HEADER APOPTOSIS 19-OCT-06 2NL9 TITLE CRYSTAL STRUCTURE OF THE MCL-1:BIM BH3 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: FUSION PROTEIN CONSISTING OF INDUCED MYELOID LEUKEMIA CELL COMPND 3 DIFFERENTIATION PROTEIN MCL-1 HOMOLOG; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: RESIDUES 171-208 AND RESIDUES 209-327; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: BCL-2-LIKE PROTEIN 11; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: BCL2-INTERACTING MEDIATOR OF CELL DEATH SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS, HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: MOUSE, HUMAN; SOURCE 4 ORGANISM_TAXID: 10090, 9606; SOURCE 5 GENE: MCL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P3; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS APOPTOSIS, BCL-2, MCL-1, BIM EXPDTA X-RAY DIFFRACTION AUTHOR P.E.CZABOTAR,P.M.COLMAN REVDAT 8 30-OCT-24 2NL9 1 REMARK REVDAT 7 27-DEC-23 2NL9 1 REMARK LINK REVDAT 6 14-JUN-17 2NL9 1 SOURCE REVDAT 5 13-JUL-11 2NL9 1 VERSN REVDAT 4 06-APR-11 2NL9 1 JRNL REVDAT 3 24-FEB-09 2NL9 1 VERSN REVDAT 2 21-AUG-07 2NL9 1 REMARK REVDAT 1 27-MAR-07 2NL9 0 JRNL AUTH P.E.CZABOTAR,E.F.LEE,M.F.VAN DELFT,C.L.DAY,B.J.SMITH, JRNL AUTH 2 D.C.HUANG,W.D.FAIRLIE,M.G.HINDS,P.M.COLMAN JRNL TITL STRUCTURAL INSIGHTS INTO THE DEGRADATION OF MCL-1 INDUCED BY JRNL TITL 2 BH3 DOMAINS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 6217 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17389404 JRNL DOI 10.1073/PNAS.0701297104 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 28898 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1469 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1046 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 47.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE SET COUNT : 52 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1349 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.53000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 0.67000 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): 0.078 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.080 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.044 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.279 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1422 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1928 ; 1.386 ; 1.939 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 180 ; 4.407 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 76 ;30.736 ;22.763 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 260 ;12.505 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;15.317 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 211 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1089 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 830 ; 0.213 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1026 ; 0.320 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 167 ; 0.157 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.044 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 39 ; 0.230 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 33 ; 0.217 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 5 ; 0.043 ; 0.200 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): 863 ; 1.061 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1357 ; 1.604 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 635 ; 2.491 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 562 ; 3.590 ; 4.500 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 172 A 322 REMARK 3 RESIDUE RANGE : B 53 B 75 REMARK 3 ORIGIN FOR THE GROUP (A): 21.1054 14.6340 41.2183 REMARK 3 T TENSOR REMARK 3 T11: -0.0190 T22: -0.0556 REMARK 3 T33: -0.0338 T12: 0.0218 REMARK 3 T13: 0.0046 T23: -0.0139 REMARK 3 L TENSOR REMARK 3 L11: 1.5437 L22: 1.1915 REMARK 3 L33: 1.4584 L12: 0.1293 REMARK 3 L13: 0.3883 L23: -0.2469 REMARK 3 S TENSOR REMARK 3 S11: -0.0281 S12: -0.1429 S13: 0.1107 REMARK 3 S21: 0.1842 S22: -0.0008 S23: 0.0233 REMARK 3 S31: -0.2472 S32: -0.0717 S33: 0.0290 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 REMARK 4 REMARK 4 2NL9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000040001. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791, 0.9792, 0.9715 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK DOUBLE CRYSTAL REMARK 200 SAGITTAL FOCUSING MONOCHROMETER REMARK 200 OPTICS : MONOCHROMETER REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29809 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 85.1 REMARK 200 DATA REDUNDANCY : 10.90 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 160.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 28.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.50300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M ZINC ACETATE, 0.2M IMIDAZOLE, 2MM REMARK 280 TCEP, PH 5.75, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 26.19000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.04000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.59000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.19000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.04000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.59000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.19000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.04000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.59000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.19000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.04000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.59000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -162.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1121.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 52.38000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 52.38000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 117.18000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 117.18000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1004.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 52.38000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 52.38000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 117.18000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 117.18000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 26.19000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 -35.04000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 58.59000 REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 26.19000 REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 35.04000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 58.59000 REMARK 350 BIOMT1 7 -1.000000 0.000000 0.000000 26.19000 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 -35.04000 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 58.59000 REMARK 350 BIOMT1 8 1.000000 0.000000 0.000000 26.19000 REMARK 350 BIOMT2 8 0.000000 -1.000000 0.000000 35.04000 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 58.59000 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 CL CL A2001 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2040 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2115 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 GLU A 171 REMARK 465 LYS A 194 REMARK 465 ASP A 195 REMARK 465 SER A 196 REMARK 465 LYS A 197 REMARK 465 PRO A 198 REMARK 465 LEU A 199 REMARK 465 GLY A 200 REMARK 465 GLU A 201 REMARK 465 ALA A 202 REMARK 465 ASP A 323 REMARK 465 LEU A 324 REMARK 465 GLU A 325 REMARK 465 GLY A 326 REMARK 465 GLY A 327 REMARK 465 ASP B 51 REMARK 465 MET B 52 REMARK 465 ARG B 76 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 173 CG OD1 OD2 REMARK 480 ARG A 176 CD NE CZ NH1 NH2 REMARK 480 GLU A 180 OE1 OE2 REMARK 480 SER A 193 CB OG REMARK 480 ARG A 207 NE CZ NH1 NH2 REMARK 480 ARG A 208 CD NE CZ NH1 NH2 REMARK 480 LYS A 276 NZ REMARK 480 GLN A 283 OE1 NE2 REMARK 480 GLU A 284 CD OE1 OE2 REMARK 480 LYS A 308 CG CD CE NZ REMARK 480 ARG B 53 CD NE CZ NH1 NH2 REMARK 480 ARG B 75 NE CZ NH1 NH2 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 NE2 HIS A 277 O HOH A 2088 2.16 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 NH2 ARG B 75 O HOH A 2137 8455 1.93 REMARK 500 OH TYR B 72 O HOH A 2144 8455 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG B 75 CD ARG B 75 NE 0.112 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 ASN A 223 -18.08 81.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 224 NE2 REMARK 620 2 ASP A 313 OD1 128.2 REMARK 620 3 GLU A 317 OE2 100.5 109.3 REMARK 620 4 GLU B 68 OE1 87.6 83.7 153.7 REMARK 620 5 GLU B 68 OE2 121.2 96.4 96.9 58.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 240 OE2 REMARK 620 2 ASP A 241 OD2 116.7 REMARK 620 3 ASP A 241 OD1 105.5 55.6 REMARK 620 4 GLU A 292 OE2 98.1 134.8 89.0 REMARK 620 5 GLU A 292 OE1 149.6 92.2 82.3 52.1 REMARK 620 6 HOH A2099 O 76.0 101.3 155.5 115.2 109.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1003 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 252 NE2 REMARK 620 2 ASP A 304 OD2 100.3 REMARK 620 3 ZN A1004 ZN 62.9 88.0 REMARK 620 4 HOH A2106 O 113.1 119.6 67.2 REMARK 620 5 HOH B1035 O 108.9 105.8 165.4 108.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1004 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 252 NE2 REMARK 620 2 ASP A 304 OD1 114.2 REMARK 620 3 ASP A 304 OD2 77.5 51.0 REMARK 620 4 HOH A2106 O 103.1 111.7 88.2 REMARK 620 5 HOH A2107 O 123.3 106.9 156.8 95.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1005 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 286 SG REMARK 620 2 CYS A 286 SG 52.9 REMARK 620 3 HOH A2102 O 123.2 130.7 REMARK 620 4 HOH A2103 O 125.5 73.5 97.1 REMARK 620 5 HOH A2104 O 115.1 148.2 81.0 105.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1006 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 286 SG REMARK 620 2 CYS A 286 SG 58.6 REMARK 620 3 HOH A2115 O 88.9 123.5 REMARK 620 4 HOH A2115 O 88.5 122.5 1.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1007 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 320 NE2 REMARK 620 2 GLU A 322 OE1 109.1 REMARK 620 3 GLU A 322 OE2 88.6 63.1 REMARK 620 4 GLU B 61 OE1 145.8 100.2 89.3 REMARK 620 5 GLU B 61 OE2 93.8 152.7 104.1 53.8 REMARK 620 6 HOH B1034 O 94.9 105.4 168.5 93.9 86.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WSX RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF MCL-1 REMARK 900 RELATED ID: 2NLA RELATED DB: PDB DBREF 2NL9 A 171 208 UNP P97287 MCL1_MOUSE 152 189 DBREF 2NL9 A 209 327 UNP Q07820 MCL1_HUMAN 209 327 DBREF 2NL9 B 51 76 UNP O43521 BIM_HUMAN 141 166 SEQRES 1 A 157 GLU ASP ASP LEU TYR ARG GLN SER LEU GLU ILE ILE SER SEQRES 2 A 157 ARG TYR LEU ARG GLU GLN ALA THR GLY SER LYS ASP SER SEQRES 3 A 157 LYS PRO LEU GLY GLU ALA GLY ALA ALA GLY ARG ARG ALA SEQRES 4 A 157 LEU GLU THR LEU ARG ARG VAL GLY ASP GLY VAL GLN ARG SEQRES 5 A 157 ASN HIS GLU THR ALA PHE GLN GLY MSE LEU ARG LYS LEU SEQRES 6 A 157 ASP ILE LYS ASN GLU ASP ASP VAL LYS SER LEU SER ARG SEQRES 7 A 157 VAL MSE ILE HIS VAL PHE SER ASP GLY VAL THR ASN TRP SEQRES 8 A 157 GLY ARG ILE VAL THR LEU ILE SER PHE GLY ALA PHE VAL SEQRES 9 A 157 ALA LYS HIS LEU LYS THR ILE ASN GLN GLU SER CYS ILE SEQRES 10 A 157 GLU PRO LEU ALA GLU SER ILE THR ASP VAL LEU VAL ARG SEQRES 11 A 157 THR LYS ARG ASP TRP LEU VAL LYS GLN ARG GLY TRP ASP SEQRES 12 A 157 GLY PHE VAL GLU PHE PHE HIS VAL GLU ASP LEU GLU GLY SEQRES 13 A 157 GLY SEQRES 1 B 26 ASP MET ARG PRO GLU ILE TRP ILE ALA GLN GLU LEU ARG SEQRES 2 B 26 ARG ILE GLY ASP GLU PHE ASN ALA TYR TYR ALA ARG ARG MODRES 2NL9 MSE A 231 MET SELENOMETHIONINE MODRES 2NL9 MSE A 250 MET SELENOMETHIONINE HET MSE A 231 8 HET MSE A 250 13 HET ZN A1001 1 HET ZN A1002 1 HET ZN A1003 1 HET ZN A1004 1 HET ZN A1005 1 HET ZN A1006 1 HET CL A2001 1 HET ZN B1007 1 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 3 ZN 7(ZN 2+) FORMUL 9 CL CL 1- FORMUL 11 HOH *201(H2 O) HELIX 1 1 ASP A 172 GLY A 192 1 21 HELIX 2 2 GLY A 203 ARG A 222 1 20 HELIX 3 3 HIS A 224 ASP A 236 1 13 HELIX 4 4 VAL A 243 PHE A 254 1 12 HELIX 5 5 SER A 255 GLY A 257 5 3 HELIX 6 6 ASN A 260 ASN A 282 1 23 HELIX 7 7 ILE A 287 LYS A 302 1 16 HELIX 8 8 LYS A 302 GLN A 309 1 8 HELIX 9 9 GLY A 311 PHE A 319 1 9 HELIX 10 10 ARG B 53 ARG B 75 1 23 LINK C GLY A 230 N MSE A 231 1555 1555 1.33 LINK C MSE A 231 N LEU A 232 1555 1555 1.33 LINK C VAL A 249 N MSE A 250 1555 1555 1.32 LINK C MSE A 250 N ILE A 251 1555 1555 1.33 LINK NE2 HIS A 224 ZN ZN A1002 8555 1555 2.04 LINK OE2 GLU A 240 ZN ZN A1001 3656 1555 2.19 LINK OD2 ASP A 241 ZN ZN A1001 3656 1555 2.24 LINK OD1 ASP A 241 ZN ZN A1001 3656 1555 2.40 LINK NE2 HIS A 252 ZN ZN A1003 1555 1555 2.00 LINK NE2 HIS A 252 ZN ZN A1004 1555 1555 2.08 LINK SG ACYS A 286 ZN ZN A1005 1555 1555 2.30 LINK SG BCYS A 286 ZN ZN A1005 1555 1555 2.95 LINK SG ACYS A 286 ZN ZN A1006 1555 1555 2.57 LINK SG BCYS A 286 ZN ZN A1006 1555 1555 2.33 LINK OE2 GLU A 292 ZN ZN A1001 1555 1555 2.10 LINK OE1 GLU A 292 ZN ZN A1001 1555 1555 2.74 LINK OD2 ASP A 304 ZN ZN A1003 2655 1555 2.01 LINK OD1 ASP A 304 ZN ZN A1004 2655 1555 1.98 LINK OD2 ASP A 304 ZN ZN A1004 2655 1555 2.77 LINK OD1 ASP A 313 ZN ZN A1002 1555 1555 2.04 LINK OE2 GLU A 317 ZN ZN A1002 1555 1555 2.00 LINK NE2 HIS A 320 ZN ZN B1007 8455 1555 1.99 LINK OE1 GLU A 322 ZN ZN B1007 8455 1555 2.20 LINK OE2 GLU A 322 ZN ZN B1007 8455 1555 1.98 LINK ZN ZN A1001 O HOH A2099 1555 3656 2.22 LINK ZN ZN A1002 OE1 GLU B 68 1555 8555 2.44 LINK ZN ZN A1002 OE2 GLU B 68 1555 8555 2.10 LINK ZN ZN A1003 ZN ZN A1004 1555 1555 1.98 LINK ZN ZN A1003 O HOH A2106 1555 1555 2.03 LINK ZN ZN A1003 O HOH B1035 1555 1555 2.26 LINK ZN ZN A1004 O HOH A2106 1555 1555 2.22 LINK ZN ZN A1004 O HOH A2107 1555 1555 2.22 LINK ZN ZN A1005 O HOH A2102 1555 1555 2.41 LINK ZN ZN A1005 O HOH A2103 1555 1555 2.34 LINK ZN ZN A1005 O HOH A2104 1555 1555 2.07 LINK ZN ZN A1006 O HOH A2115 1555 3656 2.47 LINK ZN ZN A1006 O HOH A2115 1555 1555 2.46 LINK OE1 GLU B 61 ZN ZN B1007 1555 1555 2.11 LINK OE2 GLU B 61 ZN ZN B1007 1555 1555 2.63 LINK ZN ZN B1007 O HOH B1034 1555 1555 2.26 SITE 1 AC1 4 GLU A 240 ASP A 241 GLU A 292 HOH A2099 SITE 1 AC2 4 HIS A 224 ASP A 313 GLU A 317 GLU B 68 SITE 1 AC3 5 HIS A 252 ASP A 304 ZN A1004 HOH A2106 SITE 2 AC3 5 HOH B1035 SITE 1 AC4 5 HIS A 252 ASP A 304 ZN A1003 HOH A2106 SITE 2 AC4 5 HOH A2107 SITE 1 AC5 4 CYS A 286 HOH A2102 HOH A2103 HOH A2104 SITE 1 AC6 2 CYS A 286 HOH A2115 SITE 1 AC7 4 HIS A 320 GLU A 322 GLU B 61 HOH B1034 SITE 1 AC8 1 ARG A 300 CRYST1 52.380 70.080 117.180 90.00 90.00 90.00 I 2 2 2 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 0.019091 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014269 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008534 0.00000