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- PDB-3kzv: The crystal structure of a cytoplasmic protein with unknown funct... -

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Basic information

Entry
Database: PDB / ID: 3kzv
TitleThe crystal structure of a cytoplasmic protein with unknown function from Saccharomyces cerevisiae
ComponentsUncharacterized oxidoreductase YIR035C
KeywordsOXIDOREDUCTASE / cytoplasmic protein / unknown function / structural genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / Oxidoreductases / cytoplasm
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized oxidoreductase YIR035C
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZhang, R. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a cytoplasmic protein with unknown function from Saccharomyces cerevisiae
Authors: Zhang, R. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionDec 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Uncharacterized oxidoreductase YIR035C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7854
Polymers27,5081
Non-polymers2763
Water2,342130
1
A: Uncharacterized oxidoreductase YIR035C
hetero molecules

A: Uncharacterized oxidoreductase YIR035C
hetero molecules

A: Uncharacterized oxidoreductase YIR035C
hetero molecules

A: Uncharacterized oxidoreductase YIR035C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,13916
Polymers110,0344
Non-polymers1,10512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area13100 Å2
ΔGint-78 kcal/mol
Surface area35940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.413, 117.413, 89.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

DetailsThis protein exists as tetramer. The other parts of the biological assembly is generated by the operations: -y+1/2,-x+1/2,-z+1/2 y+1/2,x-1/2,-z+1/2 x+1,-y,z

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Components

#1: Protein Uncharacterized oxidoreductase YIR035C


Mass: 27508.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: GI:6322226, YIR035C / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P40579, Oxidoreductases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M Bis-tris, 5% Iso-propanol, 2.4M NH4SO4,1/1600 chymotrypsin, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 7, 2008 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→83.05 Å / Num. all: 20314 / Num. obs: 20048 / % possible obs: 98.69 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Redundancy: 16.3 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 1.5
Reflection shellResolution: 2→2.052 Å / Redundancy: 16.3 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 36.9 / Num. unique all: 1558 / % possible all: 93.58

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→83.05 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.978 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.16
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24461 1080 5.1 %RANDOM
Rwork0.19133 ---
obs0.19409 20048 98.69 %-
all-20314 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.676 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2→83.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 18 130 2033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221932
X-RAY DIFFRACTIONr_angle_refined_deg2.2841.9682611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8395247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.45425.51378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51215328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.96156
X-RAY DIFFRACTIONr_chiral_restr0.1590.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211422
X-RAY DIFFRACTIONr_mcbond_it1.3681.51232
X-RAY DIFFRACTIONr_mcangle_it2.42321980
X-RAY DIFFRACTIONr_scbond_it3.8913700
X-RAY DIFFRACTIONr_scangle_it6.1734.5631
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 86 -
Rwork0.224 1372 -
obs--93.58 %
Refinement TLS params.Method: refined / Origin x: 42.648 Å / Origin y: 5.353 Å / Origin z: 7.607 Å
111213212223313233
T0.0453 Å20.0187 Å2-0.0216 Å2-0.0742 Å20.0028 Å2--0.0131 Å2
L0.4434 °20.1571 °20.0481 °2-0.617 °2-0.028 °2--0.4682 °2
S-0.0055 Å °0.0163 Å °-0.0028 Å °-0.0735 Å °0.0012 Å °0.04 Å °-0.043 Å °-0.0866 Å °0.0044 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 50
2X-RAY DIFFRACTION1A51 - 100
3X-RAY DIFFRACTION1A101 - 150
4X-RAY DIFFRACTION1A151 - 200
5X-RAY DIFFRACTION1A201 - 254

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