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- PDB-1jzt: Crystal structure of yeast ynu0, YNL200c -

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Basic information

Entry
Database: PDB / ID: 1jzt
TitleCrystal structure of yeast ynu0, YNL200c
ComponentsHypothetical 27.5 kDa protein in SPX19-GCR2 intergenic region
Keywordsstructural genomics / unknown function / yeast hypothetical protein / selenomethionine / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Nicotinamide salvaging / NAD(P)H-hydrate epimerase / NADHX epimerase activity / NADPHX epimerase activity / nicotinamide nucleotide metabolic process / nucleotide binding / mitochondrion / metal ion binding / cytoplasm
Similarity search - Function
YjeF N-terminal domain-containing protein NAXE-like / YjeF N-terminal domain / YjeF N-terminal domain superfamily / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NAD(P)H-hydrate epimerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.94 Å
AuthorsJiang, J.-S. / Manning, N.O. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Yeast Hypothetical Protein YNU0_YEAST
Authors: Jiang, J.-S. / Manning, N.O. / Eswaramoorthy, S. / Gerchman, S.E. / Kumaran, D. / Kycia, J.H. / Lewis, H.A. / Swaminathan, S. / Studier, F.W.
History
DepositionSep 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 26, 2014Group: Other
Revision 1.4Feb 3, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: audit_author / pdbx_unobs_or_zero_occ_atoms ...audit_author / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Hypothetical 27.5 kDa protein in SPX19-GCR2 intergenic region
B: Hypothetical 27.5 kDa protein in SPX19-GCR2 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5544
Polymers55,4832
Non-polymers712
Water5,567309
1
A: Hypothetical 27.5 kDa protein in SPX19-GCR2 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7772
Polymers27,7411
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical 27.5 kDa protein in SPX19-GCR2 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7772
Polymers27,7411
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-44 kcal/mol
Surface area20740 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.732, 68.676, 125.187
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.017708, 0.578797, 0.815279), (0.568052, -0.6652, 0.484588), (0.822802, 0.471702, -0.317008)
Vector: 19.17647, 8.37586, -28.69405)

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Components

#1: Protein Hypothetical 27.5 kDa protein in SPX19-GCR2 intergenic region


Mass: 27741.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YNL200C / Plasmid: pET 13A / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P40165
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.29 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium formate, PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9788, 0.9785, 0.9400
DetectorType: BRANDEIS - B1 / Detector: CCD / Date: May 16, 2001 / Details: toroidal mirror
RadiationMonochromator: Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.97851
30.941
ReflectionResolution: 1.9→50 Å / Num. all: 40088 / Num. obs: 39366 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 8.1 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 5.8 / % possible all: 92.3

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Processing

Software
NameClassification
ARP/wARPmodel building
SOLVEphasing
CNSrefinement
CCP4model building
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 1.94→46.26 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 165195.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: Engh & Huber
Details: LOOPS HAVE BEEN MODELLED IN AREAS OF POOR OR MISSING ELECTRON DENSITY. OCCUPANCY IS SET FOR LESS THAN 1 IN AREAS WHERE ELECTRON DENSITY IS AMBIGUOUS, AND IT IS SET EQUAL TO 0 WHERE ELECTRON ...Details: LOOPS HAVE BEEN MODELLED IN AREAS OF POOR OR MISSING ELECTRON DENSITY. OCCUPANCY IS SET FOR LESS THAN 1 IN AREAS WHERE ELECTRON DENSITY IS AMBIGUOUS, AND IT IS SET EQUAL TO 0 WHERE ELECTRON DENSITY IS NONEXISTENT. NOTE PARTICULARLY LOOPS A 119-A 123 AND B 120-B 123. THE FIRST THREE RESIDUES IN EACH CHAIN WERE NOT SEEN IN THE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1786 5.1 %RANDOM
Rwork0.2 ---
obs0.2 34978 92.9 %-
all-34978 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.6171 Å2 / ksol: 0.392074 e/Å3
Displacement parametersBiso mean: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2---1.36 Å20 Å2
3---0.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.94→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 2 309 4153
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.882.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.94→2.06 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.242 275 5.3 %
Rwork0.188 4891 -
obs-4891 83.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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