HEADER TRANSCRIPTION 13-JAN-17 5WYI TITLE THE YAF9 YEATS DOMAIN RECOGNIZING H3K122SUC PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: YAF9; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 8-169; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: YAF9; COMPND 9 CHAIN: B, C; COMPND 10 FRAGMENT: UNP RESIDUES 8-169; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: ILE-MET-PRO-LYS-ASP-ILE-GLN-LEU; COMPND 15 CHAIN: E; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN RM11-1A); SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 285006; SOURCE 5 STRAIN: RM11-1A; SOURCE 6 GENE: SCRG_03242; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR SOURCE 8 PPPARG4; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 1182032; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN RM11-1A); SOURCE 12 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 13 ORGANISM_TAXID: 285006; SOURCE 14 STRAIN: RM11-1A; SOURCE 15 GENE: SCRG_03242; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR SOURCE 17 PPPARG4; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 1182032; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 22 ORGANISM_TAXID: 9606 KEYWDS YEATS DOMAIN, SUCCINYLATION, TRANSCRIPTIONAL FACTOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.WANG,Q.HAO REVDAT 1 17-JAN-18 5WYI 0 JRNL AUTH Y.WANG,Q.HAO JRNL TITL THE YAF9 YEATS DOMAIN RECOGNIZING H3K122SUC PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 36911 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1864 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.5366 - 4.7003 1.00 2711 154 0.1872 0.1946 REMARK 3 2 4.7003 - 3.7317 1.00 2669 151 0.1657 0.1604 REMARK 3 3 3.7317 - 3.2602 1.00 2714 129 0.1810 0.2627 REMARK 3 4 3.2602 - 2.9623 1.00 2722 154 0.1983 0.2331 REMARK 3 5 2.9623 - 2.7500 1.00 2763 124 0.2159 0.2183 REMARK 3 6 2.7500 - 2.5879 1.00 2657 156 0.2159 0.2563 REMARK 3 7 2.5879 - 2.4583 1.00 2737 145 0.2207 0.2314 REMARK 3 8 2.4583 - 2.3513 1.00 2692 140 0.2206 0.2481 REMARK 3 9 2.3513 - 2.2608 1.00 2728 141 0.2188 0.2572 REMARK 3 10 2.2608 - 2.1828 1.00 2641 141 0.2226 0.2421 REMARK 3 11 2.1828 - 2.1145 1.00 2773 150 0.2323 0.2668 REMARK 3 12 2.1145 - 2.0541 0.99 2693 132 0.2275 0.2627 REMARK 3 13 2.0541 - 2.0000 0.95 2547 147 0.2501 0.2922 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5WYI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1300002603. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39259 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7800 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M BIS-TRIS REMARK 280 PH 5.5, 25% PEG 3,350, VAPOR DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 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 APPLY THE FOLLOWING TO CHAINS: A, B, C, E 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 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 HOH C 441 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 TYR A 120 REMARK 465 ALA A 121 REMARK 465 ASN A 122 REMARK 465 PRO A 123 REMARK 465 VAL A 124 REMARK 465 PRO A 125 REMARK 465 ASN A 126 REMARK 465 SER A 127 REMARK 465 ASP A 128 REMARK 465 ASN A 129 REMARK 465 GLY A 130 REMARK 465 ASN A 131 REMARK 465 GLU A 132 REMARK 465 GLN A 133 REMARK 465 ASN A 134 REMARK 465 THR A 135 REMARK 465 THR A 136 REMARK 465 ASP A 137 REMARK 465 HIS A 138 REMARK 465 ASN A 139 REMARK 465 SER A 140 REMARK 465 LYS A 141 REMARK 465 ASP A 142 REMARK 465 ALA A 143 REMARK 465 PRO B 33 REMARK 465 ASN B 34 REMARK 465 TYR B 120 REMARK 465 ALA B 121 REMARK 465 ASN B 122 REMARK 465 PRO B 123 REMARK 465 VAL B 124 REMARK 465 PRO B 125 REMARK 465 ASN B 126 REMARK 465 SER B 127 REMARK 465 ASP B 128 REMARK 465 ASN B 129 REMARK 465 GLY B 130 REMARK 465 ASN B 131 REMARK 465 GLU B 132 REMARK 465 GLN B 133 REMARK 465 ASN B 134 REMARK 465 THR B 135 REMARK 465 THR B 136 REMARK 465 ASP B 137 REMARK 465 HIS B 138 REMARK 465 ASN B 139 REMARK 465 SER B 140 REMARK 465 LYS B 141 REMARK 465 ASP B 142 REMARK 465 ALA B 143 REMARK 465 GLY C 28 REMARK 465 SER C 29 REMARK 465 VAL C 30 REMARK 465 LYS C 31 REMARK 465 PRO C 32 REMARK 465 PRO C 33 REMARK 465 ASN C 34 REMARK 465 TYR C 120 REMARK 465 ALA C 121 REMARK 465 ASN C 122 REMARK 465 PRO C 123 REMARK 465 VAL C 124 REMARK 465 PRO C 125 REMARK 465 ASN C 126 REMARK 465 SER C 127 REMARK 465 ASP C 128 REMARK 465 ASN C 129 REMARK 465 GLY C 130 REMARK 465 ASN C 131 REMARK 465 GLU C 132 REMARK 465 GLN C 133 REMARK 465 ASN C 134 REMARK 465 THR C 135 REMARK 465 THR C 136 REMARK 465 ASP C 137 REMARK 465 HIS C 138 REMARK 465 ASN C 139 REMARK 465 SER C 140 REMARK 465 LYS C 141 REMARK 465 ASP C 142 REMARK 465 ALA C 143 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 B 205 O HOH B 324 1.72 REMARK 500 O HOH B 304 O HOH B 324 1.83 REMARK 500 O HOH B 310 O HOH B 318 1.84 REMARK 500 OE1 GLU A 161 O HOH A 201 1.89 REMARK 500 O HOH C 308 O HOH C 353 1.91 REMARK 500 OE1 GLU C 38 O HOH C 301 1.95 REMARK 500 O HOH C 349 O HOH C 384 1.97 REMARK 500 O HOH C 413 O HOH C 428 1.99 REMARK 500 O HOH A 204 O HOH A 285 1.99 REMARK 500 O HOH A 204 O HOH A 335 2.04 REMARK 500 O HOH A 253 O HOH A 290 2.04 REMARK 500 O HOH B 264 O HOH B 266 2.06 REMARK 500 O HOH B 309 O HOH B 321 2.06 REMARK 500 NH1 ARG C 8 O HOH C 302 2.07 REMARK 500 O HOH C 301 O HOH C 328 2.07 REMARK 500 NE ARG C 8 O HOH C 303 2.07 REMARK 500 O HOH A 239 O HOH A 321 2.07 REMARK 500 NZ LYS E 1 C2 SIN E 101 2.08 REMARK 500 O HOH B 296 O HOH B 350 2.09 REMARK 500 OD2 ASP C 68 O HOH C 304 2.10 REMARK 500 O ARG C 169 O HOH C 305 2.10 REMARK 500 O HOH C 414 O HOH C 420 2.10 REMARK 500 O PRO B 32 O HOH B 201 2.10 REMARK 500 O HOH A 242 O HOH A 266 2.12 REMARK 500 OE2 GLU B 83 O HOH B 202 2.13 REMARK 500 OE1 GLU C 157 O HOH C 306 2.13 REMARK 500 N ALA B 35 O HOH B 203 2.14 REMARK 500 O HOH C 376 O HOH C 425 2.15 REMARK 500 O HOH C 305 O HOH C 351 2.15 REMARK 500 NE2 GLN E 4 O HOH E 201 2.16 REMARK 500 O GLU B 78 O HOH B 204 2.18 REMARK 500 O HOH A 210 O HOH A 330 2.18 REMARK 500 O HOH A 330 O HOH A 336 2.19 REMARK 500 CE LYS E 1 C1 SIN E 101 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 334 O HOH A 337 1554 1.89 REMARK 500 O HOH C 303 O HOH C 416 3555 1.92 REMARK 500 O HOH C 355 O HOH C 422 1554 1.96 REMARK 500 O HOH B 313 O HOH B 332 1554 1.99 REMARK 500 O HOH B 322 O HOH B 340 3665 2.09 REMARK 500 O HOH B 339 O HOH B 350 1556 2.09 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 LYS E 1 O - C - N ANGL. DEV. = -11.2 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 ASP A 151 -160.42 -114.56 REMARK 500 ASP B 151 -160.20 -115.01 REMARK 500 ASP C 151 -160.44 -114.92 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 LYS E 1 20.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 353 DISTANCE = 5.85 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 SLL C 201 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SLL C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide SIN E 101 and LYS E REMARK 800 1 DBREF 5WYI A 8 169 UNP B3LNW5 B3LNW5_YEAS1 8 169 DBREF 5WYI B 8 169 UNP B3LNW5 B3LNW5_YEAS1 8 169 DBREF 5WYI C 8 169 UNP B3LNW5 B3LNW5_YEAS1 8 169 DBREF 5WYI E -2 5 PDB 5WYI 5WYI -2 5 SEQADV 5WYI GLY A 6 UNP B3LNW5 EXPRESSION TAG SEQADV 5WYI ALA A 7 UNP B3LNW5 EXPRESSION TAG SEQADV 5WYI TYR A 57 UNP B3LNW5 HIS 57 ENGINEERED MUTATION SEQADV 5WYI LYS A 60 UNP B3LNW5 THR 60 ENGINEERED MUTATION SEQADV 5WYI SER A 76 UNP B3LNW5 TYR 76 ENGINEERED MUTATION SEQADV 5WYI GLY A 170 UNP B3LNW5 EXPRESSION TAG SEQADV 5WYI GLY B 6 UNP B3LNW5 EXPRESSION TAG SEQADV 5WYI ALA B 7 UNP B3LNW5 EXPRESSION TAG SEQADV 5WYI TYR B 57 UNP B3LNW5 HIS 57 ENGINEERED MUTATION SEQADV 5WYI LYS B 60 UNP B3LNW5 THR 60 ENGINEERED MUTATION SEQADV 5WYI SER B 76 UNP B3LNW5 TYR 76 ENGINEERED MUTATION SEQADV 5WYI GLY C 6 UNP B3LNW5 EXPRESSION TAG SEQADV 5WYI ALA C 7 UNP B3LNW5 EXPRESSION TAG SEQADV 5WYI TYR C 57 UNP B3LNW5 HIS 57 ENGINEERED MUTATION SEQADV 5WYI LYS C 60 UNP B3LNW5 THR 60 ENGINEERED MUTATION SEQADV 5WYI SER C 76 UNP B3LNW5 TYR 76 ENGINEERED MUTATION SEQRES 1 A 165 GLY ALA ARG ILE LYS THR LEU SER VAL SER ARG PRO ILE SEQRES 2 A 165 ILE TYR GLY ASN THR ALA LYS LYS MET GLY SER VAL LYS SEQRES 3 A 165 PRO PRO ASN ALA PRO ALA GLU HIS THR HIS LEU TRP THR SEQRES 4 A 165 ILE PHE VAL ARG GLY PRO GLN ASN GLU ASP ILE SER TYR SEQRES 5 A 165 PHE ILE LYS LYS VAL VAL PHE LYS LEU HIS ASP THR TYR SEQRES 6 A 165 PRO ASN PRO VAL ARG SER ILE GLU ALA PRO PRO PHE GLU SEQRES 7 A 165 LEU THR GLU THR GLY TRP GLY GLU PHE ASP ILE ASN ILE SEQRES 8 A 165 LYS VAL TYR PHE VAL GLU GLU ALA ASN GLU LYS VAL LEU SEQRES 9 A 165 ASN PHE TYR HIS ARG LEU ARG LEU HIS PRO TYR ALA ASN SEQRES 10 A 165 PRO VAL PRO ASN SER ASP ASN GLY ASN GLU GLN ASN THR SEQRES 11 A 165 THR ASP HIS ASN SER LYS ASP ALA GLU VAL SER SER VAL SEQRES 12 A 165 TYR PHE ASP GLU ILE VAL PHE ASN GLU PRO ASN GLU GLU SEQRES 13 A 165 PHE PHE LYS ILE LEU MET SER ARG GLY SEQRES 1 B 164 GLY ALA ARG ILE LYS THR LEU SER VAL SER ARG PRO ILE SEQRES 2 B 164 ILE TYR GLY ASN THR ALA LYS LYS MET GLY SER VAL LYS SEQRES 3 B 164 PRO PRO ASN ALA PRO ALA GLU HIS THR HIS LEU TRP THR SEQRES 4 B 164 ILE PHE VAL ARG GLY PRO GLN ASN GLU ASP ILE SER TYR SEQRES 5 B 164 PHE ILE LYS LYS VAL VAL PHE LYS LEU HIS ASP THR TYR SEQRES 6 B 164 PRO ASN PRO VAL ARG SER ILE GLU ALA PRO PRO PHE GLU SEQRES 7 B 164 LEU THR GLU THR GLY TRP GLY GLU PHE ASP ILE ASN ILE SEQRES 8 B 164 LYS VAL TYR PHE VAL GLU GLU ALA ASN GLU LYS VAL LEU SEQRES 9 B 164 ASN PHE TYR HIS ARG LEU ARG LEU HIS PRO TYR ALA ASN SEQRES 10 B 164 PRO VAL PRO ASN SER ASP ASN GLY ASN GLU GLN ASN THR SEQRES 11 B 164 THR ASP HIS ASN SER LYS ASP ALA GLU VAL SER SER VAL SEQRES 12 B 164 TYR PHE ASP GLU ILE VAL PHE ASN GLU PRO ASN GLU GLU SEQRES 13 B 164 PHE PHE LYS ILE LEU MET SER ARG SEQRES 1 C 164 GLY ALA ARG ILE LYS THR LEU SER VAL SER ARG PRO ILE SEQRES 2 C 164 ILE TYR GLY ASN THR ALA LYS LYS MET GLY SER VAL LYS SEQRES 3 C 164 PRO PRO ASN ALA PRO ALA GLU HIS THR HIS LEU TRP THR SEQRES 4 C 164 ILE PHE VAL ARG GLY PRO GLN ASN GLU ASP ILE SER TYR SEQRES 5 C 164 PHE ILE LYS LYS VAL VAL PHE LYS LEU HIS ASP THR TYR SEQRES 6 C 164 PRO ASN PRO VAL ARG SER ILE GLU ALA PRO PRO PHE GLU SEQRES 7 C 164 LEU THR GLU THR GLY TRP GLY GLU PHE ASP ILE ASN ILE SEQRES 8 C 164 LYS VAL TYR PHE VAL GLU GLU ALA ASN GLU LYS VAL LEU SEQRES 9 C 164 ASN PHE TYR HIS ARG LEU ARG LEU HIS PRO TYR ALA ASN SEQRES 10 C 164 PRO VAL PRO ASN SER ASP ASN GLY ASN GLU GLN ASN THR SEQRES 11 C 164 THR ASP HIS ASN SER LYS ASP ALA GLU VAL SER SER VAL SEQRES 12 C 164 TYR PHE ASP GLU ILE VAL PHE ASN GLU PRO ASN GLU GLU SEQRES 13 C 164 PHE PHE LYS ILE LEU MET SER ARG SEQRES 1 E 8 ILE MET PRO LYS ASP ILE GLN LEU HET SLL C 201 16 HET SIN E 101 7 HETNAM SLL (2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL) HETNAM 2 SLL AMINO]HEXANOIC ACID HETNAM SIN SUCCINIC ACID HETSYN SLL 6-N-SUCCINYL-L-LYSINE FORMUL 5 SLL C10 H18 N2 O5 FORMUL 6 SIN C4 H6 O4 FORMUL 7 HOH *478(H2 O) HELIX 1 AA1 GLY A 49 GLU A 53 5 5 HELIX 2 AA2 GLU A 102 ASN A 105 5 4 HELIX 3 AA3 ASN A 159 MET A 167 1 9 HELIX 4 AA4 GLY B 49 GLU B 53 5 5 HELIX 5 AA5 GLU B 102 ASN B 105 5 4 HELIX 6 AA6 ASN B 159 MET B 167 1 9 HELIX 7 AA7 GLY C 49 GLU C 53 5 5 HELIX 8 AA8 GLU C 102 ASN C 105 5 4 HELIX 9 AA9 ASN C 159 SER C 168 1 10 SHEET 1 AA1 4 PHE A 82 GLY A 88 0 SHEET 2 AA1 4 HIS A 41 ARG A 48 -1 N TRP A 43 O GLU A 86 SHEET 3 AA1 4 SER A 13 LYS A 26 -1 N ILE A 19 O ARG A 48 SHEET 4 AA1 4 VAL A 145 ASN A 156 -1 O TYR A 149 N TYR A 20 SHEET 1 AA2 4 VAL A 74 ILE A 77 0 SHEET 2 AA2 4 ILE A 59 LYS A 65 -1 N PHE A 64 O ARG A 75 SHEET 3 AA2 4 ASP A 93 PHE A 100 -1 O ASN A 95 N LYS A 65 SHEET 4 AA2 4 LEU A 109 ARG A 114 -1 O HIS A 113 N ILE A 94 SHEET 1 AA3 4 PHE B 82 GLY B 88 0 SHEET 2 AA3 4 HIS B 41 ARG B 48 -1 N TRP B 43 O GLU B 86 SHEET 3 AA3 4 SER B 13 LYS B 26 -1 N ILE B 19 O ARG B 48 SHEET 4 AA3 4 VAL B 145 ASN B 156 -1 O TYR B 149 N TYR B 20 SHEET 1 AA4 4 VAL B 74 ILE B 77 0 SHEET 2 AA4 4 ILE B 59 LYS B 65 -1 N PHE B 64 O ARG B 75 SHEET 3 AA4 4 ASP B 93 PHE B 100 -1 O TYR B 99 N LYS B 61 SHEET 4 AA4 4 LEU B 109 ARG B 114 -1 O HIS B 113 N ILE B 94 SHEET 1 AA5 4 PHE C 82 GLY C 88 0 SHEET 2 AA5 4 HIS C 41 ARG C 48 -1 N HIS C 41 O GLY C 88 SHEET 3 AA5 4 SER C 13 LYS C 26 -1 N ILE C 19 O ARG C 48 SHEET 4 AA5 4 VAL C 145 ASN C 156 -1 O TYR C 149 N TYR C 20 SHEET 1 AA6 4 VAL C 74 ILE C 77 0 SHEET 2 AA6 4 ILE C 59 LYS C 65 -1 N PHE C 64 O ARG C 75 SHEET 3 AA6 4 ASP C 93 PHE C 100 -1 O ASN C 95 N LYS C 65 SHEET 4 AA6 4 LEU C 109 ARG C 114 -1 O HIS C 113 N ILE C 94 LINK NZ LYS E 1 C1 SIN E 101 1555 1555 1.43 CISPEP 1 PRO A 80 PRO A 81 0 -0.81 CISPEP 2 PRO B 80 PRO B 81 0 -0.52 CISPEP 3 PRO C 80 PRO C 81 0 -0.88 SITE 1 AC1 7 HIS C 39 HIS C 67 THR C 69 TYR C 70 SITE 2 AC1 7 GLY C 88 TRP C 89 GLU C 91 SITE 1 AC2 11 HIS B 39 HIS B 67 THR B 69 TYR B 70 SITE 2 AC2 11 GLY B 88 TRP B 89 GLU B 91 PRO E 0 SITE 3 AC2 11 ASP E 2 HOH E 203 HOH E 207 CRYST1 136.932 136.932 26.168 90.00 90.00 120.00 P 3 6 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 0.007303 0.004216 0.000000 0.00000 SCALE2 0.000000 0.008433 0.000000 0.00000 SCALE3 0.000000 0.000000 0.038215 0.00000