HEADER HYDROLASE 29-JUN-21 7RA0 TITLE LC3A IN COMPLEX WITH FRAGMENT 2-10 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AUTOPHAGY-RELATED PROTEIN LC3 A,AUTOPHAGY-RELATED UBIQUITIN- COMPND 5 LIKE MODIFIER LC3 A,MAP1 LIGHT CHAIN 3-LIKE PROTEIN 1,MAP1A/MAP1B COMPND 6 LIGHT CHAIN 3 A,MAP1A/MAP1B LC3 A,MICROTUBULE-ASSOCIATED PROTEIN 1 COMPND 7 LIGHT CHAIN 3 ALPHA; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MAP1LC3A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MATG8, AUTOPHAGY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.ROUGE,M.STEFFEK,E.HELGASON,E.DUEBER,M.MULVIHILL REVDAT 3 25-OCT-23 7RA0 1 REMARK REVDAT 2 15-FEB-23 7RA0 1 JRNL REVDAT 1 12-JAN-22 7RA0 0 JRNL AUTH M.STEFFEK,E.HELGASON,N.POPOVYCH,L.ROUGE,J.M.BRUNING,K.S.LI, JRNL AUTH 2 D.J.BURDICK,J.CAI,T.CRAWFORD,J.XUE,W.DECURTINS,C.FANG, JRNL AUTH 3 F.GRUBERS,M.J.HOLLIDAY,A.LANGLEY,A.PETERSEN,A.L.SATZ,A.SONG, JRNL AUTH 4 D.STOFFLER,Q.STREBEL,J.Y.K.TOM,N.SKELTON,S.T.STABEN, JRNL AUTH 5 M.WICHERT,M.M.MULVIHILL,E.C.DUEBER JRNL TITL A MULTIFACETED HIT-FINDING APPROACH REVEALS NOVEL LC3 FAMILY JRNL TITL 2 LIGANDS. JRNL REF BIOCHEMISTRY V. 62 633 2023 JRNL REFN ISSN 0006-2960 JRNL PMID 34985287 JRNL DOI 10.1021/ACS.BIOCHEM.1C00682 REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 30883 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.490 REMARK 3 FREE R VALUE TEST SET COUNT : 2004 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 33.1000 - 3.2800 1.00 2145 150 0.1622 0.1694 REMARK 3 2 3.2800 - 2.6000 1.00 2086 144 0.1959 0.1996 REMARK 3 3 2.6000 - 2.2700 1.00 2088 144 0.2030 0.2128 REMARK 3 4 2.2700 - 2.0700 1.00 2040 140 0.1948 0.2158 REMARK 3 5 2.0600 - 1.9200 1.00 2075 146 0.1983 0.1999 REMARK 3 6 1.9200 - 1.8000 1.00 2057 146 0.2088 0.2162 REMARK 3 7 1.8000 - 1.7100 1.00 2050 141 0.2149 0.2243 REMARK 3 8 1.7100 - 1.6400 1.00 2068 142 0.2119 0.2279 REMARK 3 9 1.6400 - 1.5800 1.00 2028 142 0.2135 0.2354 REMARK 3 10 1.5800 - 1.5200 1.00 2068 145 0.2122 0.2035 REMARK 3 11 1.5200 - 1.4700 1.00 2036 140 0.2306 0.2473 REMARK 3 12 1.4700 - 1.4300 1.00 2048 142 0.2479 0.2715 REMARK 3 13 1.4300 - 1.3900 1.00 2034 141 0.2698 0.2524 REMARK 3 14 1.3900 - 1.3600 1.00 2056 141 0.2972 0.3224 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.137 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.004 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.04 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 : 0.005 1031 REMARK 3 ANGLE : 0.888 1397 REMARK 3 CHIRALITY : 0.085 149 REMARK 3 PLANARITY : 0.005 183 REMARK 3 DIHEDRAL : 19.210 405 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7RA0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000257860. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAY-18 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 : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30883 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 93.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.21700 REMARK 200 R SYM FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: 3WAL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM FORMATE, 20% PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 46.81100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 46.81100 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.42150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 46.81100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 8.21075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 46.81100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.63225 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 46.81100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.81100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 16.42150 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 46.81100 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 24.63225 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 46.81100 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 8.21075 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 411 LIES ON A SPECIAL POSITION. 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 -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 SER A 3 REMARK 465 PHE A 119 REMARK 465 GLY A 120 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 92 57.21 -92.30 REMARK 500 REMARK 500 REMARK: NULL DBREF 7RA0 A 1 120 UNP Q9H492 MLP3A_HUMAN 1 120 SEQADV 7RA0 GLY A -1 UNP Q9H492 EXPRESSION TAG SEQADV 7RA0 SER A 0 UNP Q9H492 EXPRESSION TAG SEQRES 1 A 122 GLY SER MET PRO SER ASP ARG PRO PHE LYS GLN ARG ARG SEQRES 2 A 122 SER PHE ALA ASP ARG CYS LYS GLU VAL GLN GLN ILE ARG SEQRES 3 A 122 ASP GLN HIS PRO SER LYS ILE PRO VAL ILE ILE GLU ARG SEQRES 4 A 122 TYR LYS GLY GLU LYS GLN LEU PRO VAL LEU ASP LYS THR SEQRES 5 A 122 LYS PHE LEU VAL PRO ASP HIS VAL ASN MET SER GLU LEU SEQRES 6 A 122 VAL LYS ILE ILE ARG ARG ARG LEU GLN LEU ASN PRO THR SEQRES 7 A 122 GLN ALA PHE PHE LEU LEU VAL ASN GLN HIS SER MET VAL SEQRES 8 A 122 SER VAL SER THR PRO ILE ALA ASP ILE TYR GLU GLN GLU SEQRES 9 A 122 LYS ASP GLU ASP GLY PHE LEU TYR MET VAL TYR ALA SER SEQRES 10 A 122 GLN GLU THR PHE GLY HET 2JI A 201 16 HET 2JI A 202 16 HETNAM 2JI (5-ETHYL-2-METHYL-1H-INDOL-3-YL)ACETIC ACID FORMUL 2 2JI 2(C13 H15 N O2) FORMUL 4 HOH *114(H2 O) HELIX 1 AA1 PRO A 6 ARG A 11 1 6 HELIX 2 AA2 SER A 12 HIS A 27 1 16 HELIX 3 AA3 ASN A 59 GLN A 72 1 14 HELIX 4 AA4 PRO A 94 LYS A 103 1 10 SHEET 1 AA1 5 LYS A 51 PRO A 55 0 SHEET 2 AA1 5 LYS A 30 ARG A 37 -1 N ILE A 31 O VAL A 54 SHEET 3 AA1 5 LEU A 109 ALA A 114 1 O MET A 111 N ILE A 34 SHEET 4 AA1 5 PHE A 80 VAL A 83 -1 N LEU A 82 O VAL A 112 SHEET 5 AA1 5 HIS A 86 SER A 87 -1 O HIS A 86 N VAL A 83 CRYST1 93.622 93.622 32.843 90.00 90.00 90.00 I 41 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 0.010681 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010681 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030448 0.00000