HEADER TRANSFERASE 08-JAN-08 2ZFN TITLE SELF-ACETYLATION MEDIATED HISTONE H3 LYSINE 56 ACETYLATION BY RTT109 COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATOR OF TY1 TRANSPOSITION PROTEIN 109; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RTT109; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: RTT109, KIM2, REM50; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS HISTONE H3 LYSINE 56 ACETYLATION, DNA DAMAGE, DNA REPAIR, NUCLEUS, KEYWDS 2 TRANSCRIPTION, TRANSCRIPTION REGULATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.A.YUAN REVDAT 6 15-NOV-23 2ZFN 1 REMARK REVDAT 5 01-NOV-23 2ZFN 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 2ZFN 1 VERSN REVDAT 3 24-FEB-09 2ZFN 1 VERSN REVDAT 2 04-NOV-08 2ZFN 1 JRNL REVDAT 1 23-SEP-08 2ZFN 0 JRNL AUTH C.LIN,Y.A.YUAN JRNL TITL STRUCTURAL INSIGHTS INTO HISTONE H3 LYSINE 56 ACETYLATION BY JRNL TITL 2 RTT109 JRNL REF STRUCTURE V. 16 1503 2008 JRNL REFN ISSN 0969-2126 JRNL PMID 18707894 JRNL DOI 10.1016/J.STR.2008.07.006 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 41056 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2178 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3021 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 153 REMARK 3 BIN FREE R VALUE : 0.2500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3052 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 215 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.69000 REMARK 3 B22 (A**2) : -2.56000 REMARK 3 B33 (A**2) : -2.39000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.49000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.124 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.126 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.095 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.257 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3176 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4297 ; 1.793 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 371 ; 6.625 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 139 ;32.646 ;23.597 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 559 ;16.230 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;23.146 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 479 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2331 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1396 ; 0.236 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2133 ; 0.313 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 173 ; 0.153 ; 0.200 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): 87 ; 0.239 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 25 ; 0.249 ; 0.200 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): 1952 ; 1.429 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3059 ; 1.904 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1419 ; 2.852 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1238 ; 4.154 ; 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 404 REMARK 3 ORIGIN FOR THE GROUP (A): 27.1788 30.5707 15.1305 REMARK 3 T TENSOR REMARK 3 T11: -0.1102 T22: -0.0634 REMARK 3 T33: -0.0582 T12: -0.0011 REMARK 3 T13: 0.0047 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 0.5063 L22: 1.5166 REMARK 3 L33: 1.8844 L12: -0.1357 REMARK 3 L13: 0.1971 L23: 0.2042 REMARK 3 S TENSOR REMARK 3 S11: -0.0067 S12: 0.0032 S13: 0.0296 REMARK 3 S21: -0.0349 S22: 0.0246 S23: 0.0781 REMARK 3 S31: 0.0036 S32: -0.1562 S33: -0.0179 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 2ZFN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000027911. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41056 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 73.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.07400 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: PDB ENTRY 2RIM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, TRIS, AMMONIUM CITRATE, GLYCEROL, REMARK 280 ETHYLENE GLYCOL, PH8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 73.29450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.30600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 73.29450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.30600 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 THR A 143 REMARK 465 PRO A 144 REMARK 465 ALA A 145 REMARK 465 ARG A 146 REMARK 465 THR A 147 REMARK 465 LEU A 148 REMARK 465 ARG A 149 REMARK 465 ILE A 150 REMARK 465 LEU A 151 REMARK 465 ALA A 152 REMARK 465 ARG A 153 REMARK 465 ARG A 154 REMARK 465 LEU A 155 REMARK 465 LYS A 156 REMARK 465 GLN A 157 REMARK 465 SER A 158 REMARK 465 GLY A 159 REMARK 465 SER A 160 REMARK 465 THR A 161 REMARK 465 VAL A 162 REMARK 465 LEU A 163 REMARK 465 LYS A 164 REMARK 465 GLU A 165 REMARK 465 ILE A 166 REMARK 465 GLU A 167 REMARK 465 SER A 168 REMARK 465 PRO A 169 REMARK 465 ARG A 170 REMARK 465 PHE A 171 REMARK 465 GLN A 172 REMARK 465 GLN A 173 REMARK 465 ASP A 174 REMARK 465 ARG A 405 REMARK 465 GLU A 406 REMARK 465 ARG A 407 REMARK 465 ASN A 408 REMARK 465 GLN A 409 REMARK 465 PRO A 410 REMARK 465 VAL A 411 REMARK 465 PRO A 412 REMARK 465 ALA A 413 REMARK 465 SER A 414 REMARK 465 ASN A 415 REMARK 465 ILE A 416 REMARK 465 ASN A 417 REMARK 465 THR A 418 REMARK 465 LEU A 419 REMARK 465 ALA A 420 REMARK 465 ILE A 421 REMARK 465 THR A 422 REMARK 465 MET A 423 REMARK 465 LEU A 424 REMARK 465 LYS A 425 REMARK 465 PRO A 426 REMARK 465 ARG A 427 REMARK 465 LYS A 428 REMARK 465 LYS A 429 REMARK 465 ALA A 430 REMARK 465 LYS A 431 REMARK 465 ALA A 432 REMARK 465 LEU A 433 REMARK 465 PRO A 434 REMARK 465 LYS A 435 REMARK 465 THR A 436 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 MET A 1D CG SD CE 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 701 O HOH A 816 2.12 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 134 CA SER A 134 C 0.341 REMARK 500 SER A 134 C SER A 134 O 0.444 REMARK 500 SER A 134 C PRO A 135 N 0.171 REMARK 500 PRO A 135 CD PRO A 135 N 0.158 REMARK 500 LEU A 137 C LEU A 137 O 0.289 REMARK 500 LEU A 137 C ILE A 138 N 0.168 REMARK 500 ALA A 140 C ALA A 141 N 0.233 REMARK 500 SER A 142 C SER A 142 O 0.153 REMARK 500 ALY A 290 C ALA A 291 N 0.169 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 VAL A 13 CB - CA - C ANGL. DEV. = -11.5 DEGREES REMARK 500 SER A 134 CB - CA - C ANGL. DEV. = -30.0 DEGREES REMARK 500 SER A 134 N - CA - C ANGL. DEV. = -17.7 DEGREES REMARK 500 SER A 134 O - C - N ANGL. DEV. = -13.0 DEGREES REMARK 500 ARG A 183 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 243 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 243 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 PRO A 289 CA - C - N ANGL. DEV. = 13.2 DEGREES REMARK 500 PRO A 289 O - C - N ANGL. DEV. = -15.2 DEGREES REMARK 500 ALY A 290 CA - C - N ANGL. DEV. = -16.6 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 MSE A 1 -53.90 -120.74 REMARK 500 SER A 14 7.57 57.84 REMARK 500 ASP A 38 41.93 -86.83 REMARK 500 PHE A 62 -9.23 -141.85 REMARK 500 TYR A 93 57.54 -98.81 REMARK 500 PRO A 135 -7.38 -41.69 REMARK 500 SER A 272 169.53 123.38 REMARK 500 GLU A 274 35.33 -80.88 REMARK 500 ASN A 275 160.83 65.39 REMARK 500 ALY A 290 -74.87 -40.87 REMARK 500 GLN A 319 -53.39 -129.09 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 GLU A 274 ASN A 275 -145.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER A 134 22.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACO A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RIM RELATED DB: PDB REMARK 900 THE STRUCTURE AT FREE FORM DBREF 2ZFN A 1 436 UNP Q07794 RT109_YEAST 1 436 SEQADV 2ZFN MET A -19 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN GLY A -18 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN SER A -17 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN SER A -16 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN HIS A -15 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN HIS A -14 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN HIS A -13 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN HIS A -12 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN HIS A -11 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN HIS A -10 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN SER A -9 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN SER A -8 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN GLY A -7 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN LEU A -6 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN VAL A -5 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN PRO A -4 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN ARG A -3 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN GLY A -2 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN SER A -1 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN HIS A 0 UNP Q07794 EXPRESSION TAG SEQADV 2ZFN MET A 1D UNP Q07794 EXPRESSION TAG SEQADV 2ZFN ALA A 1C UNP Q07794 EXPRESSION TAG SEQADV 2ZFN ALA A 1B UNP Q07794 EXPRESSION TAG SEQADV 2ZFN MSE A 1A UNP Q07794 EXPRESSION TAG SEQRES 1 A 460 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 460 LEU VAL PRO ARG GLY SER HIS MET ALA ALA MSE MSE SER SEQRES 3 A 460 LEU ASN ASP PHE LEU SER SER VAL LEU PRO VAL SER GLU SEQRES 4 A 460 GLN PHE GLU TYR LEU SER LEU GLN SER ILE PRO LEU GLU SEQRES 5 A 460 THR HIS ALA VAL VAL THR PRO ASN LYS ASP ASP LYS ARG SEQRES 6 A 460 VAL PRO LYS SER THR ILE LYS THR GLN HIS PHE PHE SER SEQRES 7 A 460 LEU PHE HIS GLN GLY LYS VAL PHE PHE SER LEU GLU VAL SEQRES 8 A 460 TYR VAL TYR VAL THR LEU TRP ASP GLU ALA ASP ALA GLU SEQRES 9 A 460 ARG LEU ILE PHE VAL SER LYS ALA ASP THR ASN GLY TYR SEQRES 10 A 460 CYS ASN THR ARG VAL SER VAL ARG ASP ILE THR LYS ILE SEQRES 11 A 460 ILE LEU GLU PHE ILE LEU SER ILE ASP PRO ASN TYR TYR SEQRES 12 A 460 LEU GLN LYS VAL LYS PRO ALA ILE ARG SER TYR LYS LYS SEQRES 13 A 460 ILE SER PRO GLU LEU ILE SER ALA ALA SER THR PRO ALA SEQRES 14 A 460 ARG THR LEU ARG ILE LEU ALA ARG ARG LEU LYS GLN SER SEQRES 15 A 460 GLY SER THR VAL LEU LYS GLU ILE GLU SER PRO ARG PHE SEQRES 16 A 460 GLN GLN ASP LEU TYR LEU SER PHE THR CYS PRO ARG GLU SEQRES 17 A 460 ILE LEU THR LYS ILE CYS LEU PHE THR ARG PRO ALA SER SEQRES 18 A 460 GLN TYR LEU PHE PRO ASP SER SER LYS ASN SER LYS LYS SEQRES 19 A 460 HIS ILE LEU ASN GLY GLU GLU LEU MSE LYS TRP TRP GLY SEQRES 20 A 460 PHE ILE LEU ASP ARG LEU LEU ILE GLU CYS PHE GLN ASN SEQRES 21 A 460 ASP THR GLN ALA LYS LEU ARG ILE PRO GLY GLU ASP PRO SEQRES 22 A 460 ALA ARG VAL ARG SER TYR LEU ARG GLY MSE LYS TYR PRO SEQRES 23 A 460 LEU TRP GLN VAL GLY ASP ILE PHE THR SER LYS GLU ASN SEQRES 24 A 460 SER LEU ALA VAL TYR ASN ILE PRO LEU PHE PRO ASP ASP SEQRES 25 A 460 PRO ALY ALA ARG PHE ILE HIS GLN LEU ALA GLU GLU ASP SEQRES 26 A 460 ARG LEU LEU LYS VAL SER LEU SER SER PHE TRP ILE GLU SEQRES 27 A 460 LEU GLN GLU ARG GLN GLU PHE LYS LEU SER VAL THR SER SEQRES 28 A 460 SER VAL MSE GLY ILE SER GLY TYR SER LEU ALA THR PRO SEQRES 29 A 460 SER LEU PHE PRO SER SER ALA ASP VAL ILE VAL PRO LYS SEQRES 30 A 460 SER ARG LYS GLN PHE ARG ALA ILE LYS LYS TYR ILE THR SEQRES 31 A 460 GLY GLU GLU TYR ASP THR GLU GLU GLY ALA ILE GLU ALA SEQRES 32 A 460 PHE THR ASN ILE ARG ASP PHE LEU LEU LEU ARG MSE ALA SEQRES 33 A 460 THR ASN LEU GLN SER LEU THR GLY LYS ARG GLU HIS ARG SEQRES 34 A 460 GLU ARG ASN GLN PRO VAL PRO ALA SER ASN ILE ASN THR SEQRES 35 A 460 LEU ALA ILE THR MET LEU LYS PRO ARG LYS LYS ALA LYS SEQRES 36 A 460 ALA LEU PRO LYS THR MODRES 2ZFN MSE A 1A MET SELENOMETHIONINE MODRES 2ZFN MSE A 1 MET SELENOMETHIONINE MODRES 2ZFN MSE A 219 MET SELENOMETHIONINE MODRES 2ZFN MSE A 259 MET SELENOMETHIONINE MODRES 2ZFN ALY A 290 LYS N(6)-ACETYLLYSINE MODRES 2ZFN MSE A 330 MET SELENOMETHIONINE MODRES 2ZFN MSE A 391 MET SELENOMETHIONINE HET MSE A 1A 8 HET MSE A 1 8 HET MSE A 219 8 HET MSE A 259 8 HET ALY A 290 12 HET MSE A 330 8 HET MSE A 391 8 HET ACO A 500 51 HET GOL A 601 6 HETNAM MSE SELENOMETHIONINE HETNAM ALY N(6)-ACETYLLYSINE HETNAM ACO ACETYL COENZYME *A HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 1 ALY C8 H16 N2 O3 FORMUL 2 ACO C23 H38 N7 O17 P3 S FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *215(H2 O) HELIX 1 1 SER A 2 LEU A 11 1 10 HELIX 2 2 SER A 99 SER A 113 1 15 HELIX 3 3 PRO A 116 GLN A 121 1 6 HELIX 4 4 SER A 134 ILE A 138 5 5 HELIX 5 5 ASP A 203 ASN A 207 5 5 HELIX 6 6 ASN A 214 PHE A 234 1 21 HELIX 7 7 ASP A 248 ARG A 257 1 10 HELIX 8 8 LEU A 277 ASN A 281 5 5 HELIX 9 9 ASP A 288 GLU A 300 1 13 HELIX 10 10 SER A 307 GLN A 319 1 13 HELIX 11 11 GLU A 320 SER A 324 5 5 HELIX 12 12 SER A 354 GLY A 367 1 14 HELIX 13 13 THR A 372 ALA A 392 1 21 SHEET 1 A 8 LEU A 27 THR A 29 0 SHEET 2 A 8 SER A 45 HIS A 57 -1 O LYS A 48 N LEU A 27 SHEET 3 A 8 LYS A 60 LEU A 73 -1 O LEU A 73 N SER A 45 SHEET 4 A 8 ALA A 79 THR A 90 -1 O PHE A 84 N TYR A 68 SHEET 5 A 8 LEU A 186 THR A 193 1 O LYS A 188 N ILE A 83 SHEET 6 A 8 SER A 328 GLY A 334 -1 O GLY A 334 N THR A 187 SHEET 7 A 8 GLN A 239 ARG A 243 -1 N ARG A 243 O VAL A 329 SHEET 8 A 8 TRP A 264 VAL A 266 1 O GLN A 265 N ALA A 240 SHEET 1 B 4 LEU A 27 THR A 29 0 SHEET 2 B 4 SER A 45 HIS A 57 -1 O LYS A 48 N LEU A 27 SHEET 3 B 4 GLN A 16 GLN A 23 -1 N LEU A 22 O PHE A 52 SHEET 4 B 4 GLN A 396 THR A 399 -1 O LEU A 398 N PHE A 17 LINK C ALA A 1B N MSE A 1A 1555 1555 1.33 LINK C MSE A 1A N MSE A 1 1555 1555 1.32 LINK C MSE A 1 N SER A 2 1555 1555 1.32 LINK C LEU A 218 N MSE A 219 1555 1555 1.33 LINK C MSE A 219 N LYS A 220 1555 1555 1.33 LINK C GLY A 258 N MSE A 259 1555 1555 1.34 LINK C MSE A 259 N LYS A 260 1555 1555 1.33 LINK C PRO A 289 N ALY A 290 1555 1555 1.34 LINK C ALY A 290 N ALA A 291 1555 1555 1.51 LINK C VAL A 329 N MSE A 330 1555 1555 1.33 LINK C MSE A 330 N GLY A 331 1555 1555 1.34 LINK C ARG A 390 N MSE A 391 1555 1555 1.32 LINK C MSE A 391 N ALA A 392 1555 1555 1.33 SITE 1 AC1 24 SER A 86 LYS A 87 ALA A 88 ASP A 89 SITE 2 AC1 24 THR A 90 ARG A 101 PHE A 192 ARG A 194 SITE 3 AC1 24 PRO A 195 ALA A 196 TYR A 199 LYS A 210 SITE 4 AC1 24 HIS A 211 ILE A 212 LEU A 213 LEU A 218 SITE 5 AC1 24 TRP A 221 TRP A 222 THR A 271 SER A 272 SITE 6 AC1 24 HOH A 803 HOH A 851 HOH A 867 HOH A 901 SITE 1 AC2 6 SER A 86 LYS A 87 PHE A 192 TYR A 199 SITE 2 AC2 6 ASP A 287 PRO A 289 CRYST1 146.589 68.612 55.472 90.00 95.02 90.00 C 1 2 1 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 0.006822 0.000000 0.000599 0.00000 SCALE2 0.000000 0.014575 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018096 0.00000