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- PDB-2w2k: Crystal structure of the apo forms of Rhodotorula graminis D- man... -

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Basic information

Entry
Database: PDB / ID: 2w2k
TitleCrystal structure of the apo forms of Rhodotorula graminis D- mandelate dehydrogenase at 1.8A.
Components(D-MANDELATE DEHYDROGENASE) x 2
KeywordsOXIDOREDUCTASE / MANDELATE DEHYDROGENASE / 2-HYDROXYACID DEHYDROGENASE
Function / homology
Function and homology information


hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / NAD binding / cytosol
Similarity search - Function
: / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-mandelate dehydrogenase
Similarity search - Component
Biological speciesRHODOTORULA GRAMINIS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsVachieri, S.G. / Cole, A.R. / Bagneris, C. / Baker, D.P. / Fewson, C.A. / Basak, A.K.
CitationJournal: To be Published
Title: Crystal Structure of the Apo and Holo Forms of Rhodotorula Graminis D(-)-Mandelate Dehydrogenase
Authors: Vachieri, S.G. / Cole, A.R. / Bagneris, C. / Baker, D.P. / Fewson, C.A. / Basak, A.K.
History
DepositionNov 2, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-MANDELATE DEHYDROGENASE
B: D-MANDELATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)75,9812
Polymers75,9812
Non-polymers00
Water13,349741
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-22.78 kcal/mol
Surface area28620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.030, 81.071, 93.955
Angle α, β, γ (deg.)90.00, 96.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein D-MANDELATE DEHYDROGENASE


Mass: 37997.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) RHODOTORULA GRAMINIS (fungus) / Strain: KGX39 / References: UniProt: Q7LLW9
#2: Protein D-MANDELATE DEHYDROGENASE


Mass: 37983.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: C.A.FEWSON / Source: (natural) RHODOTORULA GRAMINIS (fungus) / Strain: KGX39 / References: UniProt: Q7LLW9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 741 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIMPORTANT SEQUENCE DISCREPANCIES EXIST WITH THE UNIPROT ENTRY. THE AUTHOR OF THE ENTRY HAS BEEN ...IMPORTANT SEQUENCE DISCREPANCIES EXIST WITH THE UNIPROT ENTRY. THE AUTHOR OF THE ENTRY HAS BEEN INFORMED AND IS IN THE PROCESS OF UPDATING THE ENTRY. THE ORIGINAL ENTRY IN THE DATABANK SPECIFIED STARTING FROM RESIDUE 337 UNTIL LAST RESIDUE, THE FOLLOWING SEQUENCE VRLCPNSLRPAFRAY, INSTEAD THE STRUCTURE SHOWS THE FOLLOWING SEQUENCE PAGKVFAPSS. THIS INFORMATION OBTAINED FROM THE STRUCTURE WAS COMPARED WITH THE GENE GENOMIC SEQUENCE AND PROVED THAT THE INITIAL INTRON AND EXON ASSIGNMENT WAS INCORRECT.

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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: 2.49 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 6
Details: 100 MM MES-NAOH PH 6.0, 200 MM NACL, 20% PEG-MME5K, 1% DIOXANE, 1MM DTT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→29.8 Å / Num. obs: 59834 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 0.2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 9 / % possible all: 88.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MX3

1mx3


Resolution: 1.85→25.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.279 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PRO 2 A AND PRO 2 B WERE MODELLED AS ALA DUE TO DISORDERED SIDE CHAIN DENSITY MET 1 A, MET 1 B, SER 346 B WERE NOT MODELLED DUE TO DISORDERED DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.199 3020 5 %RANDOM
Rwork0.154 ---
obs0.156 56812 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.11 Å2
2---0.07 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 0 741 6045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225344
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9597259
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.035691
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32623.6225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01915856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.331535
X-RAY DIFFRACTIONr_chiral_restr0.0930.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024049
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1840.21857
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2850.23494
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2352
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.06823628
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.62435472
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1544.52052
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.34961785
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: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 176
Rwork0.175 3659

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