HEADER PROTEIN BINDING 08-AUG-23 8Q53 TITLE CRYSTAL STRUCTURE OF TRUNCATED HUMAN MICROTUBULE-ASSOCIATED PROTEINS TITLE 2 1A/1B LIGHT CHAIN 3B (MAP1LC3B) IN APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 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: MAP1LC3B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS AUTOPHAGY, SGC, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, KEYWDS 2 PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.KUMAR,S.KNAPP,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 1 21-AUG-24 8Q53 0 JRNL AUTH A.KUMAR,S.KNAPP JRNL TITL CRYSTAL STRUCTURE OF TRUNCATED HUMAN MICROTUBULE-ASSOCIATED JRNL TITL 2 PROTEINS 1A/1B LIGHT CHAIN 3B IN APO FORM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 26378 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.250 REMARK 3 FREE R VALUE TEST SET COUNT : 3668 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 42.6100 - 4.0200 0.99 1876 152 0.1591 0.2012 REMARK 3 2 4.0200 - 3.1900 0.93 1748 141 0.1696 0.1859 REMARK 3 3 3.1900 - 2.7900 0.99 1864 146 0.1875 0.1601 REMARK 3 4 2.7900 - 2.5300 0.99 1887 143 0.1907 0.2160 REMARK 3 5 2.5300 - 2.3500 0.98 1856 151 0.1824 0.2112 REMARK 3 6 2.3500 - 2.2100 0.98 1854 141 0.1855 0.2241 REMARK 3 7 2.2100 - 2.1000 0.97 1852 141 0.1933 0.1997 REMARK 3 8 2.1000 - 2.0100 0.97 1822 147 0.1921 0.2224 REMARK 3 9 2.0100 - 1.9300 0.90 1663 135 0.1821 0.2391 REMARK 3 10 1.9300 - 1.8700 0.95 1866 148 0.2017 0.1883 REMARK 3 11 1.8700 - 1.8100 0.97 1793 148 0.2173 0.2231 REMARK 3 12 1.8100 - 1.7600 0.97 1846 144 0.2089 0.1994 REMARK 3 13 1.7600 - 1.7100 0.96 1807 141 0.2006 0.1874 REMARK 3 14 1.7100 - 1.6700 0.97 1797 142 0.1999 0.1979 REMARK 3 15 1.6700 - 1.6300 0.95 1824 139 0.2131 0.2445 REMARK 3 16 1.6300 - 1.6000 0.97 1810 147 0.2289 0.2876 REMARK 3 17 1.6000 - 1.5600 0.94 1774 138 0.2202 0.2344 REMARK 3 18 1.5600 - 1.5400 0.95 1831 147 0.2284 0.2974 REMARK 3 19 1.5400 - 1.5100 0.96 1802 130 0.2479 0.2809 REMARK 3 20 1.5100 - 1.4800 0.94 1798 143 0.2429 0.2490 REMARK 3 21 1.4800 - 1.4600 0.95 1763 136 0.2417 0.2680 REMARK 3 22 1.4600 - 1.4400 0.87 1678 121 0.2486 0.2984 REMARK 3 23 1.4400 - 1.4100 0.94 1811 125 0.2659 0.2762 REMARK 3 24 1.4100 - 1.3900 0.94 1732 136 0.2750 0.3006 REMARK 3 25 1.3900 - 1.3800 0.94 1764 156 0.3021 0.3579 REMARK 3 26 1.3800 - 1.3600 0.92 1789 130 0.3170 0.3292 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.978 1414 REMARK 3 CHIRALITY : 0.084 156 REMARK 3 PLANARITY : 0.013 182 REMARK 3 DIHEDRAL : 7.777 152 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 8Q53 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292132593. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26382 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 42.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.04224 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.1100 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) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.73310 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 36% PEG 8000, 0.1M ACETATE PH 4.7, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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,X,Z+3/4 REMARK 290 4555 Y,-X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.46350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.19525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 8.73175 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 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 SER A 0 REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 SER A 3 REMARK 465 GLU A 4 REMARK 465 GLY A 120 REMARK 465 MET A 121 REMARK 465 LYS A 122 REMARK 465 LEU A 123 REMARK 465 SER A 124 REMARK 465 VAL A 125 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 GLN A 116 CG CD OE1 NE2 REMARK 470 THR A 118 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 O HOH A 312 O HOH A 374 1.81 REMARK 500 O HOH A 380 O HOH A 383 1.86 REMARK 500 O HOH A 322 O HOH A 351 1.91 REMARK 500 O HOH A 322 O HOH A 377 1.94 REMARK 500 NH2 ARG A 10 O HOH A 301 1.98 REMARK 500 O HOH A 325 O HOH A 370 2.09 REMARK 500 O HOH A 372 O HOH A 381 2.13 REMARK 500 OE2 GLU A 97 O HOH A 302 2.14 REMARK 500 O HOH A 350 O HOH A 376 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 364 O HOH A 377 1556 2.14 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 THR A 118 65.91 -108.57 REMARK 500 REMARK 500 REMARK: NULL DBREF 8Q53 A 1 125 UNP Q9GZQ8 MLP3B_HUMAN 1 125 SEQADV 8Q53 SER A 0 UNP Q9GZQ8 EXPRESSION TAG SEQRES 1 A 126 SER MET PRO SER GLU LYS THR PHE LYS GLN ARG ARG THR SEQRES 2 A 126 PHE GLU GLN ARG VAL GLU ASP VAL ARG LEU ILE ARG GLU SEQRES 3 A 126 GLN HIS PRO THR LYS ILE PRO VAL ILE ILE GLU ARG TYR SEQRES 4 A 126 LYS GLY GLU LYS GLN LEU PRO VAL LEU ASP LYS THR LYS SEQRES 5 A 126 PHE LEU VAL PRO ASP HIS VAL ASN MET SER GLU LEU ILE SEQRES 6 A 126 LYS ILE ILE ARG ARG ARG LEU GLN LEU ASN ALA ASN GLN SEQRES 7 A 126 ALA PHE PHE LEU LEU VAL ASN GLY HIS SER MET VAL SER SEQRES 8 A 126 VAL SER THR PRO ILE SER GLU VAL TYR GLU SER GLU LYS SEQRES 9 A 126 ASP GLU ASP GLY PHE LEU TYR MET VAL TYR ALA SER GLN SEQRES 10 A 126 GLU THR PHE GLY MET LYS LEU SER VAL HET EDO A 201 4 HET EDO A 202 4 HET EDO A 203 4 HET EDO A 204 4 HET EDO A 205 4 HET EDO A 206 4 HET EDO A 207 4 HET EDO A 208 4 HET EDO A 209 4 HET CL A 210 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 9(C2 H6 O2) FORMUL 11 CL CL 1- FORMUL 12 HOH *95(H2 O) HELIX 1 AA1 THR A 6 ARG A 11 1 6 HELIX 2 AA2 THR A 12 HIS A 27 1 16 HELIX 3 AA3 ASN A 59 LEU A 71 1 13 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 60.255 60.255 34.927 90.00 90.00 90.00 P 43 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 0.016596 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016596 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028631 0.00000