HEADER PROTEIN TRANSPORT 17-JUL-08 2ZPN TITLE THE CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE ATG8- ATG19(412-415) TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: AUTOPHAGY-RELATED PROTEIN 8; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: AUTOPHAGY-RELATED UBIQUITIN-LIKE MODIFIER ATG8, CYTOPLASM TO COMPND 5 VACUOLE TARGETING PROTEIN 5; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: SACCHAROMYCES CEREVISIAE ATG19(412-415); COMPND 9 CHAIN: E, F, G, H; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: ATG8, APG8, AUT7, CVT5, YBL078C, YBL0732; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHT1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: THIS SEQUENCE CORRESPONDS TO RESIDUES 412-415 OF SOURCE 14 SACCHAROMYCES CEREVISIAE ATG19. KEYWDS UBIQUITIN FOLD, AUTOPHAGY, CYTOPLASMIC VESICLE, LIPOPROTEIN, KEYWDS 2 MEMBRANE, PROTEIN TRANSPORT, TRANSPORT, UBL CONJUGATION PATHWAY, KEYWDS 3 VACUOLE EXPDTA X-RAY DIFFRACTION AUTHOR N.N.NODA,F.INAGAKI REVDAT 3 01-NOV-23 2ZPN 1 REMARK SEQADV REVDAT 2 30-DEC-08 2ZPN 1 JRNL REVDAT 1 09-DEC-08 2ZPN 0 JRNL AUTH N.N.NODA,H.KUMETA,H.NAKATOGAWA,K.SATOO,W.ADACHI,J.ISHII, JRNL AUTH 2 Y.FUJIOKA,Y.OHSUMI,F.INAGAKI JRNL TITL STRUCTURAL BASIS OF TARGET RECOGNITION BY ATG8/LC3 DURING JRNL TITL 2 SELECTIVE AUTOPHAGY JRNL REF GENES CELLS V. 13 1211 2008 JRNL REFN ISSN 1356-9597 JRNL PMID 19021777 JRNL DOI 10.1111/J.1365-2443.2008.01238.X REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 84615.620 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 14505 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) : 0.242 REMARK 3 FREE R VALUE : 0.302 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1476 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2007 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE : 0.3650 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 239 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3564 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 22 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.90000 REMARK 3 B22 (A**2) : 0.15000 REMARK 3 B33 (A**2) : 5.75000 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) : 0.34 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) : 0.47 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.47 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.970 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) : 1.370 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.390 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.770 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.750 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 41.03 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ZPN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000028267. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 4.2 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) : 1.0000 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 : 14927 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 41.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.26000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.120 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1GNU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 CITRATE, PH4.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 22.07500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.51000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.22500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.51000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.07500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.22500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, G 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, H 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 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 GLY A -2 REMARK 465 ALA A -1 REMARK 465 HIS A 0 REMARK 465 GLU A 112 REMARK 465 ASN A 113 REMARK 465 THR A 114 REMARK 465 PHE A 115 REMARK 465 GLY A 116 REMARK 465 GLY B -2 REMARK 465 ALA B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 SER B 3 REMARK 465 ASN B 113 REMARK 465 THR B 114 REMARK 465 PHE B 115 REMARK 465 GLY B 116 REMARK 465 GLY C -2 REMARK 465 ALA C -1 REMARK 465 HIS C 0 REMARK 465 MET C 1 REMARK 465 LYS C 2 REMARK 465 SER C 3 REMARK 465 GLU C 112 REMARK 465 ASN C 113 REMARK 465 THR C 114 REMARK 465 PHE C 115 REMARK 465 GLY C 116 REMARK 465 GLY D -2 REMARK 465 ALA D -1 REMARK 465 HIS D 0 REMARK 465 MET D 1 REMARK 465 LYS D 2 REMARK 465 SER D 3 REMARK 465 ASN D 113 REMARK 465 THR D 114 REMARK 465 PHE D 115 REMARK 465 GLY D 116 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 GLU A 8 CG CD OE1 OE2 REMARK 470 LYS A 13 CG CD CE NZ REMARK 470 LYS A 15 CG CD CE NZ REMARK 470 ARG A 24 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 26 CG CD CE NZ REMARK 470 ASN A 27 CG OD1 ND2 REMARK 470 LYS A 38 CG CD CE NZ REMARK 470 ASP A 40 CG OD1 OD2 REMARK 470 GLU A 73 CG CD OE1 OE2 REMARK 470 LYS A 74 CG CD CE NZ REMARK 470 ASN A 81 CG OD1 ND2 REMARK 470 LYS A 101 CG CD CE NZ REMARK 470 LYS B 13 CG CD CE NZ REMARK 470 LYS B 15 CG CD CE NZ REMARK 470 GLU B 19 CG CD OE1 OE2 REMARK 470 ARG B 24 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 26 CG CD CE NZ REMARK 470 ASN B 27 CG OD1 ND2 REMARK 470 GLU B 37 CG CD OE1 OE2 REMARK 470 LYS B 38 CG CD CE NZ REMARK 470 ASP B 40 CG OD1 OD2 REMARK 470 GLU B 73 CG CD OE1 OE2 REMARK 470 LYS B 74 CG CD CE NZ REMARK 470 ASN B 81 CG OD1 ND2 REMARK 470 SER B 92 OG REMARK 470 LYS B 101 CG CD CE NZ REMARK 470 GLU B 112 CG CD OE1 OE2 REMARK 470 LYS C 13 CG CD CE NZ REMARK 470 LYS C 15 CG CD CE NZ REMARK 470 LYS C 26 CG CD CE NZ REMARK 470 LYS C 38 CG CD CE NZ REMARK 470 ASP C 40 CG OD1 OD2 REMARK 470 LYS C 74 CG CD CE NZ REMARK 470 ASN C 81 CG OD1 ND2 REMARK 470 LYS C 101 CG CD CE NZ REMARK 470 GLU D 8 CG CD OE1 OE2 REMARK 470 GLU D 12 CG CD OE1 OE2 REMARK 470 LYS D 13 CG CD CE NZ REMARK 470 LYS D 15 CG CD CE NZ REMARK 470 ARG D 24 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 26 CG CD CE NZ REMARK 470 GLU D 37 CG CD OE1 OE2 REMARK 470 LYS D 38 CG CD CE NZ REMARK 470 ASP D 40 CG OD1 OD2 REMARK 470 LYS D 46 CG CD CE NZ REMARK 470 GLU D 73 CG CD OE1 OE2 REMARK 470 LYS D 74 CG CD CE NZ REMARK 470 ASN D 81 CG OD1 ND2 REMARK 470 GLU D 112 CG CD OE1 OE2 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 ASN A 27 41.27 -103.19 REMARK 500 ILE A 41 160.86 -44.52 REMARK 500 MET A 69 59.35 37.61 REMARK 500 LYS B 6 -73.32 -53.81 REMARK 500 GLU B 12 -19.59 -49.97 REMARK 500 LYS B 38 71.11 -102.58 REMARK 500 MET B 69 47.74 38.61 REMARK 500 ASN B 81 64.50 33.66 REMARK 500 LYS B 101 -9.39 -51.28 REMARK 500 SER B 110 -176.80 -171.00 REMARK 500 GLU C 37 5.01 -62.53 REMARK 500 MET C 69 64.12 32.11 REMARK 500 GLU C 73 -79.33 -62.22 REMARK 500 LYS C 74 139.46 -35.38 REMARK 500 HIS C 98 -2.11 -142.92 REMARK 500 SER C 110 -175.76 -178.27 REMARK 500 SER D 18 -70.75 -39.32 REMARK 500 ASP D 82 -7.33 68.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR C 106 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 117 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 117 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 117 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 117 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 118 DBREF 2ZPN A 1 116 UNP P38182 ATG8_YEAST 1 116 DBREF 2ZPN B 1 116 UNP P38182 ATG8_YEAST 1 116 DBREF 2ZPN C 1 116 UNP P38182 ATG8_YEAST 1 116 DBREF 2ZPN D 1 116 UNP P38182 ATG8_YEAST 1 116 DBREF 2ZPN E 1 4 PDB 2ZPN 2ZPN 1 4 DBREF 2ZPN F 1 4 PDB 2ZPN 2ZPN 1 4 DBREF 2ZPN G 1 4 PDB 2ZPN 2ZPN 1 4 DBREF 2ZPN H 1 4 PDB 2ZPN 2ZPN 1 4 SEQADV 2ZPN GLY A -2 UNP P38182 EXPRESSION TAG SEQADV 2ZPN ALA A -1 UNP P38182 EXPRESSION TAG SEQADV 2ZPN HIS A 0 UNP P38182 EXPRESSION TAG SEQADV 2ZPN GLY B -2 UNP P38182 EXPRESSION TAG SEQADV 2ZPN ALA B -1 UNP P38182 EXPRESSION TAG SEQADV 2ZPN HIS B 0 UNP P38182 EXPRESSION TAG SEQADV 2ZPN GLY C -2 UNP P38182 EXPRESSION TAG SEQADV 2ZPN ALA C -1 UNP P38182 EXPRESSION TAG SEQADV 2ZPN HIS C 0 UNP P38182 EXPRESSION TAG SEQADV 2ZPN GLY D -2 UNP P38182 EXPRESSION TAG SEQADV 2ZPN ALA D -1 UNP P38182 EXPRESSION TAG SEQADV 2ZPN HIS D 0 UNP P38182 EXPRESSION TAG SEQRES 1 A 119 GLY ALA HIS MET LYS SER THR PHE LYS SER GLU TYR PRO SEQRES 2 A 119 PHE GLU LYS ARG LYS ALA GLU SER GLU ARG ILE ALA ASP SEQRES 3 A 119 ARG PHE LYS ASN ARG ILE PRO VAL ILE CYS GLU LYS ALA SEQRES 4 A 119 GLU LYS SER ASP ILE PRO GLU ILE ASP LYS ARG LYS TYR SEQRES 5 A 119 LEU VAL PRO ALA ASP LEU THR VAL GLY GLN PHE VAL TYR SEQRES 6 A 119 VAL ILE ARG LYS ARG ILE MET LEU PRO PRO GLU LYS ALA SEQRES 7 A 119 ILE PHE ILE PHE VAL ASN ASP THR LEU PRO PRO THR ALA SEQRES 8 A 119 ALA LEU MET SER ALA ILE TYR GLN GLU HIS LYS ASP LYS SEQRES 9 A 119 ASP GLY PHE LEU TYR VAL THR TYR SER GLY GLU ASN THR SEQRES 10 A 119 PHE GLY SEQRES 1 B 119 GLY ALA HIS MET LYS SER THR PHE LYS SER GLU TYR PRO SEQRES 2 B 119 PHE GLU LYS ARG LYS ALA GLU SER GLU ARG ILE ALA ASP SEQRES 3 B 119 ARG PHE LYS ASN ARG ILE PRO VAL ILE CYS GLU LYS ALA SEQRES 4 B 119 GLU LYS SER ASP ILE PRO GLU ILE ASP LYS ARG LYS TYR SEQRES 5 B 119 LEU VAL PRO ALA ASP LEU THR VAL GLY GLN PHE VAL TYR SEQRES 6 B 119 VAL ILE ARG LYS ARG ILE MET LEU PRO PRO GLU LYS ALA SEQRES 7 B 119 ILE PHE ILE PHE VAL ASN ASP THR LEU PRO PRO THR ALA SEQRES 8 B 119 ALA LEU MET SER ALA ILE TYR GLN GLU HIS LYS ASP LYS SEQRES 9 B 119 ASP GLY PHE LEU TYR VAL THR TYR SER GLY GLU ASN THR SEQRES 10 B 119 PHE GLY SEQRES 1 C 119 GLY ALA HIS MET LYS SER THR PHE LYS SER GLU TYR PRO SEQRES 2 C 119 PHE GLU LYS ARG LYS ALA GLU SER GLU ARG ILE ALA ASP SEQRES 3 C 119 ARG PHE LYS ASN ARG ILE PRO VAL ILE CYS GLU LYS ALA SEQRES 4 C 119 GLU LYS SER ASP ILE PRO GLU ILE ASP LYS ARG LYS TYR SEQRES 5 C 119 LEU VAL PRO ALA ASP LEU THR VAL GLY GLN PHE VAL TYR SEQRES 6 C 119 VAL ILE ARG LYS ARG ILE MET LEU PRO PRO GLU LYS ALA SEQRES 7 C 119 ILE PHE ILE PHE VAL ASN ASP THR LEU PRO PRO THR ALA SEQRES 8 C 119 ALA LEU MET SER ALA ILE TYR GLN GLU HIS LYS ASP LYS SEQRES 9 C 119 ASP GLY PHE LEU TYR VAL THR TYR SER GLY GLU ASN THR SEQRES 10 C 119 PHE GLY SEQRES 1 D 119 GLY ALA HIS MET LYS SER THR PHE LYS SER GLU TYR PRO SEQRES 2 D 119 PHE GLU LYS ARG LYS ALA GLU SER GLU ARG ILE ALA ASP SEQRES 3 D 119 ARG PHE LYS ASN ARG ILE PRO VAL ILE CYS GLU LYS ALA SEQRES 4 D 119 GLU LYS SER ASP ILE PRO GLU ILE ASP LYS ARG LYS TYR SEQRES 5 D 119 LEU VAL PRO ALA ASP LEU THR VAL GLY GLN PHE VAL TYR SEQRES 6 D 119 VAL ILE ARG LYS ARG ILE MET LEU PRO PRO GLU LYS ALA SEQRES 7 D 119 ILE PHE ILE PHE VAL ASN ASP THR LEU PRO PRO THR ALA SEQRES 8 D 119 ALA LEU MET SER ALA ILE TYR GLN GLU HIS LYS ASP LYS SEQRES 9 D 119 ASP GLY PHE LEU TYR VAL THR TYR SER GLY GLU ASN THR SEQRES 10 D 119 PHE GLY SEQRES 1 E 4 TRP GLU GLU LEU SEQRES 1 F 4 TRP GLU GLU LEU SEQRES 1 G 4 TRP GLU GLU LEU SEQRES 1 H 4 TRP GLU GLU LEU HET SO4 A 117 5 HET SO4 A 118 5 HET SO4 B 117 5 HET SO4 C 117 5 HET SO4 D 117 5 HETNAM SO4 SULFATE ION FORMUL 9 SO4 5(O4 S 2-) FORMUL 14 HOH *22(H2 O) HELIX 1 1 PRO A 10 PHE A 25 1 16 HELIX 2 2 THR A 56 ILE A 68 1 13 HELIX 3 3 LEU A 90 LYS A 99 1 10 HELIX 4 4 THR B 4 TYR B 9 1 6 HELIX 5 5 PRO B 10 PHE B 25 1 16 HELIX 6 6 THR B 56 ILE B 68 1 13 HELIX 7 7 LEU B 90 LYS B 99 1 10 HELIX 8 8 THR C 4 TYR C 9 1 6 HELIX 9 9 PRO C 10 PHE C 25 1 16 HELIX 10 10 THR C 56 ILE C 68 1 13 HELIX 11 11 LEU C 90 LYS C 99 1 10 HELIX 12 12 THR D 4 TYR D 9 1 6 HELIX 13 13 PRO D 10 PHE D 25 1 16 HELIX 14 14 THR D 56 ILE D 68 1 13 HELIX 15 15 LEU D 90 LYS D 99 1 10 SHEET 1 A 5 PHE A 77 PHE A 79 0 SHEET 2 A 5 LEU A 105 SER A 110 -1 O THR A 108 N PHE A 79 SHEET 3 A 5 ARG A 28 LYS A 35 1 N ILE A 32 O VAL A 107 SHEET 4 A 5 LYS A 48 PRO A 52 -1 O VAL A 51 N ILE A 29 SHEET 5 A 5 GLU E 2 GLU E 3 1 O GLU E 2 N LEU A 50 SHEET 1 B 5 PHE B 77 VAL B 80 0 SHEET 2 B 5 LEU B 105 SER B 110 -1 O THR B 108 N PHE B 79 SHEET 3 B 5 ARG B 28 LYS B 35 1 N ILE B 32 O LEU B 105 SHEET 4 B 5 LYS B 48 PRO B 52 -1 O TYR B 49 N VAL B 31 SHEET 5 B 5 GLU F 2 GLU F 3 1 O GLU F 2 N LEU B 50 SHEET 1 C 5 PHE C 77 PHE C 79 0 SHEET 2 C 5 LEU C 105 SER C 110 -1 O SER C 110 N PHE C 77 SHEET 3 C 5 ARG C 28 LYS C 35 1 N ILE C 32 O VAL C 107 SHEET 4 C 5 LYS C 48 PRO C 52 -1 O TYR C 49 N VAL C 31 SHEET 5 C 5 GLU G 2 GLU G 3 1 O GLU G 2 N LEU C 50 SHEET 1 D 5 PHE D 77 PHE D 79 0 SHEET 2 D 5 LEU D 105 SER D 110 -1 O THR D 108 N PHE D 79 SHEET 3 D 5 ARG D 28 LYS D 35 1 N GLU D 34 O VAL D 107 SHEET 4 D 5 LYS D 48 PRO D 52 -1 O VAL D 51 N ILE D 29 SHEET 5 D 5 GLU H 2 GLU H 3 1 O GLU H 2 N LEU D 50 SITE 1 AC1 4 SER A 39 ASP A 40 ILE A 41 GLY A 111 SITE 1 AC2 6 LYS B 38 SER B 39 ASP B 40 SER B 110 SITE 2 AC2 6 GLY B 111 GLU B 112 SITE 1 AC3 4 SER C 39 ASP C 40 ILE C 41 GLY C 111 SITE 1 AC4 5 SER D 39 ASP D 40 SER D 110 GLY D 111 SITE 2 AC4 5 GLU D 112 SITE 1 AC5 4 LYS A 66 LYS B 66 ARG B 67 ALA D 88 CRYST1 44.150 104.450 113.020 90.00 90.00 90.00 P 21 21 21 16 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 0.022650 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009574 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008848 0.00000