HEADER PROTEIN BINDING, SIGNALING PROTEIN 21-AUG-09 3IQU TITLE CRYSTAL STRUCTURE OF HUMAN 14-3-3 SIGMA IN COMPLEX WITH RAF1 PEPTIDE TITLE 2 (6MER) 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: 6-MER FROM RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN COMPND 8 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 TRANSUCTION, NUCLEUS, PHOSPHOPROTEIN, SECRETED, PROTEIN KEYWDS 2 BINDING, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.OTTMANN,M.WEYAND REVDAT 6 30-OCT-24 3IQU 1 REMARK REVDAT 5 22-NOV-23 3IQU 1 REMARK REVDAT 4 01-NOV-23 3IQU 1 REMARK SEQADV LINK REVDAT 3 01-NOV-17 3IQU 1 REMARK REVDAT 2 27-NOV-13 3IQU 1 JRNL VERSN REVDAT 1 01-SEP-10 3IQU 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. 1.05 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) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 126774 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) : 0.130 REMARK 3 R VALUE (WORKING SET) : 0.129 REMARK 3 FREE R VALUE : 0.151 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6621 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) : 1.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 9002 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.1820 REMARK 3 BIN FREE R VALUE SET COUNT : 465 REMARK 3 BIN FREE R VALUE : 0.1930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1909 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 492 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : 0.90000 REMARK 3 B33 (A**2) : -0.98000 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): 0.022 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.023 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.015 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.652 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.973 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2190 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1543 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3004 ; 2.198 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3824 ; 1.159 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 315 ;12.089 ; 5.063 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 109 ;33.404 ;24.862 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 448 ;13.546 ;15.033 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;16.048 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 334 ; 0.160 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2506 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 433 ; 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): 1324 ; 2.113 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 532 ; 1.074 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2165 ; 3.108 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 866 ; 4.901 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 800 ; 6.741 ; 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): 3733 ; 2.464 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 496 ;15.637 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3666 ; 6.764 ; 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 3IQU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054750. 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 : NULL 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 : 133400 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 200 RESOLUTION RANGE LOW (A) : 34.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39700 REMARK 200 <I/SIGMA(I)> 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: 1YWT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 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 31.36500 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 31.36500 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 41.09000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.08500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.09000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.08500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 31.36500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.09000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.08500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 31.36500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.09000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.08500 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: 4840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 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 235 LIES ON A SPECIAL POSITION. 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 OE2 GLU A 86 O HOH A 478 1.58 REMARK 500 O HOH A 391 O HOH A 465 1.62 REMARK 500 O HOH A 483 O HOH A 644 1.70 REMARK 500 O HOH A 400 O HOH A 454 1.74 REMARK 500 O HOH A 392 O HOH A 466 1.78 REMARK 500 O HOH A 406 O HOH A 433 1.83 REMARK 500 N MET A -2 O HOH A 474 1.85 REMARK 500 O HOH A 390 O HOH A 474 1.86 REMARK 500 O HOH A 415 O HOH A 430 1.87 REMARK 500 O HOH A 390 O HOH A 450 1.88 REMARK 500 O HOH A 485 O HOH A 680 1.94 REMARK 500 O HOH A 423 O HOH A 428 1.98 REMARK 500 O HOH A 309 O HOH A 393 2.00 REMARK 500 O HOH A 417 O HOH A 478 2.00 REMARK 500 CE LYS A 27 O HOH A 476 2.01 REMARK 500 OD CSO A 38 O HOH A 443 2.01 REMARK 500 OE1 GLU A 115 CD1 ILE A 168 2.07 REMARK 500 O HOH A 485 O HOH A 654 2.07 REMARK 500 O HOH A 405 O HOH A 463 2.10 REMARK 500 O HOH A 401 O HOH A 486 2.11 REMARK 500 O HOH A 441 O HOH A 697 2.13 REMARK 500 O HOH A 426 O HOH A 432 2.13 REMARK 500 O HOH A 407 O HOH A 475 2.14 REMARK 500 O HOH A 421 O HOH A 434 2.14 REMARK 500 O HOH A 472 O HOH A 679 2.15 REMARK 500 O HOH A 416 O HOH A 435 2.15 REMARK 500 NZ LYS A 27 O HOH A 476 2.16 REMARK 500 O HOH A 319 O HOH A 439 2.18 REMARK 500 O HOH P 209 O HOH P 477 2.18 REMARK 500 O HOH A 309 O HOH A 413 2.18 REMARK 500 O HOH A 239 O HOH A 457 2.18 REMARK 500 O HOH A 379 O HOH A 460 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 511 O HOH A 607 6444 1.17 REMARK 500 O HOH A 251 O HOH A 625 6444 1.55 REMARK 500 O HOH A 427 O HOH A 674 6444 1.87 REMARK 500 OE1 GLU A 34 O HOH A 258 6444 1.98 REMARK 500 O HOH A 408 O HOH A 408 3454 2.07 REMARK 500 O HOH A 398 O HOH A 471 6444 2.09 REMARK 500 O HOH A 384 O HOH A 449 8545 2.10 REMARK 500 O HOH A 489 O HOH A 489 3455 2.12 REMARK 500 O HOH A 381 O HOH A 658 4555 2.14 REMARK 500 O HOH A 394 O HOH A 448 2454 2.15 REMARK 500 O HOH A 459 O HOH A 652 8445 2.15 REMARK 500 O HOH A 460 O HOH A 528 6444 2.18 REMARK 500 O ALA A -3 O HOH A 448 2454 2.18 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 GLY A -4 N GLY A -4 CA 0.095 REMARK 500 TYR A 84 CG TYR A 84 CD1 -0.126 REMARK 500 TYR A 84 CD1 TYR A 84 CE1 0.198 REMARK 500 TYR A 84 CZ TYR A 84 CE2 -0.078 REMARK 500 GLU A 91 CD GLU A 91 OE2 0.111 REMARK 500 GLU A 115 CG GLU A 115 CD 0.098 REMARK 500 GLU A 115 CD GLU A 115 OE1 0.080 REMARK 500 TYR A 130 CD1 TYR A 130 CE1 0.112 REMARK 500 TYR A 130 CZ TYR A 130 CE2 -0.089 REMARK 500 SER A 158 CB SER A 158 OG 0.099 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 3 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 GLU A 35 OE1 - CD - OE2 ANGL. DEV. = -8.0 DEGREES REMARK 500 TYR A 84 CB - CG - CD1 ANGL. DEV. = -4.4 DEGREES REMARK 500 TYR A 84 CD1 - CE1 - CZ ANGL. DEV. = -8.9 DEGREES REMARK 500 TYR A 130 CD1 - CE1 - CZ ANGL. DEV. = -7.4 DEGREES REMARK 500 ARG A 148 NH1 - CZ - NH2 ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG A 148 NE - CZ - NH2 ANGL. DEV. = -14.8 DEGREES REMARK 500 MET A 155 CG - SD - CE ANGL. DEV. = -11.7 DEGREES REMARK 500 MET A 202 CG - SD - CE ANGL. DEV. = -26.2 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 73.07 -104.29 REMARK 500 HIS A 106 34.38 -144.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ASN A 42 0.07 SIDE CHAIN 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 235 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 2 OE1 REMARK 620 2 HOH A 427 O 84.0 REMARK 620 3 HOH A 498 O 82.0 69.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 233 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 86 OE1 REMARK 620 2 GLU A 86 OE2 53.3 REMARK 620 3 GLU A 89 OE2 101.0 92.4 REMARK 620 4 HOH A 404 O 80.8 133.5 89.5 REMARK 620 5 HOH A 417 O 149.0 97.5 66.6 125.4 REMARK 620 6 HOH A 424 O 147.1 158.8 88.1 67.6 63.4 REMARK 620 7 HOH A 478 O 91.7 38.6 81.4 167.0 59.2 121.0 REMARK 620 N 1 2 3 4 5 6 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 232 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 233 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 234 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 235 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IQJ RELATED DB: PDB REMARK 900 RELATED ID: 3IQV RELATED DB: PDB REMARK 900 RELATED ID: 3CU8 RELATED DB: PDB DBREF 3IQU A 1 231 UNP P31947 1433S_HUMAN 1 231 DBREF 3IQU P 255 260 UNP P04049 RAF1_HUMAN 255 260 SEQADV 3IQU GLY A -4 UNP P31947 EXPRESSION TAG SEQADV 3IQU ALA A -3 UNP P31947 EXPRESSION TAG SEQADV 3IQU MET A -2 UNP P31947 EXPRESSION TAG SEQADV 3IQU GLY A -1 UNP P31947 EXPRESSION TAG SEQADV 3IQU 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 6 GLN ARG SER THR SEP THR MODRES 3IQU CSO A 38 CYS S-HYDROXYCYSTEINE MODRES 3IQU SEP P 259 SER PHOSPHOSERINE HET CSO A 38 7 HET SEP P 259 10 HET CL A 232 1 HET MG A 233 1 HET MG A 234 1 HET MG A 235 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 *492(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 37 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 LEU A 205 1 20 HELIX 10 10 HIS A 206 LEU A 208 5 3 HELIX 11 11 SER A 209 THR A 231 1 23 LINK C SER A 37 N CSO A 38 1555 1555 1.33 LINK C CSO A 38 N GLU A 39 1555 1555 1.31 LINK C THR P 258 N SEP P 259 1555 1555 1.32 LINK C SEP P 259 N THR P 260 1555 1555 1.32 LINK OE1 GLU A 2 MG MG A 235 1555 1555 2.39 LINK OE1 GLU A 75 MG MG A 234 1555 1555 2.49 LINK OE1BGLU A 86 MG MG A 233 1555 1555 2.42 LINK OE2BGLU A 86 MG MG A 233 1555 1555 2.51 LINK OE2 GLU A 89 MG MG A 233 1555 1555 2.35 LINK MG MG A 233 O HOH A 404 1555 1555 2.09 LINK MG MG A 233 O HOH A 417 1555 1555 1.74 LINK MG MG A 233 O HOH A 424 1555 1555 2.49 LINK MG MG A 233 O HOH A 478 1555 1555 2.23 LINK MG MG A 235 O HOH A 427 1555 1555 2.25 LINK MG MG A 235 O HOH A 498 1555 1555 2.52 CISPEP 1 SER A 105 HIS A 106 0 10.28 SITE 1 AC1 2 LYS A 9 HOH A 601 SITE 1 AC2 6 GLU A 86 GLU A 89 HOH A 404 HOH A 417 SITE 2 AC2 6 HOH A 424 HOH A 478 SITE 1 AC3 6 GLU A 75 GLU A 161 HOH A 256 HOH A 273 SITE 2 AC3 6 HOH A 292 HOH A 637 SITE 1 AC4 4 GLU A 2 HOH A 427 HOH A 498 HOH A 674 CRYST1 82.180 112.170 62.730 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 0.012168 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008915 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015941 0.00000