HEADER METAL BINDING PROTEIN/PROTEIN TRANSPORT 23-AUG-11 3VH3 TITLE CRYSTAL STRUCTURE OF ATG7CTD-ATG8 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME ATG7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN (UNP RESIDUES 295-630); COMPND 5 SYNONYM: ATG12-ACTIVATING ENZYME E1 ATG7, AUTOPHAGY-RELATED PROTEIN COMPND 6 7, CYTOPLASM TO VACUOLE TARGETING PROTEIN 2; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: AUTOPHAGY-RELATED PROTEIN 8; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: AUTOPHAGY-RELATED UBIQUITIN-LIKE MODIFIER ATG8, CYTOPLASM TO COMPND 12 VACUOLE TARGETING PROTEIN 5; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: S288C; SOURCE 6 GENE: ATG7, APG7, CVT2, YHR171W; 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: PGEX6P; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 14 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 15 ORGANISM_TAXID: 559292; SOURCE 16 STRAIN: S288C; SOURCE 17 GENE: ATG8, APG8, AUT7, CVT5, YBL078C, YBL0732; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PGEX6P KEYWDS AUTOPHAGY, E1, ZINC BINDING, METAL BINDING PROTEIN-PROTEIN TRANSPORT KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.N.NODA,K.SATOO,F.INAGAKI REVDAT 4 08-NOV-23 3VH3 1 REMARK SEQADV LINK REVDAT 3 28-MAR-12 3VH3 1 JRNL REVDAT 2 16-NOV-11 3VH3 1 JRNL REVDAT 1 21-SEP-11 3VH3 0 JRNL AUTH N.N.NODA,K.SATOO,Y.FUJIOKA,H.KUMETA,K.OGURA,H.NAKATOGAWA, JRNL AUTH 2 Y.OHSUMI,F.INAGAKI JRNL TITL STRUCTURAL BASIS OF ATG8 ACTIVATION BY A HOMODIMERIC E1, JRNL TITL 2 ATG7. JRNL REF MOL.CELL V. 44 462 2011 JRNL REFN ISSN 1097-2765 JRNL PMID 22055191 JRNL DOI 10.1016/J.MOLCEL.2011.08.035 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 169287.110 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.6 REMARK 3 NUMBER OF REFLECTIONS : 34744 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) : 0.232 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3438 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4595 REMARK 3 BIN R VALUE (WORKING SET) : 0.3150 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 475 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3290 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 168 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.86000 REMARK 3 B22 (A**2) : 8.86000 REMARK 3 B33 (A**2) : -17.71000 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) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.27 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) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.28 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740 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) : 1.380 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.230 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.010 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.880 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 57.12 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 3VH3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000095036. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU 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 : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37933 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 53.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.47500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.200 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: 2ZPN, 3VH1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEGMME 5000, 5% TACSIMATE, 0.1M REMARK 280 HEPES , PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 110.19600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.90750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.90750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 165.29400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.90750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.90750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.09800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.90750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.90750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 165.29400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.90750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.90750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.09800 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 110.19600 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -88.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 0.000000 1.000000 0.000000 -69.81500 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 69.81500 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 GLY A 291 REMARK 465 PRO A 292 REMARK 465 HIS A 293 REMARK 465 LEU A 614 REMARK 465 GLY A 615 REMARK 465 ASN A 616 REMARK 465 ASP A 617 REMARK 465 VAL A 618 REMARK 465 PHE A 619 REMARK 465 GLU A 620 REMARK 465 TRP A 621 REMARK 465 GLU A 622 REMARK 465 ASP A 623 REMARK 465 ASP A 624 REMARK 465 GLU A 625 REMARK 465 SER A 626 REMARK 465 ASP A 627 REMARK 465 GLU A 628 REMARK 465 ILE A 629 REMARK 465 ALA A 630 REMARK 465 GLY B -2 REMARK 465 PRO B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 SER B 3 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 MET A 294 CG SD CE REMARK 470 LYS A 296 CG CD CE NZ REMARK 470 LYS A 409 CG CD CE NZ REMARK 470 VAL A 411 CG1 CG2 REMARK 470 GLU A 414 CG CD OE1 OE2 REMARK 470 LYS A 418 CG CD CE NZ REMARK 470 GLU A 477 CG CD OE1 OE2 REMARK 470 GLN A 478 CG CD OE1 NE2 REMARK 470 SER A 479 OG REMARK 470 SER A 480 OG REMARK 470 LYS A 481 CG CD CE NZ REMARK 470 ARG A 501 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 504 CG OD1 OD2 REMARK 470 GLN A 505 CG CD OE1 NE2 REMARK 470 GLU A 578 CG CD OE1 OE2 REMARK 470 ASP A 582 CG OD1 OD2 REMARK 470 LYS A 589 CG CD CE NZ REMARK 470 VAL A 606 CG1 CG2 REMARK 470 GLN A 609 CG CD OE1 NE2 REMARK 470 VAL A 611 CG1 CG2 REMARK 470 GLU A 612 CG CD OE1 OE2 REMARK 470 ARG A 613 CG CD NE CZ NH1 NH2 REMARK 470 THR B 4 OG1 CG2 REMARK 470 SER B 7 OG REMARK 470 GLU B 8 CG CD OE1 OE2 REMARK 470 TYR B 9 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU B 12 CG CD OE1 OE2 REMARK 470 LYS B 13 CG CD CE NZ REMARK 470 LYS B 15 CG CD CE NZ REMARK 470 SER B 18 OG REMARK 470 ASP B 23 CG OD1 OD2 REMARK 470 ARG B 28 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 40 CG OD1 OD2 REMARK 470 ARG B 47 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 LEU B 50 CG CD1 CD2 REMARK 470 ASP B 54 CG OD1 OD2 REMARK 470 LYS B 66 CG CD CE NZ REMARK 470 ARG B 67 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 96 CG CD OE1 NE2 REMARK 470 LYS B 101 CG CD CE NZ 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 ALA A 368 11.21 -54.42 REMARK 500 GLU A 413 -70.83 -28.58 REMARK 500 SER A 480 34.87 -97.80 REMARK 500 MET A 506 144.66 -172.35 REMARK 500 SER A 535 -65.05 -25.39 REMARK 500 GLU A 538 60.30 -102.62 REMARK 500 ASP B 40 60.56 -108.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 485 SG REMARK 620 2 CYS A 488 SG 119.7 REMARK 620 3 CYS A 569 SG 100.5 115.4 REMARK 620 4 CYS A 572 SG 118.2 97.5 105.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VH1 RELATED DB: PDB REMARK 900 THE SAME PROTEIN AS A FREE FORM. REMARK 900 RELATED ID: 3VH2 RELATED DB: PDB REMARK 900 THE SAME PROTEIN AS A FREE FORM. REMARK 900 RELATED ID: 3VH4 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEX WITH MGATP. DBREF 3VH3 A 295 630 UNP P38862 ATG7_YEAST 295 630 DBREF 3VH3 B 1 116 UNP P38182 ATG8_YEAST 1 116 SEQADV 3VH3 GLY A 291 UNP P38862 EXPRESSION TAG SEQADV 3VH3 PRO A 292 UNP P38862 EXPRESSION TAG SEQADV 3VH3 HIS A 293 UNP P38862 EXPRESSION TAG SEQADV 3VH3 MET A 294 UNP P38862 EXPRESSION TAG SEQADV 3VH3 GLY B -2 UNP P38182 EXPRESSION TAG SEQADV 3VH3 PRO B -1 UNP P38182 EXPRESSION TAG SEQADV 3VH3 HIS B 0 UNP P38182 EXPRESSION TAG SEQADV 3VH3 PRO B 26 UNP P38182 LYS 26 ENGINEERED MUTATION SEQRES 1 A 340 GLY PRO HIS MET LEU LYS ILE ALA ASP GLN SER VAL ASP SEQRES 2 A 340 LEU ASN LEU LYS LEU MET LYS TRP ARG ILE LEU PRO ASP SEQRES 3 A 340 LEU ASN LEU ASP ILE ILE LYS ASN THR LYS VAL LEU LEU SEQRES 4 A 340 LEU GLY ALA GLY THR LEU GLY CYS TYR VAL SER ARG ALA SEQRES 5 A 340 LEU ILE ALA TRP GLY VAL ARG LYS ILE THR PHE VAL ASP SEQRES 6 A 340 ASN GLY THR VAL SER TYR SER ASN PRO VAL ARG GLN ALA SEQRES 7 A 340 LEU TYR ASN PHE GLU ASP CYS GLY LYS PRO LYS ALA GLU SEQRES 8 A 340 LEU ALA ALA ALA SER LEU LYS ARG ILE PHE PRO LEU MET SEQRES 9 A 340 ASP ALA THR GLY VAL LYS LEU SER ILE PRO MET ILE GLY SEQRES 10 A 340 HIS LYS LEU VAL ASN GLU GLU ALA GLN HIS LYS ASP PHE SEQRES 11 A 340 ASP ARG LEU ARG ALA LEU ILE LYS GLU HIS ASP ILE ILE SEQRES 12 A 340 PHE LEU LEU VAL ASP SER ARG GLU SER ARG TRP LEU PRO SEQRES 13 A 340 SER LEU LEU SER ASN ILE GLU ASN LYS THR VAL ILE ASN SEQRES 14 A 340 ALA ALA LEU GLY PHE ASP SER TYR LEU VAL MET ARG HIS SEQRES 15 A 340 GLY ASN ARG ASP GLU GLN SER SER LYS GLN LEU GLY CYS SEQRES 16 A 340 TYR PHE CYS HIS ASP VAL VAL ALA PRO THR ASP SER LEU SEQRES 17 A 340 THR ASP ARG THR LEU ASP GLN MET CYS THR VAL THR ARG SEQRES 18 A 340 PRO GLY VAL ALA MET MET ALA SER SER LEU ALA VAL GLU SEQRES 19 A 340 LEU MET THR SER LEU LEU GLN THR LYS TYR SER GLY SER SEQRES 20 A 340 GLU THR THR VAL LEU GLY ASP ILE PRO HIS GLN ILE ARG SEQRES 21 A 340 GLY PHE LEU HIS ASN PHE SER ILE LEU LYS LEU GLU THR SEQRES 22 A 340 PRO ALA TYR GLU HIS CYS PRO ALA CYS SER PRO LYS VAL SEQRES 23 A 340 ILE GLU ALA PHE THR ASP LEU GLY TRP GLU PHE VAL LYS SEQRES 24 A 340 LYS ALA LEU GLU HIS PRO LEU TYR LEU GLU GLU ILE SER SEQRES 25 A 340 GLY LEU SER VAL ILE LYS GLN GLU VAL GLU ARG LEU GLY SEQRES 26 A 340 ASN ASP VAL PHE GLU TRP GLU ASP ASP GLU SER ASP GLU SEQRES 27 A 340 ILE ALA SEQRES 1 B 119 GLY PRO 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 PRO 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 HET ZN A 701 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *168(H2 O) HELIX 1 1 MET A 294 ILE A 313 1 20 HELIX 2 2 ASN A 318 ASN A 324 1 7 HELIX 3 3 GLY A 333 TRP A 346 1 14 HELIX 4 4 ASN A 371 CYS A 375 5 5 HELIX 5 5 PRO A 378 PHE A 391 1 14 HELIX 6 6 ASN A 412 HIS A 430 1 19 HELIX 7 7 ARG A 440 SER A 442 5 3 HELIX 8 8 ARG A 443 GLU A 453 1 11 HELIX 9 9 PRO A 512 LEU A 530 1 19 HELIX 10 10 SER A 573 GLY A 584 1 12 HELIX 11 11 GLY A 584 HIS A 594 1 11 HELIX 12 12 HIS A 594 GLY A 603 1 10 HELIX 13 13 GLY A 603 ARG A 613 1 11 HELIX 14 14 PHE B 5 TYR B 9 5 5 HELIX 15 15 PRO B 10 PHE B 25 1 16 HELIX 16 16 THR B 56 ILE B 68 1 13 HELIX 17 17 LEU B 90 LYS B 99 1 10 SHEET 1 A 8 ASP A 395 VAL A 399 0 SHEET 2 A 8 LYS A 350 VAL A 354 1 N PHE A 353 O THR A 397 SHEET 3 A 8 LYS A 326 LEU A 330 1 N LEU A 329 O THR A 352 SHEET 4 A 8 ILE A 432 LEU A 435 1 O PHE A 434 N LEU A 328 SHEET 5 A 8 THR A 456 LEU A 462 1 O ILE A 458 N ILE A 433 SHEET 6 A 8 SER A 466 ARG A 471 -1 O MET A 470 N ASN A 459 SHEET 7 A 8 GLN A 548 PHE A 552 -1 O ILE A 549 N VAL A 469 SHEET 8 A 8 SER A 557 LEU A 561 -1 O LEU A 561 N GLN A 548 SHEET 1 B 2 THR A 539 THR A 540 0 SHEET 2 B 2 GLY A 543 ASP A 544 -1 O GLY A 543 N THR A 540 SHEET 1 C 4 LYS B 48 PRO B 52 0 SHEET 2 C 4 ARG B 28 LYS B 35 -1 N VAL B 31 O TYR B 49 SHEET 3 C 4 LEU B 105 GLY B 111 1 O VAL B 107 N ILE B 32 SHEET 4 C 4 ILE B 76 PHE B 79 -1 N PHE B 79 O THR B 108 LINK SG CYS A 485 ZN ZN A 701 1555 1555 2.36 LINK SG CYS A 488 ZN ZN A 701 1555 1555 2.23 LINK SG CYS A 569 ZN ZN A 701 1555 1555 2.29 LINK SG CYS A 572 ZN ZN A 701 1555 1555 2.36 SITE 1 AC1 4 CYS A 485 CYS A 488 CYS A 569 CYS A 572 CRYST1 69.815 69.815 220.392 90.00 90.00 90.00 P 43 21 2 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 0.014324 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014324 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004537 0.00000