1230.4765-0.00050.0058-0.0306-0.0042-0.01820.0202-0.06340.00860.01870.02270.0050.00250.05870.01360.013421.33919.689236.0181
20.42140.1657-0.00921.4283-0.4180.30910.0459-0.0332-0.01570.0484-0.1036-0.08910.01710.06730.05770.01210.01360.00190.09290.0230.0405-13.895756.216763.0025
30.3315-0.11250.14530.5511-0.41531.076-0.04220.0224-0.02890.05320.07490.0982-0.0991-0.0169-0.03270.04170.0250.00530.0650.0160.02086.117555.456114.4094
40.3596-0.170.08931.1265-0.73521.3667-0.0254-0.06950.03180.1647-0.0099-0.035-0.0047-0.01050.03540.08310.01150.00760.0620.00970.0094-22.58420.1587.578
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 399
2X-RAY DIFFRACTION2B1 - 398
3X-RAY DIFFRACTION3C1 - 399
4X-RAY DIFFRACTION4D1 - 396

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