HEADER TRANSCRIPTION/DNA 03-AUG-12 4GFB TITLE RAP1/DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-BINDING PROTEIN RAP1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 358-596; COMPND 5 SYNONYM: REPRESSOR/ACTIVATOR SITE-BINDING PROTEIN, SBF-E, TUF; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: TELOMERIC DNA; COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: TELOMERIC DNA; COMPND 13 CHAIN: D; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: RAP1, GRF1, TUF1, YNL216W, N1310; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 12 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 13 ORGANISM_TAXID: 4932; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 17 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 18 ORGANISM_TAXID: 4932 KEYWDS DOUBLE-MYB, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.-V.LE BIHAN,B.MATOT,M.-H.LE DU REVDAT 2 13-SEP-23 4GFB 1 SEQADV REVDAT 1 10-APR-13 4GFB 0 JRNL AUTH Y.V.LE BIHAN,B.MATOT,O.PIETREMENT,M.J.GIRAUD-PANIS, JRNL AUTH 2 S.GASPARINI,E.LE CAM,E.GILSON,B.SCLAVI,S.MIRON,M.H.LE DU JRNL TITL EFFECT OF RAP1 BINDING ON DNA DISTORTION AND POTASSIUM JRNL TITL 2 PERMANGANATE HYPERSENSITIVITY. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 409 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 23519416 JRNL DOI 10.1107/S0907444912049311 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.MATOT,Y.-V.LE BIHAN,R.LESCASSE,J.PEREZ,S.MIRON,G.DAVID, REMARK 1 AUTH 2 B.CASTAING,P.WEBER,B.RAYNAL,S.ZINN-JUSTIN,S.GASPARINI, REMARK 1 AUTH 3 M.-H.LE DU REMARK 1 TITL THE ORIENTATION OF THE C-TERMINAL DOMAIN OF THE REMARK 1 TITL 2 SACCHAROMYCES CEREVISIAE RAP1 PROTEIN IS DETERMINED BY ITS REMARK 1 TITL 3 BINDING TO DNA. REMARK 1 REF NUCLEIC ACIDS RES. V. 40 3197 2012 REMARK 1 REFN ISSN 0305-1048 REMARK 1 PMID 22139930 REMARK 2 REMARK 2 RESOLUTION. 2.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.8.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11279 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 603 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 : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.99 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.27 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2714 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2529 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2578 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE : 0.3652 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.01 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 136 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 : 1813 REMARK 3 NUCLEIC ACID ATOMS : 1231 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 12 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 66.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -16.21020 REMARK 3 B22 (A**2) : 7.56610 REMARK 3 B33 (A**2) : 8.64410 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) : 0.415 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.915 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.851 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3238 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4633 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1364 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 48 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 331 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3238 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 414 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 3375 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.41 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.81 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 22.54 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4GFB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074110. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11279 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.990 REMARK 200 RESOLUTION RANGE LOW (A) : 36.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.12100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.70100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 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: 3UKG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS-HCL PH 8.0, 20% PEGMME-550, REMARK 280 100MM CACL2, 5% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-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 31.91500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 74.72500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 61.32500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 74.72500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.91500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 61.32500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 31.91500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.32500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 74.72500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.32500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.91500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 74.72500 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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 LYS A 331 REMARK 465 HIS A 332 REMARK 465 HIS A 333 REMARK 465 HIS A 334 REMARK 465 HIS A 335 REMARK 465 HIS A 336 REMARK 465 HIS A 337 REMARK 465 PRO A 338 REMARK 465 MET A 339 REMARK 465 SER A 340 REMARK 465 ASP A 341 REMARK 465 TYR A 342 REMARK 465 ASP A 343 REMARK 465 ILE A 344 REMARK 465 PRO A 345 REMARK 465 THR A 346 REMARK 465 THR A 347 REMARK 465 GLU A 348 REMARK 465 ASN A 349 REMARK 465 LEU A 350 REMARK 465 TYR A 351 REMARK 465 PHE A 352 REMARK 465 GLN A 353 REMARK 465 GLY A 354 REMARK 465 ALA A 355 REMARK 465 MET A 356 REMARK 465 ALA A 357 REMARK 465 ASP A 483 REMARK 465 GLU A 484 REMARK 465 ASP A 485 REMARK 465 THR A 486 REMARK 465 PRO A 487 REMARK 465 THR A 488 REMARK 465 ALA A 489 REMARK 465 ILE A 490 REMARK 465 ALA A 491 REMARK 465 ARG A 492 REMARK 465 ARG A 493 REMARK 465 ASN A 494 REMARK 465 MET A 495 REMARK 465 THR A 496 REMARK 465 MET A 497 REMARK 465 ASP A 498 REMARK 465 PRO A 499 REMARK 465 ASN A 500 REMARK 465 HIS A 501 REMARK 465 LYS A 582 REMARK 465 ALA A 596 REMARK 465 LYS A 597 REMARK 465 ARG A 598 REMARK 465 ALA A 599 REMARK 465 ARG A 600 REMARK 465 ASN A 601 REMARK 465 TYR A 602 REMARK 465 DA C 7 REMARK 465 DC C 8 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 805 O HOH A 805 7556 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 DT D 4 O3' DT D 4 C3' -0.064 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 DG C 1 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 DT C 2 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG C 3 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT C 4 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 DG C 5 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG C 5 O4' - C1' - N9 ANGL. DEV. = 7.9 DEGREES REMARK 500 DG C 5 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 DA C 6 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA C 9 C1' - O4' - C4' ANGL. DEV. = -9.2 DEGREES REMARK 500 DA C 9 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 DA C 9 N9 - C1' - C2' ANGL. DEV. = 8.7 DEGREES REMARK 500 DA C 9 O4' - C1' - N9 ANGL. DEV. = 13.2 DEGREES REMARK 500 DA C 9 C3' - O3' - P ANGL. DEV. = 9.4 DEGREES REMARK 500 DC C 10 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 DC C 10 C3' - O3' - P ANGL. DEV. = 14.4 DEGREES REMARK 500 DC C 11 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC C 11 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES REMARK 500 DA C 12 C3' - O3' - P ANGL. DEV. = 12.8 DEGREES REMARK 500 DC C 13 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC C 13 C3' - O3' - P ANGL. DEV. = 10.9 DEGREES REMARK 500 DA C 14 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 DC C 15 C5' - C4' - O4' ANGL. DEV. = 7.2 DEGREES REMARK 500 DC C 15 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC C 18 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC C 20 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC C 21 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC C 22 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 DA C 23 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES REMARK 500 DC C 26 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 DC C 26 C3' - O3' - P ANGL. DEV. = 10.3 DEGREES REMARK 500 DA C 27 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 DA C 27 C3' - O3' - P ANGL. DEV. = 11.1 DEGREES REMARK 500 DC C 28 C3' - O3' - P ANGL. DEV. = 13.7 DEGREES REMARK 500 DG C 31 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA D 1 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 DA D 1 C3' - O3' - P ANGL. DEV. = 11.1 DEGREES REMARK 500 DC D 2 C3' - O3' - P ANGL. DEV. = 13.0 DEGREES REMARK 500 DG D 5 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES REMARK 500 DT D 7 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG D 10 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG D 10 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DG D 12 O4' - C1' - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG D 13 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 DT D 15 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG D 16 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG D 16 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES REMARK 500 DT D 18 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DG D 19 O4' - C1' - N9 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT D 20 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG D 21 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 63 ANGLE DEVIATIONS. 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 THR A 384 -169.40 -71.36 REMARK 500 GLU A 416 -61.75 70.97 REMARK 500 ASP A 432 45.45 -99.83 REMARK 500 LEU A 469 -77.69 -67.31 REMARK 500 ASP A 475 109.82 73.12 REMARK 500 THR A 476 -59.19 100.56 REMARK 500 ARG A 478 111.61 77.93 REMARK 500 PRO A 503 79.58 -68.96 REMARK 500 PHE A 509 124.85 -31.94 REMARK 500 GLN A 515 95.54 31.92 REMARK 500 SER A 516 -6.47 67.64 REMARK 500 HIS A 533 77.91 -119.41 REMARK 500 GLN A 567 24.06 -76.73 REMARK 500 ASN A 568 11.88 54.91 REMARK 500 PRO A 584 -81.01 -52.41 REMARK 500 VAL A 586 87.77 42.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UKG RELATED DB: PDB DBREF 4GFB A 358 602 UNP P11938 RAP1_YEAST 358 602 DBREF 4GFB C 1 31 PDB 4GFB 4GFB 1 31 DBREF 4GFB D 1 31 PDB 4GFB 4GFB 1 31 SEQADV 4GFB LYS A 331 UNP P11938 EXPRESSION TAG SEQADV 4GFB HIS A 332 UNP P11938 EXPRESSION TAG SEQADV 4GFB HIS A 333 UNP P11938 EXPRESSION TAG SEQADV 4GFB HIS A 334 UNP P11938 EXPRESSION TAG SEQADV 4GFB HIS A 335 UNP P11938 EXPRESSION TAG SEQADV 4GFB HIS A 336 UNP P11938 EXPRESSION TAG SEQADV 4GFB HIS A 337 UNP P11938 EXPRESSION TAG SEQADV 4GFB PRO A 338 UNP P11938 EXPRESSION TAG SEQADV 4GFB MET A 339 UNP P11938 EXPRESSION TAG SEQADV 4GFB SER A 340 UNP P11938 EXPRESSION TAG SEQADV 4GFB ASP A 341 UNP P11938 EXPRESSION TAG SEQADV 4GFB TYR A 342 UNP P11938 EXPRESSION TAG SEQADV 4GFB ASP A 343 UNP P11938 EXPRESSION TAG SEQADV 4GFB ILE A 344 UNP P11938 EXPRESSION TAG SEQADV 4GFB PRO A 345 UNP P11938 EXPRESSION TAG SEQADV 4GFB THR A 346 UNP P11938 EXPRESSION TAG SEQADV 4GFB THR A 347 UNP P11938 EXPRESSION TAG SEQADV 4GFB GLU A 348 UNP P11938 EXPRESSION TAG SEQADV 4GFB ASN A 349 UNP P11938 EXPRESSION TAG SEQADV 4GFB LEU A 350 UNP P11938 EXPRESSION TAG SEQADV 4GFB TYR A 351 UNP P11938 EXPRESSION TAG SEQADV 4GFB PHE A 352 UNP P11938 EXPRESSION TAG SEQADV 4GFB GLN A 353 UNP P11938 EXPRESSION TAG SEQADV 4GFB GLY A 354 UNP P11938 EXPRESSION TAG SEQADV 4GFB ALA A 355 UNP P11938 EXPRESSION TAG SEQADV 4GFB MET A 356 UNP P11938 EXPRESSION TAG SEQADV 4GFB ALA A 357 UNP P11938 EXPRESSION TAG SEQRES 1 A 272 LYS HIS HIS HIS HIS HIS HIS PRO MET SER ASP TYR ASP SEQRES 2 A 272 ILE PRO THR THR GLU ASN LEU TYR PHE GLN GLY ALA MET SEQRES 3 A 272 ALA HIS ASN LYS ALA SER PHE THR ASP GLU GLU ASP GLU SEQRES 4 A 272 PHE ILE LEU ASP VAL VAL ARG LYS ASN PRO THR ARG ARG SEQRES 5 A 272 THR THR HIS THR LEU TYR ASP GLU ILE SER HIS TYR VAL SEQRES 6 A 272 PRO ASN HIS THR GLY ASN SER ILE ARG HIS ARG PHE ARG SEQRES 7 A 272 VAL TYR LEU SER LYS ARG LEU GLU TYR VAL TYR GLU VAL SEQRES 8 A 272 ASP LYS PHE GLY LYS LEU VAL ARG ASP ASP ASP GLY ASN SEQRES 9 A 272 LEU ILE LYS THR LYS VAL LEU PRO PRO SER ILE LYS ARG SEQRES 10 A 272 LYS PHE SER ALA ASP GLU ASP TYR THR LEU ALA ILE ALA SEQRES 11 A 272 VAL LYS LYS GLN PHE TYR ARG ASP LEU PHE GLN ILE ASP SEQRES 12 A 272 PRO ASP THR GLY ARG SER LEU ILE THR ASP GLU ASP THR SEQRES 13 A 272 PRO THR ALA ILE ALA ARG ARG ASN MET THR MET ASP PRO SEQRES 14 A 272 ASN HIS VAL PRO GLY SER GLU PRO ASN PHE ALA ALA TYR SEQRES 15 A 272 ARG THR GLN SER ARG ARG GLY PRO ILE ALA ARG GLU PHE SEQRES 16 A 272 PHE LYS HIS PHE ALA GLU GLU HIS ALA ALA HIS THR GLU SEQRES 17 A 272 ASN ALA TRP ARG ASP ARG PHE ARG LYS PHE LEU LEU ALA SEQRES 18 A 272 TYR GLY ILE ASP ASP TYR ILE SER TYR TYR GLU ALA GLU SEQRES 19 A 272 LYS ALA GLN ASN ARG GLU PRO GLU PRO MET LYS ASN LEU SEQRES 20 A 272 THR ASN ARG PRO LYS ARG PRO GLY VAL PRO THR PRO GLY SEQRES 21 A 272 ASN TYR ASN SER ALA ALA LYS ARG ALA ARG ASN TYR SEQRES 1 C 31 DG DT DG DT DG DA DA DC DA DC DC DA DC SEQRES 2 C 31 DA DC DA DA DC DA DC DC DC DA DC DA DC SEQRES 3 C 31 DA DC DC DA DG SEQRES 1 D 31 DA DC DC DT DG DG DT DG DT DG DT DG DG SEQRES 2 D 31 DG DT DG DT DT DG DT DG DT DG DG DT DG SEQRES 3 D 31 DT DT DC DA DC HET CA A 701 1 HETNAM CA CALCIUM ION FORMUL 4 CA CA 2+ FORMUL 5 HOH *12(H2 O) HELIX 1 1 THR A 364 ASN A 378 1 15 HELIX 2 2 PRO A 379 ARG A 382 5 4 HELIX 3 3 HIS A 385 SER A 392 1 8 HELIX 4 4 THR A 399 LEU A 411 1 13 HELIX 5 5 SER A 412 LEU A 415 5 4 HELIX 6 6 SER A 450 GLN A 471 1 22 HELIX 7 7 ALA A 522 HIS A 533 1 12 HELIX 8 8 THR A 537 PHE A 548 1 12 HELIX 9 9 PHE A 548 GLY A 553 1 6 HELIX 10 10 GLY A 553 GLN A 567 1 15 SHEET 1 A 2 VAL A 418 TYR A 419 0 SHEET 2 A 2 LYS A 437 THR A 438 -1 O THR A 438 N VAL A 418 CISPEP 1 GLY A 477 ARG A 478 0 -0.82 CISPEP 2 GLY A 504 SER A 505 0 0.49 CISPEP 3 PHE A 509 ALA A 510 0 9.81 CISPEP 4 GLY A 519 PRO A 520 0 -0.29 CRYST1 63.830 122.650 149.450 90.00 90.00 90.00 I 21 21 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 0.015667 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008153 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006691 0.00000