Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Ensemble refinement of protein crystal structures: validation and application.
Journal, issue, pages	Structure, Vol. 15, Page 1040-1052, Year 2007
Publish date	May 30, 2007 (structure data deposition date)
Authors	Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N.
External links	Structure / PubMed:17850744
Methods	X-ray diffraction
Resolution	1.15 - 3.3 Å
Structure data	PDB-2q3m: Ensemble refinement of the protein crystal structure of an Arabidopsis thaliana putative steroid sulphotransferase Method: X-RAY DIFFRACTION / Resolution: 1.9 Å PDB-2q3o: Ensemble refinement of the protein crystal structure of 12-oxo-phytodienoate reductase isoform 3 Method: X-RAY DIFFRACTION / Resolution: 2 Å PDB-2q3p: Ensemble refinement of the protein crystal structure of At3g17210 from Arabidopsis thaliana Method: X-RAY DIFFRACTION / Resolution: 1.9 Å PDB-2q3q: Ensemble refinement of the protein crystal structure of At1g24000 from Arabidopsis thaliana Method: X-RAY DIFFRACTION / Resolution: 2.1 Å PDB-2q3r: Ensemble refinement of the protein crystal structure of At1g76680 from Arabidopsis thaliana Method: X-RAY DIFFRACTION / Resolution: 2 Å PDB-2q3s: Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g06450 Method: X-RAY DIFFRACTION / Resolution: 2.1 Å PDB-2q3t: Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g22680 Method: X-RAY DIFFRACTION / Resolution: 1.6 Å PDB-2q3u: Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase Method: X-RAY DIFFRACTION / Resolution: 1.53 Å PDB-2q3v: Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At2g34160 Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-2q3w: Ensemble refinement of the protein crystal structure of the cys84ala cys85ala double mutant of the [2Fe-2S] ferredoxin subunit of toluene-4-monooxygenase from Pseudomonas mendocina KR1 Method: X-RAY DIFFRACTION / Resolution: 1.48 Å PDB-2q40: Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At2g17340 Method: X-RAY DIFFRACTION / Resolution: 1.7 Å PDB-2q41: Ensemble refinement of the protein crystal structure of spermidine synthase from Arabidopsis thaliana gene At1g23820 Method: X-RAY DIFFRACTION / Resolution: 2.7 Å PDB-2q42: Ensemble refinement of the protein crystal structure of glyoxalase II from Arabidopsis thaliana gene At2g31350 Method: X-RAY DIFFRACTION / Resolution: 1.742 Å PDB-2q43: Ensemble refinement of the protein crystal structure of IAA-aminoacid hydrolase from Arabidopsis thaliana gene At5g56660 Method: X-RAY DIFFRACTION / Resolution: 2 Å PDB-2q44: Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At1g77540 Method: X-RAY DIFFRACTION / Resolution: 1.15 Å PDB-2q45: Ensemble refinement of the protein crystal structure of putative tropinone reductase from Arabidopsis thaliana gene At1g07440 Method: X-RAY DIFFRACTION / Resolution: 2.1 Å PDB-2q46: Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g02240 Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-2q47: Ensemble refinement of the protein crystal structure of a putative phosphoprotein phosphatase from Arabidopsis thaliana gene At1g05000 Method: X-RAY DIFFRACTION / Resolution: 3.3 Å PDB-2q48: Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g48480 Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-2q49: Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At2g19940 Method: X-RAY DIFFRACTION / Resolution: 2.19 Å PDB-2q4a: Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g21360 Method: X-RAY DIFFRACTION / Resolution: 2.39 Å PDB-2q4b: Ensemble refinement of the protein crystal structure of selenomethionyl gene product from Arabidopsis thaliana At5g02240 in space group P21212 Method: X-RAY DIFFRACTION / Resolution: 2.096 Å PDB-2q4c: Ensemble refinement of the protein crystal structure of annexin from Arabidopsis thaliana gene At1g35720 Method: X-RAY DIFFRACTION / Resolution: 2.508 Å PDB-2q4d: Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950 Method: X-RAY DIFFRACTION / Resolution: 2.152 Å PDB-2q4e: Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At4g09670 Method: X-RAY DIFFRACTION / Resolution: 2.49 Å PDB-2q4f: Ensemble refinement of the crystal structure of putative histidine-containing phosphotransfer protein from rice, Ak104879 Method: X-RAY DIFFRACTION / Resolution: 2 Å PDB-2q4h: Ensemble refinement of the crystal structure of GALT-like protein from Arabidopsis thaliana At5g18200 Method: X-RAY DIFFRACTION / Resolution: 1.834 Å PDB-2q4i: Ensemble refinement of the protein crystal structure of allene oxide cyclase from Arabidopsis thaliana At3g25770 Method: X-RAY DIFFRACTION / Resolution: 1.71 Å PDB-2q4j: Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g03250, a putative UDP-glucose pyrophosphorylase Method: X-RAY DIFFRACTION / Resolution: 1.863 Å PDB-2q4k: Ensemble refinement of the protein crystal structure of gene product from Homo sapiens Hs.433573 Method: X-RAY DIFFRACTION / Resolution: 2.5 Å PDB-2q4l: Ensemble refinement of the crystal structure of GALT-like protein from Arabidopsis thaliana At5g18200 Method: X-RAY DIFFRACTION / Resolution: 2.3 Å PDB-2q4m: Ensemble refinement of the crystal structure of protein from Arabidopsis thaliana At5g01750 Method: X-RAY DIFFRACTION / Resolution: 1.7 Å PDB-2q4n: Ensemble refinement of the crystal structure of protein from Arabidopsis thaliana At1g79260 Method: X-RAY DIFFRACTION / Resolution: 1.32 Å PDB-2q4o: Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At2g37210 Method: X-RAY DIFFRACTION / Resolution: 1.95 Å PDB-2q4p: Ensemble refinement of the crystal structure of protein from Mus musculus Mm.29898 Method: X-RAY DIFFRACTION / Resolution: 2.32 Å PDB-2q4q: Ensemble refinement of the protein crystal structure of gene product from Homo sapiens Hs.95870 Method: X-RAY DIFFRACTION / Resolution: 2.59 Å PDB-2q4r: Ensemble refinement of the protein crystal structure of human phosphomannomutase 2 (PMM2) Method: X-RAY DIFFRACTION / Resolution: 2.09 Å PDB-2q4s: Ensemble refinement of the protein crystal structure of cysteine dioxygenase type I from Mus musculus Mm.241056 Method: X-RAY DIFFRACTION / Resolution: 1.75 Å PDB-2q4t: Ensemble refinement of the protein crystal structure of a cytosolic 5'-nucleotidase III from Mus musculus Mm.158936 Method: X-RAY DIFFRACTION / Resolution: 2.35 Å PDB-2q4u: Ensemble refinement of the crystal structure of an EF-hand protein from Danio rerio Dr.36843 Method: X-RAY DIFFRACTION / Resolution: 2.1 Å PDB-2q4v: Ensemble refinement of the protein crystal structure of thialysine n-acetyltransferase (SSAT2) from Homo sapiens Method: X-RAY DIFFRACTION / Resolution: 1.842 Å PDB-2q4x: Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g16990 Method: X-RAY DIFFRACTION / Resolution: 2.1 Å PDB-2q4y: Ensemble refinement of the protein crystal structure of At1g77540-coenzyme A complex Method: X-RAY DIFFRACTION / Resolution: 2.06 Å PDB-2q4z: Ensemble refinement of the protein crystal structure of an aspartoacylase from Rattus norvegicus Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-2q50: Ensemble refinement of the protein crystal structure of a glyoxylate/hydroxypyruvate reductase from Homo sapiens Method: X-RAY DIFFRACTION / Resolution: 2.45 Å PDB-2q51: Ensemble refinement of the protein crystal structure of an aspartoacylase from Homo sapiens Method: X-RAY DIFFRACTION / Resolution: 2.8 Å PDB-2q52: Ensemble refinement of the crystal structure of a glycolipid transfer-like protein from Galdieria sulphuraria Method: X-RAY DIFFRACTION / Resolution: 1.38 Å
Chemicals	ChemComp-MLA: MALONIC ACID / Malonic acid ChemComp-HOH: WATER / Water ChemComp-FMN: FLAVIN MONONUCLEOTIDE / Flavin mononucleotide ChemComp-MG: Unknown entry ChemComp-SO4: SULFATE ION / Sulfate ChemComp-CPS: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / detergentYM / CHAPS detergent ChemComp-EDO: 1,2-ETHANEDIOL / Ethylene glycol ChemComp-MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID / pH bufferYM / MOPS ChemComp-K: Unknown entry ChemComp-NO3: NITRATE ION / Nitrate ChemComp-FES: FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster ChemComp-ZN: Unknown entry ChemComp-FE: Unknown entry / Iron ChemComp-ACY: ACETIC ACID / Acetic acid ChemComp-PEG: DI(HYDROXYETHYL)ETHER / Diethylene glycol ChemComp-BR: BROMIDE ION / Bromide ChemComp-NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate ChemComp-AMP: ADENOSINE MONOPHOSPHATE / AMPYM / Adenosine monophosphate ChemComp-GLY: GLYCINE / Glycine ChemComp-NI: NICKEL (II) ION / Nickel ChemComp-EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH bufferYM / HEPES ChemComp-ACO: ACETYL COENZYME A / Acetyl-CoA ChemComp-HMH: 4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE / 4-Amino-5-hydroxymethyl-2-methylpyrimidine ChemComp-COA: COENZYME A / Coenzyme A ChemComp-PO4*: PHOSPHATE ION / Phosphate
Source	arabidopsis thaliana (thale cress) pseudomonas mendocina (bacteria) oryza sativa (Asian cultivated rice) homo sapiens (human) mus musculus (house mouse) danio rerio (zebrafish) rattus norvegicus (Norway rat) galdieria sulphuraria (eukaryote)
Keywords	TRANSFERASE / Ensemble Refinement / Refinement Methodology Development / Steroid Sulphotransferase / Apo / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG / OXIDOREDUCTASE / Flavoprotein / flavoenzyme / xenobiotic reductase / old yellow enzyme / secondary messenger / UNKNOWN FUNCTION / PLANT PROTEIN / Protein / homohexamer / At5g06450 / HYDROLASE / At5g08170 / POLYAMINE BIOSYNTHESIS / AGMATINE IMINOHYDROLASE / AIH / AGMATINE DEIMINASE / N-CARBAMOYLPUTRESCINE / PUTRESCINE / At2g34160 / Nitrate / ELECTRON TRANSPORT / FERREDOXIN / FES / [2FE-2S] CLUSTER / RIESKE PROTEIN / TOLUENE-4-MONOOXYGENASE SUBUNIT / AT2G17340 / AT1G23820 / PUTRESCINE AMINOPROPYL TRANSFERASE / SPERMIDINE SYNTHASE / SPDS1 / POLYAMINE / AT2G31350 / METALLO-HYDROLASE / ZINC/IRON BINUCLEAR CENTER / B-LACTAMASE FOLD / THIOESTER HYDROLASE / mitochondrial isozyme / AT5G56660 / ILL2 / indole-3-acetic acid / auxin / AT1G77540 / PUTATIVE ACETYLTRANSFERASE / AT1G07440 / REDUCTIVELY METHYLATED PROTEIN / PUTATIVE TROPINONE REDUCTASE / AT5G02240 / NADP / AT1G05000 / phosphoprotein phosphatase / AT5G48480 / CATH 3.10.180 FOLD / DIMER / AT2G19940 / CATH 3.40.50 FOLD / SEMIALDEHYDE DEHYDROGENASE FAMILY / TETRAMER / AT3G21360 / METAL BINDING PROTEIN / AT1G35720 / ANNEXIN / MEMBRANE-BINDING / CALCIUM-BINDING / AT5G11950 / LYSINE DECARBOXYLASE-LIKE PROTEIN / AT4G09670 / SIGNALING PROTEIN / AK104879 / PHOSPHORELAY MEDIATOR / HP1 / GALT / AMP / ISOMERASE / AT3G25770 / jasmonic acid biosynthesis / AT3G03250 / PUTATIVE UDP-GLUCOSE PYROPHOSPHORYLASE / Hs.433573 / P5326 / BLES03 / BC010512 / AT5G18200 / AT5G01750 / PFAM PF01167 / TULP / AT1G79260 / AT2G37210 / MM.29898 / BC004623 / 2410015N17RIK / HS.95870 / DUF498 / HS.459855 / HS.313504 / BC008310 / PHOSPHATASE / PFAM PF03332 / HAD SUPERFAMILY / JAECKEN DISEASE / CARBOHYDRATE-DEFICIENT GLYCOPROTEIN SYNDROME / Mm.241056 / pfam05995.2 CDO_I / BC013638 / CUPIN FAMILY / UMPH-1 / CYTOSOLIC 5'-NUCLEOTIDASE III / NT5C3 PROTEIN / AAH38029 / BC038029 / MM.158936 / Dr.36843 / BC083168 / CALICIUM BINDING / EF-HAND SUPERFAMILY / SSAT2 / BC011751 / AAH11751 / THIALYSINE N-ACETYLTRANSFERASE / TENA_THI-4 DOMAIN / TENA/THI-4/PQQC FAMILY / AT3G16990 / CoA / Coenzyme-A / COG2388 Family / acetyltransferase / Aspartoacylase family / Aminoacylase-2 / ACY-2 / ACY2_RAT / Q9UBQ7 / Glyoxylate reductase / hydroxypyruvate reductase / Canavan disease / N-acetyl-L-aspartate / Zinc-dependent hydrolase / ACY2 / ASPA / GLTP superfamily / GLTP-like