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

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Basic information

Entry
Database: PDB / ID: 4tmb
TitleCRYSTAL STRUCTURE of OLD YELLOW ENZYME from CANDIDA MACEDONIENSIS AKU4588
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 StrPapers
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)185,6168
Polyers183,7914
Non-polymers1,8254
Water16,880937
#1
A: Old yellow enzyme
B: Old yellow enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8084
Polyers91,8952
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3670
ΔGint (kcal/M)-23
Surface area (Å2)28860
MethodPISA
#2
C: Old yellow enzyme
D: Old yellow enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8084
Polyers91,8952
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3220
ΔGint (kcal/M)-20
Surface area (Å2)28530
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)287.510, 59.620, 100.290
Angle α, β, γ (deg.)90.00, 109.89, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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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: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 937 / 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: 2.2 / Density percent sol: 44.06
Crystal growTemp: 293 K / Method: VAPOR DIFFUSION, SITTING DROP / pH: 8
Details: 25%(V/V) PEG3350, 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: Oct 14, 2009
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionD resolution high: 1.8 Å / D resolution low: 2 Å / Number obs: 148617 / NetI over sigmaI: 21.7 / Redundancy: 3.5 / Percent possible obs: 97.6

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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: 0.955 / Correlation coeff Fo to Fc free: 0.937 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING / Overall SU B: 4.713 / Overall SU ML: 0.078 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.124 / 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: 25.8 Å2 / Aniso B11: -0.03 Å2 / Aniso B12: 0 Å2 / Aniso B13: -0.03 Å2 / Aniso B22: 0.03 Å2 / Aniso B23: 0 Å2 / Aniso B33: 0.01 Å2
Least-squares processR factor R free: 0.21 / R factor R work: 0.172 / R factor obs: 0.173 / Highest resolution: 1.8 Å / Lowest resolution: 19.82 Å / Number reflection R free: 7364 / Number reflection obs: 146754 / Percent reflection R free: 5 / Percent reflection obs: 98.9
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 19.82 Å
Number of atoms included #LASTProtein: 12235 / Nucleic acid: 0 / Ligand: 124 / Solvent: 937 / Total: 13296
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02012677
X-RAY DIFFRACTIONr_bond_other_d0.0010.02011799
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.96917207
X-RAY DIFFRACTIONr_angle_other_deg0.9473.00027183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3745.0001521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44224.194620
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96215.0002094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.53915.00081
X-RAY DIFFRACTIONr_chiral_restr0.1230.2001781
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02114413
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0202956
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: 0.262 / R factor R work: 0.193 / Lowest resolution: 1.85 Å / Number reflection R free: 550 / Number reflection R work: 10074 / Total number of bins used: 20 / Percent reflection obs: 98.75
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.2907-0.1403-0.32860.23110.09410.4820-0.00940.0379-0.00590.0296-0.01940.01700.0096-0.04780.02880.0208-0.01620.01590.0806-0.02030.018763.224748.5324-19.2629
20.31060.06690.07310.1899-0.00340.40780.01150.0385-0.01100.0311-0.0252-0.03650.0539-0.03450.01370.0513-0.00770.01290.01710.00450.0175101.625730.1290-30.1640
31.38370.46130.48400.43010.14270.5563-0.03590.3422-0.0267-0.00020.12560.0026-0.06270.2029-0.08960.0197-0.02710.01430.1101-0.02100.0317138.589244.3931-36.5556
40.3801-0.30490.20500.7093-0.34530.3601-0.0078-0.0566-0.0884-0.05740.06680.0457-0.0040-0.0309-0.05900.02630.00500.00040.01580.01390.0591170.64959.121-8.356
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS ID
1A3A3921
2B3B3922
3C1C3923
4D1D3994

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