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- PDB-2c5q: Crystal structure of yeast YER010Cp -

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Basic information

Entry
Database: PDB / ID: 2c5q
TitleCrystal structure of yeast YER010Cp
ComponentsRRAA-LIKE PROTEIN YER010C
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSEUDO-KNOT / RRAA
Function / homology
Function and homology information


4-hydroxy-4-methyl-2-oxoglutarate aldolase / 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity / oxaloacetate decarboxylase / 3,4-dihydroxybenzoate catabolic process / oxaloacetate decarboxylase activity / metal ion binding
Similarity search - Function
Ribonuclease E inhibitor RraA/RraA-like / Ribonuclease E inhibitor RraA/RraA-like protein / Ribonuclease E inhibitor RraA/RraA-like superfamily / Aldolase/RraA / Glucose Oxidase; domain 1 / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-hydroxy-4-methyl-2-oxoglutarate aldolase
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsLeulliot, N. / Quevillon-Cheruel, S. / Graille, M. / Schiltz, M. / Blondeau, K. / Janin, J. / van Tilbeurgh, H.
CitationJournal: Protein Sci. / Year: 2005
Title: Crystal Structure of Yeast Yer010Cp, a Knotable Member of the Rraa Protein Family.
Authors: Leulliot, N. / Quevillon-Cheruel, S. / Graille, M. / Schiltz, M. / Blondeau, K. / Janin, J. / Van Tilbeurgh, H.
History
DepositionOct 31, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RRAA-LIKE PROTEIN YER010C
B: RRAA-LIKE PROTEIN YER010C
C: RRAA-LIKE PROTEIN YER010C
D: RRAA-LIKE PROTEIN YER010C
E: RRAA-LIKE PROTEIN YER010C
F: RRAA-LIKE PROTEIN YER010C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,76619
Polymers158,9596
Non-polymers80713
Water30,0671669
1
A: RRAA-LIKE PROTEIN YER010C
B: RRAA-LIKE PROTEIN YER010C
C: RRAA-LIKE PROTEIN YER010C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7287
Polymers79,4803
Non-polymers2484
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: RRAA-LIKE PROTEIN YER010C
E: RRAA-LIKE PROTEIN YER010C
F: RRAA-LIKE PROTEIN YER010C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,03812
Polymers79,4803
Non-polymers5599
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)128.193, 255.073, 48.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.01, 0.3006, -0.9537), (-0.95058, -0.29312, -0.10236), (-0.31032, 0.90759, 0.28281)107.93973, 140.84962, 14.76893
2given(-0.99274, 0.12023, -0.00203), (0.12023, 0.99274, 0.00178), (0.00223, 0.00153, -1)127.28513, -15.53921, 26.1184
3given(-0.12245, -0.33105, 0.93563), (-0.94775, -0.24081, -0.20924), (0.29458, -0.91237, -0.28427)36.79715, 137.3335, 13.30418
4given(0.04882, 0.91108, 0.40934), (0.30049, -0.40423, 0.86389), (0.95254, 0.08083, -0.2935)-11.79119, -3.58381, -85.7367
5given(-0.00751, -0.95506, -0.29633), (0.30647, -0.28427, 0.90844), (-0.95185, -0.084, 0.29483)138.94739, -5.42174, 112.19878

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Components

#1: Protein
RRAA-LIKE PROTEIN YER010C / HYPOTHETICAL 25.6 KDA PROTEIN IN NTF2-SRP1 INTERGENIC REGION


Mass: 26493.215 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GOLD(DE3) / References: UniProt: P40011
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1669 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.25 %
Crystal growpH: 6
Details: 18% PEG 8K, 0.1M SODIUM CACODYLATE PH6, 0.1M MAGNESIUM SULPHATE, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 956280 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 5.49 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.2
Reflection shellResolution: 1.7→1.74 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SHARPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MAD / Resolution: 1.7→19.94 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.535 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.183 8721 5 %RANDOM
Rwork0.155 ---
obs0.156 165607 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--0.52 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10703 0 52 1669 12424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210956
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210100
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9814906
X-RAY DIFFRACTIONr_angle_other_deg0.855323585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27951384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00724.89454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.081151796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5631554
X-RAY DIFFRACTIONr_chiral_restr0.0980.21751
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212084
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021994
X-RAY DIFFRACTIONr_nbd_refined0.2150.22358
X-RAY DIFFRACTIONr_nbd_other0.1880.211045
X-RAY DIFFRACTIONr_nbtor_refined0.1780.25657
X-RAY DIFFRACTIONr_nbtor_other0.0840.26489
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.21342
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.266
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2341.58833
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.542211373
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.81934549
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0174.53533
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: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.225 582
Rwork0.176 11550

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