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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
DescriptorOld yellow enzyme
KeywordsFLAVOPROTEIN / TIM BARREL MOTIF / DEHYDROGENASE
Specimen sourceKluyveromyces marxianus / yeast
MethodX-ray diffraction (1.8 Å resolution / Molecular replacement)
AuthorsHorita, S. / Kataoka, M. / Kitamura, N. / Nakagawa, T. / Miyakawa, T. / Ohtsuka, J. / Nagata, K. / Shimizu, S. / Tanokura, M.
CitationChembiochem, 2015, 16, 440-445

Chembiochem, 2015, 16, 440-445 Yorodumi Papers
An Engineered Old Yellow Enzyme that Enables Efficient Synthesis of (4R,6R)-Actinol in a One-Pot Reduction System
Horita, S. / Kataoka, M. / Kitamura, N. / Nakagawa, T. / Miyakawa, T. / Ohtsuka, J. / Nagata, K. / Shimizu, S. / Tanokura, M.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 31, 2014 / Release: Feb 11, 2015

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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
Polyers183,7914
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
Polyers91,8952
Non-polymers1,1574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4310
ΔGint (kcal/M)-0
Surface area (Å2)28640
MethodPISA
#2
B: Old yellow enzyme
D: Old yellow enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0526
Polyers91,8952
Non-polymers1,1574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4250
ΔGint (kcal/M)-3
Surface area (Å2)28460
MethodPISA
Unit cell
γ
α
β
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-MP 21 21 21

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Components

#1: Polypeptide(L)
Old yellow enzyme


Mass: 45947.645 Da / Num. of mol.: 4 / Source: (gene. exp.) Kluyveromyces marxianus / yeast / References: UniProt: Q6I7B7

Molecular function

#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 122.121 Da / Num. of mol.: 4 / Formula: C7H6O2
#4: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1050 / 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 / Density percent sol: 42.83
Crystal growTemp: 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 kelvins
SourceSource: SYNCHROTRON / Type: PHOTON FACTORY BEAMLINE AR-NW12A / Synchrotron site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Collection date: Dec 7, 2009
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
11.00001.0
21.01.0
ReflectionD resolution high: 1.8 Å / D resolution low: 2 Å / Number obs: 147656 / NetI over sigmaI: 23 / Redundancy: 7.3 / Percent possible obs: 99.9

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Processing

Software
NameVersionClassification
PHASERmodel building
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OYA
Correlation coeff Fo to Fc: 0.965 / Correlation coeff Fo to Fc free: 0.95 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING / Overall SU B: 4.952 / Overall SU ML: 0.082 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.125 / Overall ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 39.08 Å2 / Aniso B11: 0.01 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -0.09 Å2 / Aniso B23: - Å2 / Aniso B33: 0.08 Å2
Least-squares processR factor R free: 0.205 / R factor R work: 0.167 / R factor obs: 0.169 / Highest resolution: 1.8 Å / Lowest resolution: 19.95 Å / Number reflection R free: 7378 / Number reflection obs: 147411 / Percent reflection R free: 5 / Percent reflection obs: 99.7
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 19.95 Å
Number of atoms included #LASTProtein: 12800 / Nucleic acid: 0 / Ligand: 160 / Solvent: 1050 / Total: 14010
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02013304
X-RAY DIFFRACTIONr_bond_other_d0.0010.02012362
X-RAY DIFFRACTIONr_angle_refined_deg1.8921.97118050
X-RAY DIFFRACTIONr_angle_other_deg0.9473.00028496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4955.0001588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51824.154650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58615.0002204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.61015.00084
X-RAY DIFFRACTIONr_chiral_restr0.1240.2001852
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02115108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0203124
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
Refine LS shellHighest resolution: 1.8 Å / R factor R free: 0.261 / R factor R work: 0.22 / Lowest resolution: 1.85 Å / Number reflection R free: 524 / Number reflection R work: 10001 / Total number of bins used: 20 / Percent reflection obs: 98.59
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.1979-0.1926-0.01900.7003-0.12300.4765-0.00050.0058-0.0306-0.0042-0.01820.0202-0.06340.00860.01870.02270.00500.00250.05870.01360.013421.339019.689236.0181
20.42140.1657-0.00921.4283-0.41800.30910.0459-0.0332-0.01570.0484-0.1036-0.08910.01710.06730.05770.01210.01360.00190.09290.02300.0405-13.895756.216763.0025
30.3315-0.11250.14530.5511-0.41531.0760-0.04220.0224-0.02890.05320.07490.0982-0.0991-0.0169-0.03270.04170.02500.00530.06500.01600.02086.117555.456114.4094
40.3596-0.17000.08931.1265-0.73521.3667-0.0254-0.06950.03180.1647-0.0099-0.0350-0.0047-0.01050.03540.08310.01150.00760.06200.00970.0094-22.58420.15087.578
Refine TLS group

Beg auth seq ID: 1 / Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDEnd auth asym IDEnd auth seq IDRefine TLS ID
1AA3991
2BB3982
3CC3993
4DD3964

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