HEADER LIGASE 20-NOV-12 3W1S TITLE CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE ATG12-ATG5 CONJUGATE TITLE 2 BOUND TO THE N-TERMINAL DOMAIN OF ATG16 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AUTOPHAGY PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-284; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: AUTOPHAGY PROTEIN 16; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 1-46; COMPND 10 SYNONYM: CYTOPLASM TO VACUOLE TARGETING PROTEIN 11, SAP18 HOMOLOG; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: UBIQUITIN-LIKE PROTEIN ATG12; COMPND 14 CHAIN: C; COMPND 15 FRAGMENT: UNP RESIDUES 100-186; COMPND 16 SYNONYM: AUTOPHAGY-RELATED PROTEIN 12; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: APG5, ATG5, ATG5(AMINO ACIDS 1-284), P2601, YPL149W; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PACYC184; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 14 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 15 ORGANISM_TAXID: 559292; SOURCE 16 STRAIN: ATCC 204508 / S288C; SOURCE 17 GENE: APG15, APG16, ATG16, ATG16(AMINO ACIDS 1-46), CVT11, SAP18, SOURCE 18 YM8520.08C, YMR159C; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 21 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 22 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 23 EXPRESSION_SYSTEM_PLASMID: PGEX6P; SOURCE 24 MOL_ID: 3; SOURCE 25 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 26 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 27 ORGANISM_TAXID: 559292; SOURCE 28 STRAIN: ATCC 204508 / S288C; SOURCE 29 GENE: APG12, ATG12, ATG12(AMINO ACIDS 100-186), YBR1506, YBR217W; SOURCE 30 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 31 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 32 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 33 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 34 EXPRESSION_SYSTEM_PLASMID: PACYC184 KEYWDS UBIQUITIN FOLD, E3-LIKE, ATG3 BINDING, ISOPEPTIDE BOND BETWEEN ATG12 KEYWDS 2 GLY186 AND ATG5 LYS149, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR N.N.NODA,Y.FUJIOKA,T.HANADA,Y.OHSUMI,F.INAGAKI REVDAT 3 08-NOV-23 3W1S 1 SEQADV REVDAT 2 26-JUN-13 3W1S 1 JRNL REVDAT 1 26-DEC-12 3W1S 0 JRNL AUTH N.N.NODA,Y.FUJIOKA,T.HANADA,Y.OHSUMI,F.INAGAKI JRNL TITL STRUCTURE OF THE ATG12-ATG5 CONJUGATE REVEALS A PLATFORM FOR JRNL TITL 2 STIMULATING ATG8-PE CONJUGATION JRNL REF EMBO REP. V. 14 206 2013 JRNL REFN ISSN 1469-221X JRNL PMID 23238393 JRNL DOI 10.1038/EMBOR.2012.208 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 167335.040 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 16822 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1679 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2345 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 247 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2868 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 27 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.38000 REMARK 3 B22 (A**2) : -5.38000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.36 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.41 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.830 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.500 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.560 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.940 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.870 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 48.36 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3W1S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000095777. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17173 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 42.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05500 REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.30300 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 2DYM, 1WZ3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG10000, 0.5M POTASSIUM REMARK 280 THIOCYANATE, 0.1M ADA, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.53550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.53550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 36.07450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.04200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.07450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.04200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 71.53550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.07450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 53.04200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 71.53550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.07450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 53.04200 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLY A 96 REMARK 465 LYS A 97 REMARK 465 SER A 98 REMARK 465 ALA A 99 REMARK 465 THR A 100 REMARK 465 PHE A 101 REMARK 465 THR A 102 REMARK 465 THR A 103 REMARK 465 SER A 104 REMARK 465 PHE A 105 REMARK 465 GLU A 106 REMARK 465 ASN A 107 REMARK 465 GLN A 108 REMARK 465 VAL A 109 REMARK 465 LYS A 110 REMARK 465 SER A 135 REMARK 465 SER A 136 REMARK 465 GLY A 242 REMARK 465 ILE A 243 REMARK 465 ASN A 244 REMARK 465 GLY A 245 REMARK 465 ASN A 246 REMARK 465 GLY B -2 REMARK 465 PRO B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 ASN B 3 REMARK 465 PHE B 4 REMARK 465 ILE B 5 REMARK 465 ILE B 6 REMARK 465 THR B 7 REMARK 465 GLU B 8 REMARK 465 ARG B 9 REMARK 465 LYS B 10 REMARK 465 LYS B 11 REMARK 465 ALA B 12 REMARK 465 LYS B 13 REMARK 465 GLU B 14 REMARK 465 GLU B 15 REMARK 465 ARG B 16 REMARK 465 SER B 17 REMARK 465 ASN B 18 REMARK 465 PRO B 19 REMARK 465 GLN B 20 REMARK 465 THR B 21 REMARK 465 GLY C 96 REMARK 465 ALA C 97 REMARK 465 HIS C 98 REMARK 465 MET C 99 REMARK 465 ASN C 100 REMARK 465 SER C 113 REMARK 465 ILE C 114 REMARK 465 GLY C 115 REMARK 465 GLN C 116 REMARK 465 LEU C 117 REMARK 465 LYS C 118 REMARK 465 PRO C 119 REMARK 465 SER C 182 REMARK 465 VAL C 183 REMARK 465 ALA C 184 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 26 CG CD CE NZ REMARK 470 ARG A 30 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 31 CG CD OE1 OE2 REMARK 470 THR A 66 OG1 CG2 REMARK 470 ASP A 67 CG OD1 OD2 REMARK 470 SER A 68 OG REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 VAL A 112 CG1 CG2 REMARK 470 SER A 125 OG REMARK 470 LYS A 137 CG CD CE NZ REMARK 470 THR A 138 OG1 CG2 REMARK 470 GLN A 139 CG CD OE1 NE2 REMARK 470 LYS A 142 CG CD CE NZ REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 THR A 209 OG1 CG2 REMARK 470 SER A 210 OG REMARK 470 ARG A 214 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 230 CG CD CE NZ REMARK 470 LYS A 240 CG CD CE NZ REMARK 470 GLU A 241 CG CD OE1 OE2 REMARK 470 VAL A 248 CG1 CG2 REMARK 470 ASP B 22 CG OD1 OD2 REMARK 470 LYS B 38 CG CD CE NZ REMARK 470 ILE C 101 CG1 CG2 CD1 REMARK 470 GLN C 102 CG CD OE1 NE2 REMARK 470 SER C 120 OG REMARK 470 LYS C 142 CG CD CE NZ REMARK 470 PHE C 185 CG CD1 CD2 CE1 CE2 CZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS A 149 C GLY C 186 1.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 20 155.18 -41.69 REMARK 500 THR A 66 7.38 -157.34 REMARK 500 ASN A 84 39.70 -79.91 REMARK 500 ILE A 133 -94.82 -106.09 REMARK 500 THR A 138 73.82 -167.96 REMARK 500 THR A 209 -74.87 -73.08 REMARK 500 ASN A 226 56.76 -148.31 REMARK 500 MET C 143 -164.29 -126.80 REMARK 500 ASP C 144 -32.24 -150.13 REMARK 500 ASN C 151 33.70 38.11 REMARK 500 ASP C 173 -18.93 70.29 REMARK 500 REMARK 500 REMARK: NULL DBREF 3W1S A 1 284 UNP Q12380 ATG5_YEAST 1 284 DBREF 3W1S B 1 46 UNP Q03818 ATG16_YEAST 1 46 DBREF 3W1S C 100 186 UNP P38316 ATG12_YEAST 100 186 SEQADV 3W1S GLY B -2 UNP Q03818 EXPRESSION TAG SEQADV 3W1S PRO B -1 UNP Q03818 EXPRESSION TAG SEQADV 3W1S HIS B 0 UNP Q03818 EXPRESSION TAG SEQADV 3W1S GLY C 96 UNP P38316 EXPRESSION TAG SEQADV 3W1S ALA C 97 UNP P38316 EXPRESSION TAG SEQADV 3W1S HIS C 98 UNP P38316 EXPRESSION TAG SEQADV 3W1S MET C 99 UNP P38316 EXPRESSION TAG SEQRES 1 A 284 MET ASN ASP ILE LYS GLN LEU LEU TRP ASN GLY GLU LEU SEQRES 2 A 284 ASN VAL LEU VAL SER ILE ASP PRO SER PHE LEU MET LYS SEQRES 3 A 284 GLY SER PRO ARG GLU ILE ALA VAL LEU ARG ILE ARG VAL SEQRES 4 A 284 PRO ARG GLU THR TYR LEU VAL ASN TYR MET PRO LEU ILE SEQRES 5 A 284 TRP ASN LYS ILE LYS SER PHE LEU SER PHE ASP PRO LEU SEQRES 6 A 284 THR ASP SER GLU LYS TYR PHE TRP PHE GLU HIS ASN LYS SEQRES 7 A 284 THR PRO ILE PRO TRP ASN TYR PRO VAL GLY VAL LEU PHE SEQRES 8 A 284 ASP CYS LEU ALA GLY LYS SER ALA THR PHE THR THR SER SEQRES 9 A 284 PHE GLU ASN GLN VAL LYS ASP VAL LEU THR PHE LEU ARG SEQRES 10 A 284 ILE HIS LEU VAL MET GLY ASP SER LEU PRO PRO THR ILE SEQRES 11 A 284 ILE PRO ILE ALA SER SER LYS THR GLN ALA GLU LYS PHE SEQRES 12 A 284 TRP PHE HIS GLN TRP LYS GLN VAL CYS PHE ILE LEU ASN SEQRES 13 A 284 GLY SER SER LYS ALA ILE MET SER LEU SER VAL ASN GLU SEQRES 14 A 284 ALA ARG LYS PHE TRP GLY SER VAL ILE THR ARG ASN PHE SEQRES 15 A 284 GLN ASP PHE ILE GLU ILE SER ASN LYS ILE SER SER SER SEQRES 16 A 284 ARG PRO ARG HIS ILE PRO LEU ILE ILE GLN THR SER ARG SEQRES 17 A 284 THR SER GLY THR PHE ARG ILE SER GLN PRO THR ILE SER SEQRES 18 A 284 MET THR GLY VAL ASN PRO THR LEU LYS ASP ILE GLU GLY SEQRES 19 A 284 ASP ILE LEU ASP VAL LYS GLU GLY ILE ASN GLY ASN ASP SEQRES 20 A 284 VAL MET VAL ILE CYS GLN GLY ILE GLU ILE PRO TRP HIS SEQRES 21 A 284 MET LEU LEU TYR ASP LEU TYR SER LYS LEU ARG SER PHE SEQRES 22 A 284 ASP GLY PHE LEU TYR ILE THR LEU VAL PRO ILE SEQRES 1 B 49 GLY PRO HIS MET GLY ASN PHE ILE ILE THR GLU ARG LYS SEQRES 2 B 49 LYS ALA LYS GLU GLU ARG SER ASN PRO GLN THR ASP SER SEQRES 3 B 49 MET ASP ASP LEU LEU ILE ARG ARG LEU THR ASP ARG ASN SEQRES 4 B 49 ASP LYS GLU ALA HIS LEU ASN GLU LEU PHE SEQRES 1 C 91 GLY ALA HIS MET ASN ILE GLN LYS ILE GLN ILE LYS PHE SEQRES 2 C 91 GLN PRO ILE GLY SER ILE GLY GLN LEU LYS PRO SER VAL SEQRES 3 C 91 CYS LYS ILE SER MET SER GLN SER PHE ALA MET VAL ILE SEQRES 4 C 91 LEU PHE LEU LYS ARG ARG LEU LYS MET ASP HIS VAL TYR SEQRES 5 C 91 CYS TYR ILE ASN ASN SER PHE ALA PRO SER PRO GLN GLN SEQRES 6 C 91 ASN ILE GLY GLU LEU TRP MET GLN PHE LYS THR ASN ASP SEQRES 7 C 91 GLU LEU ILE VAL SER TYR CYS ALA SER VAL ALA PHE GLY FORMUL 4 HOH *27(H2 O) HELIX 1 1 ASN A 2 GLY A 11 1 10 HELIX 2 2 PRO A 21 LEU A 24 5 4 HELIX 3 3 PRO A 29 ALA A 33 1 5 HELIX 4 4 TYR A 44 ASN A 47 5 4 HELIX 5 5 TYR A 48 LYS A 57 1 10 HELIX 6 6 SER A 58 LEU A 60 5 3 HELIX 7 7 PRO A 86 ALA A 95 1 10 HELIX 8 8 GLN A 139 GLY A 157 1 19 HELIX 9 9 SER A 159 SER A 164 1 6 HELIX 10 10 SER A 166 ARG A 180 1 15 HELIX 11 11 ASN A 181 LYS A 191 1 11 HELIX 12 12 LEU A 229 ASP A 231 5 3 HELIX 13 13 ILE A 232 LEU A 237 1 6 HELIX 14 14 ASP A 238 LYS A 240 5 3 HELIX 15 15 LEU A 262 ARG A 271 1 10 HELIX 16 16 SER B 23 HIS B 41 1 19 HELIX 17 17 LEU B 42 PHE B 46 5 5 HELIX 18 18 SER C 129 LYS C 142 1 14 HELIX 19 19 ASN C 161 LYS C 170 1 10 SHEET 1 A 5 VAL A 34 PRO A 40 0 SHEET 2 A 5 GLU A 12 ILE A 19 -1 N VAL A 17 O LEU A 35 SHEET 3 A 5 LEU A 116 GLY A 123 1 O LEU A 116 N LEU A 16 SHEET 4 A 5 TYR A 71 HIS A 76 -1 N TYR A 71 O GLY A 123 SHEET 5 A 5 THR A 79 PRO A 80 -1 O THR A 79 N HIS A 76 SHEET 1 B 5 ILE A 215 SER A 216 0 SHEET 2 B 5 LEU A 202 GLN A 205 -1 N ILE A 204 O SER A 216 SHEET 3 B 5 LEU A 277 PRO A 283 1 O ILE A 279 N GLN A 205 SHEET 4 B 5 VAL A 248 CYS A 252 -1 N ILE A 251 O THR A 280 SHEET 5 B 5 ILE A 255 GLU A 256 -1 O ILE A 255 N CYS A 252 SHEET 1 C 4 VAL C 121 SER C 125 0 SHEET 2 C 4 LYS C 103 PRO C 110 -1 N ILE C 106 O CYS C 122 SHEET 3 C 4 GLU C 174 CYS C 180 1 O VAL C 177 N LYS C 107 SHEET 4 C 4 TYR C 147 ILE C 150 -1 N TYR C 149 O SER C 178 CRYST1 72.149 106.084 143.071 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013860 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009426 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006990 0.00000