HEADER PROTEIN BINDING, SIGNALING PROTEIN 20-AUG-09 3IQJ TITLE CRYSTAL STRUCTURE OF HUMAN 14-3-3 SIGMA IN COMPLEX WITH RAF1 PEPTIDE TITLE 2 (10MER) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 14-3-3 PROTEIN SIGMA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-231; COMPND 5 SYNONYM: STRATIFIN, EPITHELIAL CELL MARKER PROTEIN 1; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 10-MER PEPTIDE FROM RAF PROTO-ONCOGENE SERINE/THREONINE- COMPND 8 PROTEIN KINASE; COMPND 9 CHAIN: P; COMPND 10 SYNONYM: C-RAF, CRAF, RAF-1; 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 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 8 OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN) KEYWDS SIGNAL TRANSDUCTION, NUCLEUS, PHOSPHOPROTEIN, SECRETED, ATP-BINDING, KEYWDS 2 DISEASE MUTATION, KINASE, METAL-BINDING, NUCLEOTIDE-BINDING, KEYWDS 3 PHORBOL-ESTER BINDING, PROTO-ONCOGENE, SERINE/THREONINE-PROTEIN KEYWDS 4 KINASE, TRANSFERASE, ZINC-FINGER, PROTEIN BINDING, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.OTTMANN,M.WEYAND REVDAT 6 30-OCT-24 3IQJ 1 REMARK REVDAT 5 22-NOV-23 3IQJ 1 REMARK REVDAT 4 01-NOV-23 3IQJ 1 REMARK SEQADV LINK REVDAT 3 01-NOV-17 3IQJ 1 REMARK REVDAT 2 27-NOV-13 3IQJ 1 JRNL VERSN REVDAT 1 01-SEP-10 3IQJ 0 JRNL AUTH M.MOLZAN,B.SCHUMACHER,C.OTTMANN,A.BALJULS,L.POLZIEN, JRNL AUTH 2 M.WEYAND,P.THIEL,R.ROSE,M.ROSE,P.KUHENNE,M.KAISER,U.R.RAPP, JRNL AUTH 3 J.KUHLMANN,C.OTTMANN JRNL TITL IMPAIRED BINDING OF 14-3-3 TO C-RAF IN NOONAN SYNDROME JRNL TITL 2 SUGGESTS NEW APPROACHES IN DISEASES WITH INCREASED RAS JRNL TITL 3 SIGNALING. JRNL REF MOL.CELL.BIOL. V. 30 4698 2010 JRNL REFN ISSN 0270-7306 JRNL PMID 20679480 JRNL DOI 10.1128/MCB.01636-09 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 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) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 97849 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) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.127 REMARK 3 FREE R VALUE : 0.153 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5105 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) : 1.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7187 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.1520 REMARK 3 BIN FREE R VALUE SET COUNT : 368 REMARK 3 BIN FREE R VALUE : 0.1770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1895 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 429 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.32000 REMARK 3 B22 (A**2) : -0.29000 REMARK 3 B33 (A**2) : -0.03000 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): 0.027 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.029 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.015 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.711 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2149 ; 0.027 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1486 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2953 ; 2.140 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3682 ; 1.116 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 315 ;14.475 ; 5.127 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;30.694 ;24.902 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 419 ;11.348 ;15.036 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;16.528 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 335 ; 0.145 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2458 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 423 ; 0.001 ; 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): 1323 ; 2.389 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 532 ; 1.144 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2158 ; 3.492 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 826 ; 5.080 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 757 ; 7.061 ; 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): 3635 ; 2.556 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 433 ;15.853 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3570 ; 6.352 ; 3.000 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 : 1.40 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 3IQJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054739. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.87314 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 102954 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 34.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.46900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.800 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: 1YWT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES/NAOH PH 7.5, 0.2M CACL2, REMARK 280 28% PEG 400, 5% GLYCEROL, 2MM DTT, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 31.34000 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 31.34000 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 41.30500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.28000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.30500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.28000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 31.34000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.30500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.28000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 31.34000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.30500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.28000 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P 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 0.00000 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 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 MG MG A 265 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 VAL P 263 REMARK 465 HIS P 264 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 LYS A 68 CD CE NZ REMARK 470 GLU A 72 CG CD OE1 OE2 REMARK 470 GLU A 76 CG CD OE1 OE2 REMARK 470 GLU A 110 CD OE1 OE2 REMARK 470 ASP A 138 CG OD1 OD2 REMARK 470 LYS A 160 CE NZ REMARK 470 LYS A 214 CE NZ REMARK 470 ARG P 256 CG CD 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 O HOH A 325 O HOH A 414 1.47 REMARK 500 O HOH A 331 O HOH A 420 1.50 REMARK 500 O LYS A 77 O HOH A 420 1.67 REMARK 500 O HOH A 379 O HOH A 496 1.68 REMARK 500 O HOH A 381 O HOH A 409 1.69 REMARK 500 CG2 THR P 260 O HOH P 404 1.69 REMARK 500 O HOH A 341 O HOH A 400 1.78 REMARK 500 OG SER A 177 O HOH A 414 1.84 REMARK 500 O HOH A 327 O HOH A 418 1.90 REMARK 500 NH2 ARG A 60 O HOH A 392 1.91 REMARK 500 O HOH A 402 O HOH A 464 1.93 REMARK 500 O HOH A 335 O HOH A 406 1.95 REMARK 500 O HOH A 390 O HOH A 403 2.01 REMARK 500 OD1 ASN A 42 O HOH A 397 2.05 REMARK 500 O ALA A -3 O HOH A 349 2.12 REMARK 500 O HOH A 346 O HOH A 416 2.13 REMARK 500 O HOH A 398 O HOH A 424 2.15 REMARK 500 O HOH A 376 O HOH A 436 2.17 REMARK 500 O HOH A 287 O HOH A 368 2.18 REMARK 500 CB THR P 258 O HOH P 344 2.18 REMARK 500 OE2 GLU A 89 O HOH A 346 2.18 REMARK 500 O HOH A 286 O HOH A 349 2.19 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 O HOH A 311 O HOH A 452 4555 1.39 REMARK 500 CD ARG A 142 O HOH A 366 3455 1.55 REMARK 500 O HOH A 362 O HOH A 555 6444 1.88 REMARK 500 OD CSO A 259 O HOH A 483 6444 1.99 REMARK 500 O HOH A 277 O HOH A 277 3454 2.05 REMARK 500 O HOH A 382 O HOH A 415 3555 2.07 REMARK 500 O HOH A 271 O HOH A 499 8445 2.12 REMARK 500 SG CSO A 259 O HOH A 516 6444 2.12 REMARK 500 O HOH A 345 O HOH A 407 4555 2.14 REMARK 500 O HOH A 464 O HOH A 532 3454 2.19 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 SER A 0 CB SER A 0 OG 0.081 REMARK 500 GLU A 256 CD GLU A 256 OE2 -0.072 REMARK 500 TYR A 84 CG TYR A 84 CD1 -0.086 REMARK 500 TYR A 84 CD1 TYR A 84 CE1 0.132 REMARK 500 TYR A 84 CE2 TYR A 84 CD2 -0.099 REMARK 500 GLU A 91 CD GLU A 91 OE2 0.100 REMARK 500 GLU A 115 CD GLU A 115 OE1 0.075 REMARK 500 SER A 177 CB SER A 177 OG -0.083 REMARK 500 GLU A 182 CD GLU A 182 OE1 0.071 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 TYR A 84 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 TYR A 84 CD1 - CE1 - CZ ANGL. DEV. = -7.1 DEGREES REMARK 500 GLU A 86 OE1 - CD - OE2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ARG A 129 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 GLY A 137 C - N - CA ANGL. DEV. = -15.2 DEGREES REMARK 500 ARG A 148 NE - CZ - NH2 ANGL. DEV. = -8.1 DEGREES REMARK 500 MET A 162 CG - SD - CE ANGL. DEV. = -9.7 DEGREES REMARK 500 GLU A 182 CG - CD - OE1 ANGL. DEV. = 16.8 DEGREES REMARK 500 GLU A 182 CG - CD - OE2 ANGL. DEV. = -13.0 DEGREES 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 ARG A 18 72.95 -106.03 REMARK 500 HIS A 106 35.21 -147.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 137 ASP A 138 -146.17 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 MG A 265 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 2 OE1 REMARK 620 2 HOH A 362 O 80.6 REMARK 620 3 HOH A 626 O 80.1 69.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 264 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 89 OE2 REMARK 620 2 HOH A 238 O 103.2 REMARK 620 3 HOH A 338 O 89.5 77.7 REMARK 620 4 HOH A 346 O 63.8 153.8 122.4 REMARK 620 5 HOH A 367 O 94.7 55.4 132.7 101.2 REMARK 620 6 HOH A 416 O 83.2 146.0 68.8 58.6 158.5 REMARK 620 7 HOH A 417 O 167.3 89.3 95.9 103.7 90.2 87.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 266 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 188 OE2 REMARK 620 2 HOH A 453 O 99.7 REMARK 620 3 HOH A 459 O 73.0 85.6 REMARK 620 N 1 2 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 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 265 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 266 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CU8 RELATED DB: PDB REMARK 900 RELATED ID: 3IQU RELATED DB: PDB REMARK 900 RELATED ID: 3IQV RELATED DB: PDB DBREF 3IQJ A 1 231 UNP P31947 1433S_HUMAN 1 231 DBREF 3IQJ P 255 264 UNP P04049 RAF1_HUMAN 255 264 SEQADV 3IQJ GLY A -4 UNP P31947 EXPRESSION TAG SEQADV 3IQJ ALA A -3 UNP P31947 EXPRESSION TAG SEQADV 3IQJ MET A -2 UNP P31947 EXPRESSION TAG SEQADV 3IQJ GLY A -1 UNP P31947 EXPRESSION TAG SEQADV 3IQJ SER A 0 UNP P31947 EXPRESSION TAG SEQRES 1 A 236 GLY ALA MET GLY SER MET GLU ARG ALA SER LEU ILE GLN SEQRES 2 A 236 LYS ALA LYS LEU ALA GLU GLN ALA GLU ARG TYR GLU ASP SEQRES 3 A 236 MET ALA ALA PHE MET LYS GLY ALA VAL GLU LYS GLY GLU SEQRES 4 A 236 GLU LEU SER CSO GLU GLU ARG ASN LEU LEU SER VAL ALA SEQRES 5 A 236 TYR LYS ASN VAL VAL GLY GLY GLN ARG ALA ALA TRP ARG SEQRES 6 A 236 VAL LEU SER SER ILE GLU GLN LYS SER ASN GLU GLU GLY SEQRES 7 A 236 SER GLU GLU LYS GLY PRO GLU VAL ARG GLU TYR ARG GLU SEQRES 8 A 236 LYS VAL GLU THR GLU LEU GLN GLY VAL CYS ASP THR VAL SEQRES 9 A 236 LEU GLY LEU LEU ASP SER HIS LEU ILE LYS GLU ALA GLY SEQRES 10 A 236 ASP ALA GLU SER ARG VAL PHE TYR LEU LYS MET LYS GLY SEQRES 11 A 236 ASP TYR TYR ARG TYR LEU ALA GLU VAL ALA THR GLY ASP SEQRES 12 A 236 ASP LYS LYS ARG ILE ILE ASP SER ALA ARG SER ALA TYR SEQRES 13 A 236 GLN GLU ALA MET ASP ILE SER LYS LYS GLU MET PRO PRO SEQRES 14 A 236 THR ASN PRO ILE ARG LEU GLY LEU ALA LEU ASN PHE SER SEQRES 15 A 236 VAL PHE HIS TYR GLU ILE ALA ASN SER PRO GLU GLU ALA SEQRES 16 A 236 ILE SER LEU ALA LYS THR THR PHE ASP GLU ALA MET ALA SEQRES 17 A 236 ASP LEU HIS THR LEU SER GLU ASP SER TYR LYS ASP SER SEQRES 18 A 236 THR LEU ILE MET GLN LEU LEU ARG ASP ASN LEU THR LEU SEQRES 19 A 236 TRP THR SEQRES 1 P 10 GLN ARG SER THR SEP THR PRO ASN VAL HIS MODRES 3IQJ CSO A 259 CYS S-HYDROXYCYSTEINE MODRES 3IQJ SEP P 259 SER PHOSPHOSERINE HET CSO A 259 11 HET SEP P 259 10 HET CL A 263 1 HET MG A 264 1 HET MG A 265 1 HET MG A 266 1 HETNAM CSO S-HYDROXYCYSTEINE HETNAM SEP PHOSPHOSERINE HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETSYN SEP PHOSPHONOSERINE FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 SEP C3 H8 N O6 P FORMUL 3 CL CL 1- FORMUL 4 MG 3(MG 2+) FORMUL 7 HOH *429(H2 O) HELIX 1 1 GLU A 2 ALA A 16 1 15 HELIX 2 2 ARG A 18 LYS A 32 1 15 HELIX 3 3 SER A 258 ASN A 70 1 34 HELIX 4 4 PRO A 79 SER A 105 1 27 HELIX 5 5 HIS A 106 ALA A 111 1 6 HELIX 6 6 ASP A 113 ALA A 135 1 23 HELIX 7 7 ASP A 139 MET A 162 1 24 HELIX 8 8 ASN A 166 ILE A 183 1 18 HELIX 9 9 SER A 186 ALA A 203 1 18 HELIX 10 10 ASP A 204 LEU A 208 5 5 HELIX 11 11 SER A 209 THR A 231 1 23 LINK C SER A 258 N CSO A 259 1555 1555 1.33 LINK C CSO A 259 N GLU A 260 1555 1555 1.32 LINK C THR P 258 N SEP P 259 1555 1555 1.29 LINK C SEP P 259 N THR P 260 1555 1555 1.33 LINK OE1 GLU A 2 MG MG A 265 1555 1555 2.42 LINK OE2 GLU A 89 MG MG A 264 1555 1555 2.31 LINK OE2 GLU A 188 MG MG A 266 1555 1555 2.32 LINK O HOH A 238 MG MG A 264 1555 1555 2.41 LINK MG MG A 264 O HOH A 338 1555 1555 2.03 LINK MG MG A 264 O HOH A 346 1555 1555 1.71 LINK MG MG A 264 O HOH A 367 1555 1555 2.47 LINK MG MG A 264 O HOH A 416 1555 1555 2.44 LINK MG MG A 264 O HOH A 417 1555 1555 2.46 LINK MG MG A 265 O HOH A 362 1555 1555 2.29 LINK MG MG A 265 O HOH A 626 1555 1555 2.56 LINK MG MG A 266 O HOH A 453 1555 1555 2.35 LINK MG MG A 266 O HOH A 459 1555 1555 2.39 CISPEP 1 SER A 105 HIS A 106 0 15.46 SITE 1 AC1 2 LYS A 9 HOH A 495 SITE 1 AC2 7 GLU A 89 HOH A 238 HOH A 338 HOH A 346 SITE 2 AC2 7 HOH A 367 HOH A 416 HOH A 417 SITE 1 AC3 4 GLU A 2 HOH A 362 HOH A 555 HOH A 626 SITE 1 AC4 6 GLU A 110 GLU A 188 GLU A 256 HOH A 453 SITE 2 AC4 6 HOH A 459 HOH A 462 CRYST1 82.610 112.560 62.680 90.00 90.00 90.00 C 2 2 21 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 0.012105 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008884 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015954 0.00000