HEADER STRUCTURAL PROTEIN 10-AUG-23 7GAS TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF MAP1LC3B IN TITLE 2 COMPLEX WITH Z952016136 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; COMPND 9 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, MAP1ALC3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SGC - DIAMOND I04-1 FRAGMENT SCREENING, PANDDA, XCHEMEXPLORER, KEYWDS 2 STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.KUMAR,P.G.MARPLES,C.W.E.TOMLINSON,D.FEARON,F.VON-DELFT,S.KNAPP, AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 1 04-SEP-24 7GAS 0 JRNL AUTH A.KUMAR,S.KNAPP,STRUCTURAL GENOMICS CONSORTIUM (SGC) JRNL TITL PANDDA ANALYSIS GROUP DEPOSITION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 9624 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 + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 400 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.96 REMARK 3 REFLECTION IN BIN (WORKING SET) : 592 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.4080 REMARK 3 BIN FREE R VALUE SET COUNT : 31 REMARK 3 BIN FREE R VALUE : 0.3690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 954 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.61000 REMARK 3 B22 (A**2) : -0.61000 REMARK 3 B33 (A**2) : 1.22000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.227 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.196 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.241 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.095 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1348 ; 0.008 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 1198 ; 0.001 ; 0.014 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1646 ; 1.549 ; 1.667 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2748 ; 1.199 ; 1.583 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 156 ; 6.362 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 70 ;28.003 ;19.429 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 224 ;14.969 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;24.616 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 152 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1415 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 313 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 625 ; 4.465 ; 5.278 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 623 ; 4.451 ; 5.271 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 740 ; 5.910 ; 7.915 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7GAS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1001405949. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-23 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 : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.92124 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 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10191 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 30.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : 0.14100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 14.40 REMARK 200 R MERGE FOR SHELL (I) : 7.31000 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 8Q53 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 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 17.74800 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 26.62200 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 8.87400 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 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 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 367 O HOH A 373 1.90 REMARK 500 O HOH A 349 O HOH A 362 1.92 REMARK 500 O HOH A 324 O HOH A 371 1.96 REMARK 500 O HOH A 364 O HOH A 388 2.00 REMARK 500 OG1 THR A 6 O HOH A 301 2.05 REMARK 500 O HOH A 325 O HOH A 346 2.17 REMARK 500 O HOH A 312 O HOH A 385 2.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 7GAS A 1 120 UNP Q9GZQ8 MLP3B_HUMAN 1 120 SEQADV 7GAS SER A 0 UNP Q9GZQ8 EXPRESSION TAG SEQRES 1 A 121 SER MET PRO SER GLU LYS THR PHE LYS GLN ARG ARG THR SEQRES 2 A 121 PHE GLU GLN ARG VAL GLU ASP VAL ARG LEU ILE ARG GLU SEQRES 3 A 121 GLN HIS PRO THR LYS ILE PRO VAL ILE ILE GLU ARG TYR SEQRES 4 A 121 LYS GLY GLU LYS GLN LEU PRO VAL LEU ASP LYS THR LYS SEQRES 5 A 121 PHE LEU VAL PRO ASP HIS VAL ASN MET SER GLU LEU ILE SEQRES 6 A 121 LYS ILE ILE ARG ARG ARG LEU GLN LEU ASN ALA ASN GLN SEQRES 7 A 121 ALA PHE PHE LEU LEU VAL ASN GLY HIS SER MET VAL SER SEQRES 8 A 121 VAL SER THR PRO ILE SER GLU VAL TYR GLU SER GLU LYS SEQRES 9 A 121 ASP GLU ASP GLY PHE LEU TYR MET VAL TYR ALA SER GLN SEQRES 10 A 121 GLU THR PHE GLY HET KBU A 201 10 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 KBU 4-CHLORO-1H-BENZIMIDAZOLE HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 KBU C7 H5 CL N2 FORMUL 3 EDO 8(C2 H6 O2) FORMUL 11 CL CL 1- FORMUL 12 HOH *93(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 VAL A 33 O PHE A 52 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 60.854 60.854 35.496 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 0.016433 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016433 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028172 0.00000