HEADER APOPTOSIS 29-AUG-18 6MBE TITLE HUMAN MCL-1 IN COMPLEX WITH THE DESIGNED PEPTIDE DM7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL- COMPND 3 1; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: BCL-2-LIKE PROTEIN 3,BCL2-L-3,BCL-2-RELATED PROTEIN COMPND 6 EAT/MCL1,MCL1/EAT; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DM7; COMPND 10 CHAIN: B; COMPND 11 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: MCL1, BCL2L3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS ANTI-APOPTOTIC BCL-2, INHIBITOR, DESIGN, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR J.M.JENSON,A.E.KEATING REVDAT 4 11-OCT-23 6MBE 1 REMARK REVDAT 3 01-JAN-20 6MBE 1 REMARK REVDAT 2 10-APR-19 6MBE 1 JRNL REVDAT 1 06-MAR-19 6MBE 0 JRNL AUTH V.FRAPPIER,J.M.JENSON,J.ZHOU,G.GRIGORYAN,A.E.KEATING JRNL TITL TERTIARY STRUCTURAL MOTIF SEQUENCE STATISTICS ENABLE FACILE JRNL TITL 2 PREDICTION AND DESIGN OF PEPTIDES THAT BIND ANTI-APOPTOTIC JRNL TITL 3 BFL-1 AND MCL-1. JRNL REF STRUCTURE V. 27 606 2019 JRNL REFN ISSN 1878-4186 JRNL PMID 30773399 JRNL DOI 10.1016/J.STR.2019.01.008 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 10414 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) : 0.192 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1051 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 29.9430 - 4.4899 1.00 1266 146 0.1652 0.1879 REMARK 3 2 4.4899 - 3.5656 1.00 1217 130 0.1663 0.2160 REMARK 3 3 3.5656 - 3.1154 1.00 1196 137 0.2088 0.2221 REMARK 3 4 3.1154 - 2.8308 1.00 1204 134 0.2189 0.2625 REMARK 3 5 2.8308 - 2.6281 1.00 1177 130 0.2199 0.2590 REMARK 3 6 2.6281 - 2.4732 1.00 1210 135 0.2198 0.2248 REMARK 3 7 2.4732 - 2.3494 0.97 1136 128 0.2314 0.2550 REMARK 3 8 2.3494 - 2.2471 0.82 957 111 0.2493 0.2586 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.34 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6MBE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1000236554. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JAN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10429 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 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 (%) : 97.3 REMARK 200 DATA REDUNDANCY : 17.60 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.60400 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: 3PK1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M SODIUM CITRATE PH 6.5, 0.1 M REMARK 280 HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.63333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.31667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 19.31667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 38.63333 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 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 ACE B 0 REMARK 465 NH2 B 23 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 401 DBREF 6MBE A 172 323 UNP Q07820 MCL1_HUMAN 172 323 DBREF 6MBE B 0 23 PDB 6MBE 6MBE 0 23 SEQADV 6MBE GLY A 170 UNP Q07820 EXPRESSION TAG SEQADV 6MBE SER A 171 UNP Q07820 EXPRESSION TAG SEQRES 1 A 154 GLY SER ASP GLU LEU TYR ARG GLN SER LEU GLU ILE ILE SEQRES 2 A 154 SER ARG TYR LEU ARG GLU GLN ALA THR GLY ALA LYS ASP SEQRES 3 A 154 THR LYS PRO MET GLY ARG SER GLY ALA THR SER ARG LYS SEQRES 4 A 154 ALA LEU GLU THR LEU ARG ARG VAL GLY ASP GLY VAL GLN SEQRES 5 A 154 ARG ASN HIS GLU THR ALA PHE GLN GLY MET LEU ARG LYS SEQRES 6 A 154 LEU ASP ILE LYS ASN GLU ASP ASP VAL LYS SER LEU SER SEQRES 7 A 154 ARG VAL MET ILE HIS VAL PHE SER ASP GLY VAL THR ASN SEQRES 8 A 154 TRP GLY ARG ILE VAL THR LEU ILE SER PHE GLY ALA PHE SEQRES 9 A 154 VAL ALA LYS HIS LEU LYS THR ILE ASN GLN GLU SER CYS SEQRES 10 A 154 ILE GLU PRO LEU ALA GLU SER ILE THR ASP VAL LEU VAL SEQRES 11 A 154 ARG THR LYS ARG ASP TRP LEU VAL LYS GLN ARG GLY TRP SEQRES 12 A 154 ASP GLY PHE VAL GLU PHE PHE HIS VAL GLU ASP SEQRES 1 B 24 ACE ASP LYS THR LEU GLU GLU ILE ALA ARG GLU LEU LEU SEQRES 2 B 24 LYS LEU ALA LEU GLU ILE ASP LYS GLU ILE NH2 HET CL A 401 1 HETNAM CL CHLORIDE ION FORMUL 3 CL CL 1- FORMUL 4 HOH *47(H2 O) HELIX 1 AA1 ASP A 172 GLY A 192 1 21 HELIX 2 AA2 SER A 202 HIS A 224 1 23 HELIX 3 AA3 HIS A 224 ASP A 236 1 13 HELIX 4 AA4 ASN A 239 SER A 245 1 7 HELIX 5 AA5 LEU A 246 ILE A 251 1 6 HELIX 6 AA6 HIS A 252 SER A 255 5 4 HELIX 7 AA7 ASN A 260 ILE A 281 1 22 HELIX 8 AA8 ASN A 282 SER A 285 5 4 HELIX 9 AA9 CYS A 286 GLN A 309 1 24 HELIX 10 AB1 ARG A 310 PHE A 319 1 10 HELIX 11 AB2 LYS B 2 LYS B 20 1 19 SITE 1 AC1 4 PRO A 198 MET A 199 ARG A 207 PHE A 318 CRYST1 80.758 80.758 57.950 90.00 90.00 120.00 P 32 2 1 6 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 0.012383 0.007149 0.000000 0.00000 SCALE2 0.000000 0.014298 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017256 0.00000