PDB Short entry for 1MX4 HEADER CELL CYCLE INHIBITOR 01-OCT-02 1MX4 TITLE STRUCTURE OF P18INK4C (F82Q) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-DEPENDENT KINASE 6 INHIBITOR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: P18-INK6, CYCLIN-DEPENDENT KINASE 4 INHIBITOR C, P18-INK4C; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRSETA KEYWDS ANKYRIN REPEATS, CELL CYCLE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR R.MARMORSTEIN,R.N.VENKATARAMANI,T.K.MACLACHLAN,X.CHAI,W.S.EL-DEIRY REVDAT 4 27-OCT-21 1MX4 1 SEQADV REVDAT 3 24-FEB-09 1MX4 1 VERSN REVDAT 2 25-JAN-05 1MX4 1 JRNL REVDAT 1 16-OCT-02 1MX4 0 JRNL AUTH R.N.VENKATARAMANI,T.K.MACLACHLAN,X.CHAI,W.S.EL-DEIRY, JRNL AUTH 2 R.MARMORSTEIN JRNL TITL STRUCTURE-BASED DESIGN OF P18INK4C PROTEINS WITH INCREASED JRNL TITL 2 THERMODYNAMIC STABILITY AND CELL CYCLE INHIBITORY ACTIVITY JRNL REF J.BIOL.CHEM. V. 277 48827 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 12370184 JRNL DOI 10.1074/JBC.M208061200 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 22818 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 SET) : 0.231 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2282 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2402 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 179 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) : -1.03000 REMARK 3 B22 (A**2) : 3.88600 REMARK 3 B33 (A**2) : -2.85600 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.240 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MX4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-OCT-02. REMARK 100 THE DEPOSITION ID IS D_1000017269. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 8.5 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 : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22818 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : 0.03900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.13800 REMARK 200 R SYM FOR SHELL (I) : 0.13800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 16.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1IHB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5 MG/ML PROTEIN, 20 MM TRIS (PH 8.5), REMARK 280 0.5 MM DTT, 14 % PEG 6000, 2 M NACL, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 273K 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 27.53500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 75.58700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.53500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 75.58700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLU A 3 REMARK 465 PRO A 4 REMARK 465 ALA A 161 REMARK 465 GLY A 162 REMARK 465 GLY A 163 REMARK 465 ALA A 164 REMARK 465 THR A 165 REMARK 465 ASN A 166 REMARK 465 LEU A 167 REMARK 465 GLN A 168 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLU B 3 REMARK 465 GLY B 163 REMARK 465 ALA B 164 REMARK 465 THR B 165 REMARK 465 ASN B 166 REMARK 465 LEU B 167 REMARK 465 GLN B 168 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 ARG A 145 NH2 ARG B 54 3546 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MX2 RELATED DB: PDB REMARK 900 STRUCTURE OF P18INK4C (F71N) REMARK 900 RELATED ID: 1MX6 RELATED DB: PDB REMARK 900 STRUCTURE OF P18INK4C (F92N) DBREF 1MX4 A 1 168 UNP P42773 CDN2C_HUMAN 1 168 DBREF 1MX4 B 1 168 UNP P42773 CDN2C_HUMAN 1 168 SEQADV 1MX4 GLN A 82 UNP P42773 PHE 82 ENGINEERED MUTATION SEQADV 1MX4 GLN B 82 UNP P42773 PHE 82 ENGINEERED MUTATION SEQRES 1 A 168 MET ALA GLU PRO TRP GLY ASN GLU LEU ALA SER ALA ALA SEQRES 2 A 168 ALA ARG GLY ASP LEU GLU GLN LEU THR SER LEU LEU GLN SEQRES 3 A 168 ASN ASN VAL ASN VAL ASN ALA GLN ASN GLY PHE GLY ARG SEQRES 4 A 168 THR ALA LEU GLN VAL MET LYS LEU GLY ASN PRO GLU ILE SEQRES 5 A 168 ALA ARG ARG LEU LEU LEU ARG GLY ALA ASN PRO ASP LEU SEQRES 6 A 168 LYS ASP ARG THR GLY PHE ALA VAL ILE HIS ASP ALA ALA SEQRES 7 A 168 ARG ALA GLY GLN LEU ASP THR LEU GLN THR LEU LEU GLU SEQRES 8 A 168 PHE GLN ALA ASP VAL ASN ILE GLU ASP ASN GLU GLY ASN SEQRES 9 A 168 LEU PRO LEU HIS LEU ALA ALA LYS GLU GLY HIS LEU ARG SEQRES 10 A 168 VAL VAL GLU PHE LEU VAL LYS HIS THR ALA SER ASN VAL SEQRES 11 A 168 GLY HIS ARG ASN HIS LYS GLY ASP THR ALA CYS ASP LEU SEQRES 12 A 168 ALA ARG LEU TYR GLY ARG ASN GLU VAL VAL SER LEU MET SEQRES 13 A 168 GLN ALA ASN GLY ALA GLY GLY ALA THR ASN LEU GLN SEQRES 1 B 168 MET ALA GLU PRO TRP GLY ASN GLU LEU ALA SER ALA ALA SEQRES 2 B 168 ALA ARG GLY ASP LEU GLU GLN LEU THR SER LEU LEU GLN SEQRES 3 B 168 ASN ASN VAL ASN VAL ASN ALA GLN ASN GLY PHE GLY ARG SEQRES 4 B 168 THR ALA LEU GLN VAL MET LYS LEU GLY ASN PRO GLU ILE SEQRES 5 B 168 ALA ARG ARG LEU LEU LEU ARG GLY ALA ASN PRO ASP LEU SEQRES 6 B 168 LYS ASP ARG THR GLY PHE ALA VAL ILE HIS ASP ALA ALA SEQRES 7 B 168 ARG ALA GLY GLN LEU ASP THR LEU GLN THR LEU LEU GLU SEQRES 8 B 168 PHE GLN ALA ASP VAL ASN ILE GLU ASP ASN GLU GLY ASN SEQRES 9 B 168 LEU PRO LEU HIS LEU ALA ALA LYS GLU GLY HIS LEU ARG SEQRES 10 B 168 VAL VAL GLU PHE LEU VAL LYS HIS THR ALA SER ASN VAL SEQRES 11 B 168 GLY HIS ARG ASN HIS LYS GLY ASP THR ALA CYS ASP LEU SEQRES 12 B 168 ALA ARG LEU TYR GLY ARG ASN GLU VAL VAL SER LEU MET SEQRES 13 B 168 GLN ALA ASN GLY ALA GLY GLY ALA THR ASN LEU GLN FORMUL 3 HOH *179(H2 O) HELIX 1 1 TRP A 5 GLY A 16 1 12 HELIX 2 2 ASP A 17 LEU A 25 1 9 HELIX 3 3 THR A 40 MET A 45 1 6 HELIX 4 4 ASN A 49 ARG A 59 1 11 HELIX 5 5 ALA A 72 ALA A 80 1 9 HELIX 6 6 GLN A 82 PHE A 92 1 11 HELIX 7 7 LEU A 105 GLY A 114 1 10 HELIX 8 8 HIS A 115 THR A 126 1 12 HELIX 9 9 THR A 139 TYR A 147 1 9 HELIX 10 10 ARG A 149 ASN A 159 1 11 HELIX 11 11 PRO B 4 GLY B 16 1 13 HELIX 12 12 ASP B 17 ASN B 27 1 11 HELIX 13 13 THR B 40 MET B 45 1 6 HELIX 14 14 ASN B 49 ARG B 59 1 11 HELIX 15 15 ALA B 72 ALA B 80 1 9 HELIX 16 16 GLN B 82 PHE B 92 1 11 HELIX 17 17 LEU B 105 GLU B 113 1 9 HELIX 18 18 HIS B 115 THR B 126 1 12 HELIX 19 19 THR B 139 TYR B 147 1 9 HELIX 20 20 ARG B 149 ASN B 159 1 11 CRYST1 55.070 151.174 40.149 90.00 90.00 90.00 P 21 21 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 0.018159 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006615 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024907 0.00000