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- PDB-1nkq: Crystal structure of yeast ynq8, a fumarylacetoacetate hydrolase ... -

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Basic information

Entry
Database: PDB / ID: 1nkq
TitleCrystal structure of yeast ynq8, a fumarylacetoacetate hydrolase family protein
ComponentsHypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
KeywordsStructural Genomics / Unknown Function / dimer / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


acetylpyruvate hydrolase activity / Citric acid cycle (TCA cycle) / Hydrolases / mitochondrion / metal ion binding
Similarity search - Function
Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Uncharacterized mitochondrial hydrolase FMP41
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsEswaramoorthy, S. / Kumaran, D. / Daniels, B. / Studier, F.W. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crtystal Structure of Yeast Hypothetical Protein YNQ8_YEAST
Authors: Eswaramoorthy, S. / Kumaran, D. / Daniels, B. / Studier, F.W. / Swaminathan, S.
History
DepositionJan 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: DIMER THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 ...BIOMOLECULE: DIMER THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAINS OR 3 DIMERS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL DIMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
B: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
C: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
D: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
E: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
F: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,30231
Polymers174,6696
Non-polymers1,63425
Water11,422634
1
A: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
B: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,02413
Polymers58,2232
Non-polymers80111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-104 kcal/mol
Surface area18780 Å2
MethodPISA
2
C: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
D: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6399
Polymers58,2232
Non-polymers4167
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-65 kcal/mol
Surface area18470 Å2
MethodPISA
3
E: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
F: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6399
Polymers58,2232
Non-polymers4167
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-65 kcal/mol
Surface area18310 Å2
MethodPISA
4
A: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
B: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
hetero molecules

E: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
F: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
hetero molecules

C: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
D: Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,30231
Polymers174,6696
Non-polymers1,63425
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_545x,y-1,z1
Buried area16370 Å2
ΔGint-259 kcal/mol
Surface area52840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.705, 85.990, 316.704
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region


Mass: 29111.441 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YNL168C or N1696 / Production host: Escherichia coli (E. coli) / References: UniProt: P53889
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 634 / 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: 6

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.28 %
Description: High resolution data were collected with X25 of NSLS.
Crystal growTemperature: 293 K / Method: evaporation / pH: 4.5
Details: PEG 4000, CaCl2, Ammonium Sulfate, pH 4.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9785 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Oct 1, 2002 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 78576 / Num. obs: 78576 / % possible obs: 73.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 6.1
Reflection shellResolution: 2→2.1 Å / Redundancy: 12 % / Rmerge(I) obs: 0.484 / Num. unique all: 3257 / % possible all: 30.9

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Processing

Software
NameVersionClassification
MARMADdata collection
DENZO2000data reduction
SCALEPACK2000data scaling
SnBphasing
SHARPphasing
CNSrefinement
MARMADdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.262 2028 RANDOM
Rwork0.216 --
all-65711 -
obs-65711 -
Displacement parametersBiso mean: 18.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11365 0 41 682 12088
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4

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