HEADER PROTEIN BINDING 10-APR-21 7ELG TITLE LC3B MODIFICATED WITH A COVALENT PROBE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AUTOPHAGY-RELATED PROTEIN LC3 B,AUTOPHAGY-RELATED UBIQUITIN- COMPND 5 LIKE MODIFIER LC3 B,MAP1 LIGHT CHAIN 3-LIKE PROTEIN 2,MAP1A/MAP1B COMPND 6 LIGHT CHAIN 3 B,MAP1A/MAP1B LC3 B,MICROTUBULE-ASSOCIATED PROTEIN 1 COMPND 7 LIGHT CHAIN 3 BETA; 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: MAP1LC3B, MAP1ALC3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, COMPLEX, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.FAN,W.WAN REVDAT 3 29-NOV-23 7ELG 1 REMARK REVDAT 2 16-FEB-22 7ELG 1 JRNL REVDAT 1 13-OCT-21 7ELG 0 JRNL AUTH S.FAN,L.YUE,W.WAN,Y.ZHANG,B.ZHANG,C.OTOMO,Q.LI,T.LIN,J.HU, JRNL AUTH 2 P.XU,M.ZHU,H.TAO,Z.CHEN,L.LI,H.DING,Z.YAO,J.LU,Y.WEN, JRNL AUTH 3 N.ZHANG,M.TAN,K.CHEN,Y.XIE,T.OTOMO,B.ZHOU,H.JIANG,Y.DANG, JRNL AUTH 4 C.LUO JRNL TITL INHIBITION OF AUTOPHAGY BY A SMALL MOLECULE THROUGH COVALENT JRNL TITL 2 MODIFICATION OF THE LC3 PROTEIN. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 60 26105 2021 JRNL REFN ESSN 1521-3773 JRNL PMID 34590387 JRNL DOI 10.1002/ANIE.202109464 REMARK 2 REMARK 2 RESOLUTION. 1.60 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 16025 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 770 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 2.7338 - 2.1701 1.00 3056 151 0.2044 0.2450 REMARK 3 2 2.1701 - 1.8958 1.00 3006 172 0.1916 0.2180 REMARK 3 3 1.8958 - 1.7225 1.00 3023 147 0.2046 0.2265 REMARK 3 4 1.7225 - 1.5990 1.00 3002 131 0.2109 0.2560 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.50 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 : 0.007 1056 REMARK 3 ANGLE : 1.013 1423 REMARK 3 CHIRALITY : 0.058 155 REMARK 3 PLANARITY : 0.005 183 REMARK 3 DIHEDRAL : 16.493 651 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): 12.8016 -2.7713 -3.2960 REMARK 3 T TENSOR REMARK 3 T11: 0.1716 T22: 0.1640 REMARK 3 T33: 0.1797 T12: -0.0053 REMARK 3 T13: 0.0119 T23: 0.0212 REMARK 3 L TENSOR REMARK 3 L11: 1.5216 L22: 1.4787 REMARK 3 L33: 2.4187 L12: 0.3864 REMARK 3 L13: 0.3419 L23: 0.3930 REMARK 3 S TENSOR REMARK 3 S11: -0.0254 S12: 0.0482 S13: -0.0154 REMARK 3 S21: -0.0111 S22: 0.0668 S23: -0.0466 REMARK 3 S31: -0.0463 S32: 0.1495 S33: 0.0001 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 7ELG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-APR-21. REMARK 100 THE DEPOSITION ID IS D_1300021567. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-16 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 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 : 16025 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.599 REMARK 200 RESOLUTION RANGE LOW (A) : 30.402 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.03709 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.7200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.46900 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: 3VTU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULFATE, 0.1M TRI-SODIUM REMARK 280 CITRATE (PH 5.6), 0.2M POTASSIUM SODIUM TARTRATE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.15K 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 17.55400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.39600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.38300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.39600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.55400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.38300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 TOTAL BURIED SURFACE AREA: 160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 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 DBREF 7ELG A 6 123 UNP Q9GZQ8 MLP3B_HUMAN 2 119 SEQADV 7ELG GLY A 1 UNP Q9GZQ8 EXPRESSION TAG SEQADV 7ELG SER A 2 UNP Q9GZQ8 EXPRESSION TAG SEQADV 7ELG PRO A 3 UNP Q9GZQ8 EXPRESSION TAG SEQADV 7ELG GLU A 4 UNP Q9GZQ8 EXPRESSION TAG SEQADV 7ELG PHE A 5 UNP Q9GZQ8 EXPRESSION TAG SEQRES 1 A 123 GLY SER PRO GLU PHE PRO SER GLU LYS THR PHE LYS GLN SEQRES 2 A 123 ARG ARG THR PHE GLU GLN ARG VAL GLU ASP VAL ARG LEU SEQRES 3 A 123 ILE ARG GLU GLN HIS PRO THR LYS ILE PRO VAL ILE ILE SEQRES 4 A 123 GLU ARG TYR LYS GLY GLU LYS GLN LEU PRO VAL LEU ASP SEQRES 5 A 123 LYS THR LYS PHE LEU VAL PRO ASP HIS VAL ASN MET SER SEQRES 6 A 123 GLU LEU ILE LYS ILE ILE ARG ARG ARG LEU GLN LEU ASN SEQRES 7 A 123 ALA ASN GLN ALA PHE PHE LEU LEU VAL ASN GLY HIS SER SEQRES 8 A 123 MET VAL SER VAL SER THR PRO ILE SER GLU VAL TYR GLU SEQRES 9 A 123 SER GLU LYS ASP GLU ASP GLY PHE LEU TYR MET VAL TYR SEQRES 10 A 123 ALA SER GLN GLU THR PHE HET 8Z6 A 201 14 HET SO4 A 202 5 HETNAM 8Z6 2-METHYLIDENE-5-THIOPHEN-2-YL-CYCLOHEXANE-1,3-DIONE HETNAM SO4 SULFATE ION FORMUL 2 8Z6 C11 H10 O2 S FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *77(H2 O) HELIX 1 AA1 THR A 10 ARG A 15 1 6 HELIX 2 AA2 THR A 16 HIS A 31 1 16 HELIX 3 AA3 ASN A 63 LEU A 75 1 13 HELIX 4 AA4 PRO A 98 LYS A 107 1 10 SHEET 1 AA1 5 LYS A 55 PRO A 59 0 SHEET 2 AA1 5 LYS A 34 ARG A 41 -1 N VAL A 37 O PHE A 56 SHEET 3 AA1 5 LEU A 113 ALA A 118 1 O MET A 115 N ILE A 38 SHEET 4 AA1 5 PHE A 84 VAL A 87 -1 N LEU A 86 O VAL A 116 SHEET 5 AA1 5 HIS A 90 SER A 91 -1 O HIS A 90 N VAL A 87 LINK NZ LYS A 53 CAA 8Z6 A 201 1555 1555 1.39 CRYST1 35.108 54.766 60.792 90.00 90.00 90.00 P 21 21 21 4 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 0.028484 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018260 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016450 0.00000