PDB Short entry for 5XUY HEADER PROTEIN BINDING 26-JUN-17 5XUY TITLE CRYSTAL STRUCTURE OF ATG101-ATG13HORMA COMPND MOL_ID: 1; COMPND 2 MOLECULE: AUTOPHAGY-RELATED PROTEIN 13; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: UNP RESIDUES 1-190; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: AUTOPHAGY-RELATED PROTEIN 101; COMPND 8 CHAIN: B, D; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ATG13, KIAA0652; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: ATG101, C12ORF44, PP894; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AUTOPHAGY, ATG101, ATG13, HORMA, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR B.-W.KIM,H.K.SONG REVDAT 3 27-MAR-24 5XUY 1 REMARK REVDAT 2 16-JAN-19 5XUY 1 JRNL REVDAT 1 04-JUL-18 5XUY 0 JRNL AUTH B.-W.KIM,Y.JIN,J.KIM,J.H.KIM,J.JUNG,S.KANG,I.Y.KIM,J.KIM, JRNL AUTH 2 H.CHEONG,H.K.SONG JRNL TITL THE C-TERMINAL REGION OF ATG101 BRIDGES ULK1 AND PTDINS3K JRNL TITL 2 COMPLEX IN AUTOPHAGY INITIATION. JRNL REF AUTOPHAGY V. 14 2104 2018 JRNL REFN ESSN 1554-8635 JRNL PMID 30081750 JRNL DOI 10.1080/15548627.2018.1504716 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 53556 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.730 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 31.4668 - 5.2872 0.90 3422 132 0.2043 0.2451 REMARK 3 2 5.2872 - 4.1998 0.99 3703 144 0.1832 0.2034 REMARK 3 3 4.1998 - 3.6698 0.99 3712 144 0.2056 0.2515 REMARK 3 4 3.6698 - 3.3347 1.00 3734 144 0.2289 0.2426 REMARK 3 5 3.3347 - 3.0959 1.00 3755 147 0.2481 0.2889 REMARK 3 6 3.0959 - 2.9135 1.00 3700 143 0.2602 0.3290 REMARK 3 7 2.9135 - 2.7677 1.00 3730 144 0.2648 0.3414 REMARK 3 8 2.7677 - 2.6473 1.00 3695 143 0.2748 0.3471 REMARK 3 9 2.6473 - 2.5454 1.00 3729 145 0.2879 0.3104 REMARK 3 10 2.5454 - 2.4576 1.00 3710 144 0.3185 0.3850 REMARK 3 11 2.4576 - 2.3808 1.00 3693 143 0.3521 0.3867 REMARK 3 12 2.3808 - 2.3128 1.00 3725 145 0.3802 0.4253 REMARK 3 13 2.3128 - 2.2519 0.99 3678 141 0.4343 0.4954 REMARK 3 14 2.2519 - 2.1970 0.97 3572 139 0.4716 0.4831 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 6037 REMARK 3 ANGLE : 0.700 8192 REMARK 3 CHIRALITY : 0.044 974 REMARK 3 PLANARITY : 0.004 1035 REMARK 3 DIHEDRAL : 14.339 3602 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 63.7379 28.7810 221.3517 REMARK 3 T TENSOR REMARK 3 T11: 0.3030 T22: 0.3816 REMARK 3 T33: 0.3846 T12: 0.0008 REMARK 3 T13: -0.0120 T23: -0.0114 REMARK 3 L TENSOR REMARK 3 L11: 0.2575 L22: 2.2236 REMARK 3 L33: 2.1880 L12: 0.2995 REMARK 3 L13: -0.4286 L23: -1.7733 REMARK 3 S TENSOR REMARK 3 S11: -0.0010 S12: -0.0048 S13: -0.0186 REMARK 3 S21: -0.1928 S22: -0.0772 S23: -0.0143 REMARK 3 S31: 0.2281 S32: -0.0440 S33: -0.0025 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5XUY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1300004218. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53628 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.63600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES (PH7.5), 0.2M MGCL2, 6-8% REMARK 280 (W/V) PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 43.99500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 62.58850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 43.99500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 62.58850 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 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: 2660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 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: 2600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 THR A 3 REMARK 465 ASP A 4 REMARK 465 LEU A 5 REMARK 465 ASP A 92 REMARK 465 LYS A 112 REMARK 465 VAL A 113 REMARK 465 GLY A 145 REMARK 465 HIS A 146 REMARK 465 MET B 1 REMARK 465 GLY B 94 REMARK 465 MET B 208 REMARK 465 ARG B 209 REMARK 465 ARG B 210 REMARK 465 LEU B 211 REMARK 465 ILE B 212 REMARK 465 LYS B 213 REMARK 465 ASP B 214 REMARK 465 THR B 215 REMARK 465 LEU B 216 REMARK 465 ALA B 217 REMARK 465 LEU B 218 REMARK 465 MET C 1 REMARK 465 GLU C 2 REMARK 465 THR C 3 REMARK 465 ASP C 4 REMARK 465 LEU C 5 REMARK 465 GLY C 145 REMARK 465 LEU D 216 REMARK 465 ALA D 217 REMARK 465 LEU D 218 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 11 CG CD CE NZ REMARK 470 ARG A 40 CG CD NE CZ NH1 NH2 REMARK 470 SER A 44 OG REMARK 470 LYS A 67 CG CD CE NZ REMARK 470 ARG A 78 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 87 CG CD CE NZ REMARK 470 GLU A 90 CG CD OE1 OE2 REMARK 470 GLU A 105 CG CD OE1 OE2 REMARK 470 LYS A 106 CG CD CE NZ REMARK 470 LYS A 109 CG CD CE NZ REMARK 470 GLU A 110 CG CD OE1 OE2 REMARK 470 SER A 114 OG REMARK 470 LEU A 140 CG CD1 CD2 REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 GLN A 144 CG CD OE1 NE2 REMARK 470 GLU A 147 CG CD OE1 OE2 REMARK 470 TYR A 148 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 151 CG CD1 CD2 REMARK 470 GLU A 158 CG CD OE1 OE2 REMARK 470 GLN A 160 CG CD OE1 NE2 REMARK 470 GLU A 166 CG CD OE1 OE2 REMARK 470 ARG A 172 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 190 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 9 CG CD OE1 OE2 REMARK 470 GLU B 18 CG CD OE1 OE2 REMARK 470 GLU B 71 CG CD OE1 OE2 REMARK 470 ARG B 88 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 89 CG OD1 ND2 REMARK 470 SER B 90 OG REMARK 470 ASP B 93 CG OD1 OD2 REMARK 470 LEU B 95 CG CD1 CD2 REMARK 470 LYS B 107 CG CD CE NZ REMARK 470 ARG B 109 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 134 CG CD OE1 OE2 REMARK 470 ARG B 161 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 163 CG CD OE1 OE2 REMARK 470 LYS B 167 CG CD CE NZ REMARK 470 LEU B 200 CG CD1 CD2 REMARK 470 SER B 203 OG REMARK 470 THR B 205 OG1 CG2 REMARK 470 LYS C 11 CG CD CE NZ REMARK 470 SER C 44 OG REMARK 470 GLU C 60 CG CD OE1 OE2 REMARK 470 LYS C 87 CG CD CE NZ REMARK 470 GLU C 90 CG CD OE1 OE2 REMARK 470 ASP C 92 CG OD1 OD2 REMARK 470 GLU C 105 CG CD OE1 OE2 REMARK 470 LYS C 106 CG CD CE NZ REMARK 470 LYS C 109 CG CD CE NZ REMARK 470 GLU C 110 CG CD OE1 OE2 REMARK 470 LYS C 112 CG CD CE NZ REMARK 470 VAL C 113 CG1 CG2 REMARK 470 SER C 114 OG REMARK 470 ARG C 139 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 158 CG CD OE1 OE2 REMARK 470 SER C 162 OG REMARK 470 GLU C 166 CG CD OE1 OE2 REMARK 470 MET D 1 CG SD CE REMARK 470 GLU D 18 CG CD OE1 OE2 REMARK 470 GLU D 70 CG CD OE1 OE2 REMARK 470 LYS D 107 CG CD CE NZ REMARK 470 ARG D 109 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 134 CG CD OE1 OE2 REMARK 470 GLN D 135 CG CD OE1 NE2 REMARK 470 LYS D 167 CG CD CE NZ REMARK 470 LEU D 200 CG CD1 CD2 REMARK 470 VAL D 204 CG1 CG2 REMARK 470 THR D 205 OG1 CG2 REMARK 470 MET D 208 CG SD CE REMARK 470 ARG D 209 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 210 CG CD NE CZ NH1 NH2 REMARK 470 ILE D 212 CG1 CG2 CD1 REMARK 470 LYS D 213 CG CD CE NZ REMARK 470 ASP D 214 CG OD1 OD2 REMARK 470 THR D 215 OG1 CG2 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 ND2 ASN C 104 OG1 THR C 182 2.05 REMARK 500 O TYR D 164 O HOH D 301 2.14 REMARK 500 NH1 ARG C 153 O HOH C 201 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU D 131 CB - CG - CD1 ANGL. DEV. = -22.6 DEGREES 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 SER A 44 78.61 -118.05 REMARK 500 ARG B 15 4.27 -62.26 REMARK 500 ARG B 32 54.57 -109.02 REMARK 500 VAL B 204 41.53 -97.21 REMARK 500 SER C 44 72.78 -118.71 REMARK 500 SER C 114 73.43 -68.66 REMARK 500 TYR C 115 -13.31 94.04 REMARK 500 GLU C 158 75.19 57.37 REMARK 500 ASN D 2 19.17 59.33 REMARK 500 ARG D 32 55.09 -113.10 REMARK 500 ASP D 61 81.72 -62.67 REMARK 500 ALA D 132 -25.12 -144.66 REMARK 500 THR D 197 -163.40 -122.10 REMARK 500 SER D 203 40.41 75.80 REMARK 500 VAL D 204 17.24 49.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 327 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH D 331 DISTANCE = 7.42 ANGSTROMS DBREF 5XUY A 1 190 UNP O75143 ATG13_HUMAN 1 190 DBREF 5XUY B 1 218 UNP Q9BSB4 ATGA1_HUMAN 1 218 DBREF 5XUY C 1 190 UNP O75143 ATG13_HUMAN 1 190 DBREF 5XUY D 1 218 UNP Q9BSB4 ATGA1_HUMAN 1 218 SEQADV 5XUY ALA B 40 UNP Q9BSB4 LYS 40 ENGINEERED MUTATION SEQADV 5XUY ALA B 41 UNP Q9BSB4 LYS 41 ENGINEERED MUTATION SEQADV 5XUY ALA B 42 UNP Q9BSB4 GLU 42 ENGINEERED MUTATION SEQADV 5XUY ALA D 40 UNP Q9BSB4 LYS 40 ENGINEERED MUTATION SEQADV 5XUY ALA D 41 UNP Q9BSB4 LYS 41 ENGINEERED MUTATION SEQADV 5XUY ALA D 42 UNP Q9BSB4 GLU 42 ENGINEERED MUTATION SEQRES 1 A 190 MET GLU THR ASP LEU ASN SER GLN ASP ARG LYS ASP LEU SEQRES 2 A 190 ASP LYS PHE ILE LYS PHE PHE ALA LEU LYS THR VAL GLN SEQRES 3 A 190 VAL ILE VAL GLN ALA ARG LEU GLY GLU LYS ILE CYS THR SEQRES 4 A 190 ARG SER SER SER SER PRO THR GLY SER ASP TRP PHE ASN SEQRES 5 A 190 LEU ALA ILE LYS ASP ILE PRO GLU VAL THR HIS GLU ALA SEQRES 6 A 190 LYS LYS ALA LEU ALA GLY GLN LEU PRO ALA VAL GLY ARG SEQRES 7 A 190 SER MET CYS VAL GLU ILE SER LEU LYS THR SER GLU GLY SEQRES 8 A 190 ASP SER MET GLU LEU GLU ILE TRP CYS LEU GLU MET ASN SEQRES 9 A 190 GLU LYS CYS ASP LYS GLU ILE LYS VAL SER TYR THR VAL SEQRES 10 A 190 TYR ASN ARG LEU SER LEU LEU LEU LYS SER LEU LEU ALA SEQRES 11 A 190 ILE THR ARG VAL THR PRO ALA TYR ARG LEU SER ARG LYS SEQRES 12 A 190 GLN GLY HIS GLU TYR VAL ILE LEU TYR ARG ILE TYR PHE SEQRES 13 A 190 GLY GLU VAL GLN LEU SER GLY LEU GLY GLU GLY PHE GLN SEQRES 14 A 190 THR VAL ARG VAL GLY THR VAL GLY THR PRO VAL GLY THR SEQRES 15 A 190 ILE THR LEU SER CYS ALA TYR ARG SEQRES 1 B 218 MET ASN CYS ARG SER GLU VAL LEU GLU VAL SER VAL GLU SEQRES 2 B 218 GLY ARG GLN VAL GLU GLU ALA MET LEU ALA VAL LEU HIS SEQRES 3 B 218 THR VAL LEU LEU HIS ARG SER THR GLY LYS PHE HIS TYR SEQRES 4 B 218 ALA ALA ALA GLY THR TYR SER ILE GLY THR VAL GLY THR SEQRES 5 B 218 GLN ASP VAL ASP CYS ASP PHE ILE ASP PHE THR TYR VAL SEQRES 6 B 218 ARG VAL SER SER GLU GLU LEU ASP ARG ALA LEU ARG LYS SEQRES 7 B 218 VAL VAL GLY GLU PHE LYS ASP ALA LEU ARG ASN SER GLY SEQRES 8 B 218 GLY ASP GLY LEU GLY GLN MET SER LEU GLU PHE TYR GLN SEQRES 9 B 218 LYS LYS LYS SER ARG TRP PRO PHE SER ASP GLU CYS ILE SEQRES 10 B 218 PRO TRP GLU VAL TRP THR VAL LYS VAL HIS VAL VAL ALA SEQRES 11 B 218 LEU ALA THR GLU GLN GLU ARG GLN ILE CYS ARG GLU LYS SEQRES 12 B 218 VAL GLY GLU LYS LEU CYS GLU LYS ILE ILE ASN ILE VAL SEQRES 13 B 218 GLU VAL MET ASN ARG HIS GLU TYR LEU PRO LYS MET PRO SEQRES 14 B 218 THR GLN SER GLU VAL ASP ASN VAL PHE ASP THR GLY LEU SEQRES 15 B 218 ARG ASP VAL GLN PRO TYR LEU TYR LYS ILE SER PHE GLN SEQRES 16 B 218 ILE THR ASP ALA LEU GLY THR SER VAL THR THR THR MET SEQRES 17 B 218 ARG ARG LEU ILE LYS ASP THR LEU ALA LEU SEQRES 1 C 190 MET GLU THR ASP LEU ASN SER GLN ASP ARG LYS ASP LEU SEQRES 2 C 190 ASP LYS PHE ILE LYS PHE PHE ALA LEU LYS THR VAL GLN SEQRES 3 C 190 VAL ILE VAL GLN ALA ARG LEU GLY GLU LYS ILE CYS THR SEQRES 4 C 190 ARG SER SER SER SER PRO THR GLY SER ASP TRP PHE ASN SEQRES 5 C 190 LEU ALA ILE LYS ASP ILE PRO GLU VAL THR HIS GLU ALA SEQRES 6 C 190 LYS LYS ALA LEU ALA GLY GLN LEU PRO ALA VAL GLY ARG SEQRES 7 C 190 SER MET CYS VAL GLU ILE SER LEU LYS THR SER GLU GLY SEQRES 8 C 190 ASP SER MET GLU LEU GLU ILE TRP CYS LEU GLU MET ASN SEQRES 9 C 190 GLU LYS CYS ASP LYS GLU ILE LYS VAL SER TYR THR VAL SEQRES 10 C 190 TYR ASN ARG LEU SER LEU LEU LEU LYS SER LEU LEU ALA SEQRES 11 C 190 ILE THR ARG VAL THR PRO ALA TYR ARG LEU SER ARG LYS SEQRES 12 C 190 GLN GLY HIS GLU TYR VAL ILE LEU TYR ARG ILE TYR PHE SEQRES 13 C 190 GLY GLU VAL GLN LEU SER GLY LEU GLY GLU GLY PHE GLN SEQRES 14 C 190 THR VAL ARG VAL GLY THR VAL GLY THR PRO VAL GLY THR SEQRES 15 C 190 ILE THR LEU SER CYS ALA TYR ARG SEQRES 1 D 218 MET ASN CYS ARG SER GLU VAL LEU GLU VAL SER VAL GLU SEQRES 2 D 218 GLY ARG GLN VAL GLU GLU ALA MET LEU ALA VAL LEU HIS SEQRES 3 D 218 THR VAL LEU LEU HIS ARG SER THR GLY LYS PHE HIS TYR SEQRES 4 D 218 ALA ALA ALA GLY THR TYR SER ILE GLY THR VAL GLY THR SEQRES 5 D 218 GLN ASP VAL ASP CYS ASP PHE ILE ASP PHE THR TYR VAL SEQRES 6 D 218 ARG VAL SER SER GLU GLU LEU ASP ARG ALA LEU ARG LYS SEQRES 7 D 218 VAL VAL GLY GLU PHE LYS ASP ALA LEU ARG ASN SER GLY SEQRES 8 D 218 GLY ASP GLY LEU GLY GLN MET SER LEU GLU PHE TYR GLN SEQRES 9 D 218 LYS LYS LYS SER ARG TRP PRO PHE SER ASP GLU CYS ILE SEQRES 10 D 218 PRO TRP GLU VAL TRP THR VAL LYS VAL HIS VAL VAL ALA SEQRES 11 D 218 LEU ALA THR GLU GLN GLU ARG GLN ILE CYS ARG GLU LYS SEQRES 12 D 218 VAL GLY GLU LYS LEU CYS GLU LYS ILE ILE ASN ILE VAL SEQRES 13 D 218 GLU VAL MET ASN ARG HIS GLU TYR LEU PRO LYS MET PRO SEQRES 14 D 218 THR GLN SER GLU VAL ASP ASN VAL PHE ASP THR GLY LEU SEQRES 15 D 218 ARG ASP VAL GLN PRO TYR LEU TYR LYS ILE SER PHE GLN SEQRES 16 D 218 ILE THR ASP ALA LEU GLY THR SER VAL THR THR THR MET SEQRES 17 D 218 ARG ARG LEU ILE LYS ASP THR LEU ALA LEU FORMUL 5 HOH *101(H2 O) HELIX 1 AA1 SER A 7 ARG A 32 1 26 HELIX 2 AA2 ASP A 49 LEU A 53 5 5 HELIX 3 AA3 ILE A 58 ALA A 70 1 13 HELIX 4 AA4 TYR A 115 THR A 132 1 18 HELIX 5 AA5 THR A 135 ARG A 142 1 8 HELIX 6 AA6 GLN B 16 ARG B 32 1 17 HELIX 7 AA7 GLU B 71 GLY B 91 1 21 HELIX 8 AA8 THR B 133 HIS B 162 1 30 HELIX 9 AA9 GLU B 173 VAL B 177 5 5 HELIX 10 AB1 SER C 7 ARG C 32 1 26 HELIX 11 AB2 ASP C 49 LEU C 53 5 5 HELIX 12 AB3 ILE C 58 ALA C 70 1 13 HELIX 13 AB4 TYR C 115 THR C 132 1 18 HELIX 14 AB5 THR C 135 ARG C 142 1 8 HELIX 15 AB6 LEU C 161 GLY C 165 5 5 HELIX 16 AB7 GLN D 16 ARG D 32 1 17 HELIX 17 AB8 SER D 69 SER D 90 1 22 HELIX 18 AB9 THR D 133 ASN D 160 1 28 HELIX 19 AC1 GLU D 173 VAL D 177 5 5 HELIX 20 AC2 THR D 205 THR D 215 1 11 SHEET 1 AA1 5 ILE A 150 GLY A 157 0 SHEET 2 AA1 5 SER A 79 LEU A 86 -1 N SER A 79 O GLY A 157 SHEET 3 AA1 5 MET A 94 MET A 103 -1 O GLU A 97 N ILE A 84 SHEET 4 AA1 5 GLY A 181 TYR A 189 -1 O THR A 184 N GLU A 102 SHEET 5 AA1 5 GLN A 169 THR A 178 -1 N GLY A 174 O LEU A 185 SHEET 1 AA2 4 ARG B 4 GLU B 13 0 SHEET 2 AA2 4 GLU B 115 VAL B 129 1 O HIS B 127 N VAL B 10 SHEET 3 AA2 4 GLY B 96 LYS B 106 -1 N PHE B 102 O GLU B 120 SHEET 4 AA2 4 TYR B 190 ILE B 196 -1 O SER B 193 N SER B 99 SHEET 1 AA3 2 SER B 33 THR B 34 0 SHEET 2 AA3 2 GLN B 186 PRO B 187 -1 O GLN B 186 N THR B 34 SHEET 1 AA4 2 PHE B 37 TYR B 39 0 SHEET 2 AA4 2 TYR B 45 ILE B 47 -1 O SER B 46 N HIS B 38 SHEET 1 AA5 2 THR B 52 ASP B 56 0 SHEET 2 AA5 2 THR B 63 VAL B 67 -1 O TYR B 64 N VAL B 55 SHEET 1 AA6 5 TYR C 148 GLY C 157 0 SHEET 2 AA6 5 SER C 79 THR C 88 -1 N GLU C 83 O ARG C 153 SHEET 3 AA6 5 SER C 93 ASN C 104 -1 O LEU C 101 N MET C 80 SHEET 4 AA6 5 GLY C 181 TYR C 189 -1 O THR C 184 N GLU C 102 SHEET 5 AA6 5 GLN C 169 THR C 178 -1 N GLN C 169 O TYR C 189 SHEET 1 AA7 4 ARG D 4 GLU D 13 0 SHEET 2 AA7 4 GLU D 115 VAL D 129 1 O THR D 123 N GLU D 6 SHEET 3 AA7 4 LEU D 95 LYS D 106 -1 N LEU D 100 O TRP D 122 SHEET 4 AA7 4 TYR D 190 ILE D 196 -1 O SER D 193 N SER D 99 SHEET 1 AA8 2 SER D 33 THR D 34 0 SHEET 2 AA8 2 GLN D 186 PRO D 187 -1 O GLN D 186 N THR D 34 SHEET 1 AA9 2 PHE D 37 TYR D 39 0 SHEET 2 AA9 2 TYR D 45 ILE D 47 -1 O SER D 46 N HIS D 38 SHEET 1 AB1 2 THR D 52 ASP D 56 0 SHEET 2 AB1 2 THR D 63 VAL D 67 -1 O ARG D 66 N GLN D 53 CISPEP 1 GLY A 157 GLU A 158 0 -1.35 CISPEP 2 TRP B 110 PRO B 111 0 4.41 CISPEP 3 GLY C 157 GLU C 158 0 -4.99 CISPEP 4 MET D 1 ASN D 2 0 -1.29 CISPEP 5 TRP D 110 PRO D 111 0 2.92 CISPEP 6 GLY D 201 THR D 202 0 -2.70 CRYST1 87.990 125.177 100.760 90.00 102.08 90.00 C 1 2 1 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 0.011365 0.000000 0.002432 0.00000 SCALE2 0.000000 0.007989 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010149 0.00000