PDB Short entry for 4LWU HEADER LIGASE/LIGASE INHIBITOR 28-JUL-13 4LWU TITLE THE 1.14A CRYSTAL STRUCTURE OF HUMANIZED XENOPUS MDM2 WITH RO5499252 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE MDM2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN (UNP RESIDUES 21-105); COMPND 5 SYNONYM: DOUBLE MINUTE 2 PROTEIN, XDM2, P53-BINDING PROTEIN MDM2; COMPND 6 EC: 6.3.2.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: CLAWED FROG,COMMON PLATANNA,PLATANNA; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 GENE: MDM2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PUBS 520 KEYWDS MDM2, SPIROINDOLINONE, E3 UBIQUITIN LIGASE, P53, NUCLEUS, LIGASE- KEYWDS 2 LIGASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.J.GRAVES,C.LUKACS,C.A.JANSON REVDAT 3 28-FEB-24 4LWU 1 REMARK SEQADV REVDAT 2 13-AUG-14 4LWU 1 JRNL REVDAT 1 16-JUL-14 4LWU 0 JRNL AUTH Z.ZHANG,Q.DING,J.J.LIU,J.ZHANG,N.JIANG,X.J.CHU,D.BARTKOVITZ, JRNL AUTH 2 K.C.LUK,C.JANSON,C.TOVAR,Z.M.FILIPOVIC,B.HIGGINS,K.GLENN, JRNL AUTH 3 K.PACKMAN,L.T.VASSILEV,B.GRAVES JRNL TITL DISCOVERY OF POTENT AND SELECTIVE SPIROINDOLINONE MDM2 JRNL TITL 2 INHIBITOR, RO8994, FOR CANCER THERAPY. JRNL REF BIOORG.MED.CHEM. V. 22 4001 2014 JRNL REFN ISSN 0968-0896 JRNL PMID 24997575 JRNL DOI 10.1016/J.BMC.2014.05.072 REMARK 2 REMARK 2 RESOLUTION. 1.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2005 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 889077.520 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 29315 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1471 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.2170 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.2170 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1471 REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : 0.0060 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 29315 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.14 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.20 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3857 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 202 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 690 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 131 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.64000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.65000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.14 REMARK 3 ESD FROM SIGMAA (A) : 0.10 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.15 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.230 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.800 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.150 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.150 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 37.56 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARA REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : RO5499252.PRX REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : RO5499252.TPX REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4LWU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000081185. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99998 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29503 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.140 REMARK 200 RESOLUTION RANGE LOW (A) : 40.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.34700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40-50% SATURATED AMMONIUM SULFATE, REMARK 280 0.1M MES, PH 6.5, 5% PEG200, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z 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 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 20.27700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.17050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.27700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.17050 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 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 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 N THR A 27 O HOH A 399 2.17 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 GLN A 67 -115.62 -119.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 20U A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LWT RELATED DB: PDB REMARK 900 RELATED ID: 4LWV RELATED DB: PDB DBREF 4LWU A 21 105 UNP P56273 MDM2_XENLA 21 105 SEQADV 4LWU LEU A 50 UNP P56273 ILE 50 ENGINEERED MUTATION SEQADV 4LWU HIS A 92 UNP P56273 PRO 92 ENGINEERED MUTATION SEQADV 4LWU ILE A 95 UNP P56273 LEU 95 ENGINEERED MUTATION SEQRES 1 A 85 GLU LYS LEU VAL GLN PRO THR PRO LEU LEU LEU SER LEU SEQRES 2 A 85 LEU LYS SER ALA GLY ALA GLN LYS GLU THR PHE THR MET SEQRES 3 A 85 LYS GLU VAL LEU TYR HIS LEU GLY GLN TYR ILE MET ALA SEQRES 4 A 85 LYS GLN LEU TYR ASP GLU LYS GLN GLN HIS ILE VAL HIS SEQRES 5 A 85 CYS SER ASN ASP PRO LEU GLY GLU LEU PHE GLY VAL GLN SEQRES 6 A 85 GLU PHE SER VAL LYS GLU HIS ARG ARG ILE TYR ALA MET SEQRES 7 A 85 ILE SER ARG ASN LEU VAL SER HET 20U A 201 40 HET SO4 A 202 5 HETNAM 20U (2'S,3R,4'S,5'R)-N-(4-CARBAMOYLPHENYL)-6-CHLORO-4'-(3- HETNAM 2 20U CHLORO-2-FLUOROPHENYL)-2'-(2,2-DIMETHYLPROPYL)-2-OXO- HETNAM 3 20U 1,2-DIHYDROSPIRO[INDOLE-3,3'-PYRROLIDINE]-5'- HETNAM 4 20U CARBOXAMIDE HETNAM SO4 SULFATE ION FORMUL 2 20U C30 H29 CL2 F N4 O3 FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *131(H2 O) HELIX 1 1 THR A 27 ALA A 37 1 11 HELIX 2 2 THR A 45 LYS A 60 1 16 HELIX 3 3 ASP A 76 GLY A 83 1 8 HELIX 4 4 GLU A 91 ARG A 101 1 11 SHEET 1 A 2 ILE A 70 HIS A 72 0 SHEET 2 A 2 GLU A 86 SER A 88 -1 O PHE A 87 N VAL A 71 SITE 1 AC1 15 LEU A 50 ILE A 57 HIS A 69 PHE A 82 SITE 2 AC1 15 GLN A 85 PHE A 87 VAL A 89 LYS A 90 SITE 3 AC1 15 HIS A 92 ILE A 95 TYR A 96 SO4 A 202 SITE 4 AC1 15 HOH A 316 HOH A 375 HOH A 419 SITE 1 AC2 9 TYR A 63 GLU A 65 LYS A 66 HIS A 69 SITE 2 AC2 9 20U A 201 HOH A 304 HOH A 397 HOH A 400 SITE 3 AC2 9 HOH A 419 CRYST1 40.554 78.341 24.703 90.00 90.00 90.00 P 21 21 2 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 0.024658 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012765 0.000000 0.00000 SCALE3 0.000000 0.000000 0.040481 0.00000