HEADER DNA BINDING PROTEIN/DNA 09-NOV-11 3UKG TITLE CRYSTAL STRUCTURE OF RAP1/DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-BINDING PROTEIN RAP1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA BINDING DOMAIN, UNP RESIDUES 360-601; 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 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES KEYWDS DOUBLE MYB, TRANSCRIPTION REGULATION, TELOMERES LENGTH REGULATION, KEYWDS 2 TELOMERES PROTECTION, NUCLEUS, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.MATOT,Y.-V.LE BIHAN,S.GASPARINI,M.H.LEDU REVDAT 4 13-SEP-23 3UKG 1 REMARK LINK REVDAT 3 09-MAY-12 3UKG 1 JRNL REVDAT 2 11-JAN-12 3UKG 1 JRNL REVDAT 1 07-DEC-11 3UKG 0 JRNL AUTH B.MATOT,Y.V.LE BIHAN,R.LESCASSE,J.PEREZ,S.MIRON,G.DAVID, JRNL AUTH 2 B.CASTAING,P.WEBER,B.RAYNAL,S.ZINN-JUSTIN,S.GASPARINI, JRNL AUTH 3 M.H.LE DU JRNL TITL THE ORIENTATION OF THE C-TERMINAL DOMAIN OF THE JRNL TITL 2 SACCHAROMYCES CEREVISIAE RAP1 PROTEIN IS DETERMINED BY ITS JRNL TITL 3 BINDING TO DNA. JRNL REF NUCLEIC ACIDS RES. V. 40 3197 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22139930 JRNL DOI 10.1093/NAR/GKR1166 REMARK 2 REMARK 2 RESOLUTION. 2.95 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) : 2.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 10759 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.930 REMARK 3 FREE R VALUE TEST SET COUNT : 961 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 : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.95 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.30 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2911 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2291 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2645 REMARK 3 BIN R VALUE (WORKING SET) : 0.2228 REMARK 3 BIN FREE R VALUE : 0.2943 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.14 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 266 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 : 1854 REMARK 3 NUCLEIC ACID ATOMS : 1271 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 12 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 78.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -11.84680 REMARK 3 B22 (A**2) : 20.46150 REMARK 3 B33 (A**2) : -8.61470 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) : 0.452 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 : 0.902 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.819 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3329 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4766 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1411 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 49 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 343 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3329 ; 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 : 424 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 1 ; 1.000 ; HARMONIC 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 : 3530 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.48 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.05 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 23.16 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|360 - A|447 } REMARK 3 ORIGIN FOR THE GROUP (A): -24.7280 8.9443 -24.8040 REMARK 3 T TENSOR REMARK 3 T11: -0.3040 T22: 0.0160 REMARK 3 T33: 0.3040 T12: 0.0326 REMARK 3 T13: 0.0095 T23: -0.1520 REMARK 3 L TENSOR REMARK 3 L11: 7.7624 L22: 3.6560 REMARK 3 L33: 6.2454 L12: 0.3537 REMARK 3 L13: 2.9104 L23: 2.9104 REMARK 3 S TENSOR REMARK 3 S11: 0.2384 S12: 0.3329 S13: -0.4997 REMARK 3 S21: -0.4133 S22: -0.2792 S23: 0.5151 REMARK 3 S31: 0.5442 S32: -0.5442 S33: 0.0409 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|448 - A|479 A|499 - A|601 } REMARK 3 ORIGIN FOR THE GROUP (A): -4.0240 35.0650 -16.8153 REMARK 3 T TENSOR REMARK 3 T11: -0.3040 T22: 0.1824 REMARK 3 T33: 0.3040 T12: 0.0191 REMARK 3 T13: -0.0099 T23: 0.0195 REMARK 3 L TENSOR REMARK 3 L11: 5.2410 L22: 4.0685 REMARK 3 L33: 0.3647 L12: 2.1284 REMARK 3 L13: -0.0400 L23: 0.0331 REMARK 3 S TENSOR REMARK 3 S11: 0.0396 S12: 0.5442 S13: 0.5442 REMARK 3 S21: -0.3837 S22: -0.1176 S23: -0.3025 REMARK 3 S31: -0.5378 S32: 0.0492 S33: 0.0780 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { C|1 -C|31 D|1 - D|31 } REMARK 3 ORIGIN FOR THE GROUP (A): -19.5357 5.9875 -7.6423 REMARK 3 T TENSOR REMARK 3 T11: -0.3040 T22: -0.3040 REMARK 3 T33: 0.3040 T12: -0.0198 REMARK 3 T13: 0.0206 T23: 0.0057 REMARK 3 L TENSOR REMARK 3 L11: 2.5594 L22: 3.0414 REMARK 3 L33: 2.1242 L12: 1.5555 REMARK 3 L13: 0.2468 L23: -0.0363 REMARK 3 S TENSOR REMARK 3 S11: 0.2560 S12: -0.0253 S13: -0.5442 REMARK 3 S21: 0.5442 S22: -0.2521 S23: -0.0608 REMARK 3 S31: 0.5442 S32: -0.0048 S33: -0.0039 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3UKG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068866. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 140 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 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10759 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.950 REMARK 200 RESOLUTION RANGE LOW (A) : 35.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.13800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PDB ENTRY 1IGN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS-HCL PH 8.0, 20% (V/V) REMARK 280 PEGMME-550, 100MM CACL2, AND 5% (V/V) GLYCEROL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 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 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 20.29750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.37750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.47200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.37750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.29750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.47200 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 LEU A 480 REMARK 465 ILE A 481 REMARK 465 THR A 482 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 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 582 CD 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 7 O3' DT D 7 C3' -0.043 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 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA C 2 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA C 2 C3' - O3' - P ANGL. DEV. = 11.2 DEGREES REMARK 500 DA C 3 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 DA C 3 C3' - O3' - P ANGL. DEV. = 11.8 DEGREES REMARK 500 DC C 4 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC C 4 C3' - O3' - P ANGL. DEV. = 12.1 DEGREES REMARK 500 DA C 5 O4' - C1' - N9 ANGL. DEV. = 8.8 DEGREES REMARK 500 DC C 6 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 DC C 6 C3' - O3' - P ANGL. DEV. = 13.3 DEGREES REMARK 500 DC C 7 O4' - C1' - N1 ANGL. DEV. = 7.5 DEGREES REMARK 500 DA C 8 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DA C 8 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES REMARK 500 DC C 9 O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES REMARK 500 DC C 9 C1' - O4' - C4' ANGL. DEV. = -10.4 DEGREES REMARK 500 DC C 9 N1 - C1' - C2' ANGL. DEV. = 11.3 DEGREES REMARK 500 DC C 9 O4' - C1' - N1 ANGL. DEV. = 6.5 DEGREES REMARK 500 DA C 10 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES REMARK 500 DC C 11 N1 - C1' - C2' ANGL. DEV. = 8.4 DEGREES REMARK 500 DC C 11 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 DC C 11 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 DA C 13 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 DC C 14 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DA C 15 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 DC C 16 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC C 16 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DC C 18 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC C 18 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 DA C 19 P - O5' - C5' ANGL. DEV. = 11.2 DEGREES REMARK 500 DA C 19 C5' - C4' - C3' ANGL. DEV. = 7.6 DEGREES REMARK 500 DA C 19 C3' - O3' - P ANGL. DEV. = 14.0 DEGREES REMARK 500 DC C 20 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES REMARK 500 DA C 21 O4' - C1' - N9 ANGL. DEV. = -5.9 DEGREES REMARK 500 DC C 22 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DC C 22 C3' - O3' - P ANGL. DEV. = 14.1 DEGREES REMARK 500 DA C 23 O4' - C4' - C3' ANGL. DEV. = -3.1 DEGREES REMARK 500 DC C 24 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 DC C 24 C3' - O3' - P ANGL. DEV. = 10.3 DEGREES REMARK 500 DC C 25 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG C 27 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 DT C 29 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG C 30 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG C 30 C3' - O3' - P ANGL. DEV. = 10.3 DEGREES REMARK 500 DT C 31 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DT C 31 O4' - C1' - N1 ANGL. DEV. = 9.3 DEGREES REMARK 500 DA D 1 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DA D 1 C3' - O3' - P ANGL. DEV. = 11.2 DEGREES REMARK 500 DC D 2 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 DT D 4 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 DT D 7 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 73 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 PRO A 396 -80.76 -43.80 REMARK 500 ASN A 397 -3.14 -55.56 REMARK 500 GLU A 416 -62.01 65.57 REMARK 500 ASP A 430 -165.73 -78.01 REMARK 500 SER A 444 -157.49 -84.99 REMARK 500 ILE A 472 -53.16 -122.74 REMARK 500 ASP A 473 115.02 73.93 REMARK 500 THR A 476 -141.71 -133.08 REMARK 500 ARG A 478 135.43 73.38 REMARK 500 ASN A 500 165.46 77.93 REMARK 500 HIS A 501 45.49 -144.91 REMARK 500 VAL A 502 101.81 70.25 REMARK 500 PRO A 507 -50.06 -28.79 REMARK 500 ASN A 508 123.64 28.50 REMARK 500 PHE A 509 -47.01 -173.84 REMARK 500 GLN A 515 -123.11 57.78 REMARK 500 PHE A 548 -63.74 -108.81 REMARK 500 GLN A 567 20.00 -79.93 REMARK 500 ASN A 568 18.53 56.12 REMARK 500 ARG A 583 66.80 -114.46 REMARK 500 VAL A 586 78.12 61.81 REMARK 500 ASN A 591 75.85 -158.62 REMARK 500 ALA A 596 97.96 76.88 REMARK 500 LYS A 597 -121.24 34.41 REMARK 500 ARG A 598 59.26 16.23 REMARK 500 ARG A 600 19.60 52.54 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 CA A 1 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 506 OE2 REMARK 620 2 GLU A 506 OE1 46.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1 DBREF 3UKG A 360 601 UNP P11938 RAP1_YEAST 360 601 DBREF 3UKG C 1 31 PDB 3UKG 3UKG 1 31 DBREF 3UKG D 1 31 PDB 3UKG 3UKG 1 31 SEQRES 1 A 242 LYS ALA SER PHE THR ASP GLU GLU ASP GLU PHE ILE LEU SEQRES 2 A 242 ASP VAL VAL ARG LYS ASN PRO THR ARG ARG THR THR HIS SEQRES 3 A 242 THR LEU TYR ASP GLU ILE SER HIS TYR VAL PRO ASN HIS SEQRES 4 A 242 THR GLY ASN SER ILE ARG HIS ARG PHE ARG VAL TYR LEU SEQRES 5 A 242 SER LYS ARG LEU GLU TYR VAL TYR GLU VAL ASP LYS PHE SEQRES 6 A 242 GLY LYS LEU VAL ARG ASP ASP ASP GLY ASN LEU ILE LYS SEQRES 7 A 242 THR LYS VAL LEU PRO PRO SER ILE LYS ARG LYS PHE SER SEQRES 8 A 242 ALA ASP GLU ASP TYR THR LEU ALA ILE ALA VAL LYS LYS SEQRES 9 A 242 GLN PHE TYR ARG ASP LEU PHE GLN ILE ASP PRO ASP THR SEQRES 10 A 242 GLY ARG SER LEU ILE THR ASP GLU ASP THR PRO THR ALA SEQRES 11 A 242 ILE ALA ARG ARG ASN MET THR MET ASP PRO ASN HIS VAL SEQRES 12 A 242 PRO GLY SER GLU PRO ASN PHE ALA ALA TYR ARG THR GLN SEQRES 13 A 242 SER ARG ARG GLY PRO ILE ALA ARG GLU PHE PHE LYS HIS SEQRES 14 A 242 PHE ALA GLU GLU HIS ALA ALA HIS THR GLU ASN ALA TRP SEQRES 15 A 242 ARG ASP ARG PHE ARG LYS PHE LEU LEU ALA TYR GLY ILE SEQRES 16 A 242 ASP ASP TYR ILE SER TYR TYR GLU ALA GLU LYS ALA GLN SEQRES 17 A 242 ASN ARG GLU PRO GLU PRO MET LYS ASN LEU THR ASN ARG SEQRES 18 A 242 PRO LYS ARG PRO GLY VAL PRO THR PRO GLY ASN TYR ASN SEQRES 19 A 242 SER ALA ALA LYS ARG ALA ARG ASN SEQRES 1 C 31 DG DA DA DC DA DC DC DA DC DA DC DA DA SEQRES 2 C 31 DC DA DC DC DC DA DC DA DC DA DC DC DA SEQRES 3 C 31 DG DG DT DG DT 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 1 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 HIS A 385 SER A 392 1 8 HELIX 3 3 THR A 399 LEU A 411 1 13 HELIX 4 4 SER A 412 LEU A 415 5 4 HELIX 5 5 SER A 450 GLN A 471 1 22 HELIX 6 6 ALA A 522 HIS A 533 1 12 HELIX 7 7 THR A 537 PHE A 548 1 12 HELIX 8 8 PHE A 548 GLY A 553 1 6 HELIX 9 9 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 LINK CA CA A 1 OE2 GLU A 506 1555 1555 2.21 LINK CA CA A 1 OE1 GLU A 506 1555 1555 3.06 CISPEP 1 PHE A 424 GLY A 425 0 -2.72 CISPEP 2 LYS A 426 LEU A 427 0 4.34 CISPEP 3 PRO A 474 ASP A 475 0 0.56 CISPEP 4 PRO A 499 ASN A 500 0 7.21 CISPEP 5 ASN A 500 HIS A 501 0 6.58 CISPEP 6 ASN A 508 PHE A 509 0 -11.83 CISPEP 7 GLY A 519 PRO A 520 0 2.09 CISPEP 8 ALA A 596 LYS A 597 0 5.64 SITE 1 AC1 3 PRO A 503 GLY A 504 GLU A 506 CRYST1 40.595 102.944 116.755 90.00 90.00 90.00 P 21 21 21 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 0.024634 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009714 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008565 0.00000