HEADER TRANSCRIPTION REGULATOR 20-MAR-15 4YWC TITLE CRYSTAL STRUCTURE OF MYC3(5-242) FRAGMENT IN COMPLEX WITH JAZ9(218- TITLE 2 239) PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR MYC3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN (UNP RESIDUES 5-242); COMPND 5 SYNONYM: BASIC HELIX-LOOP-HELIX PROTEIN 5,BHLH 5,PROTEIN ALTERED COMPND 6 TRYPTOPHAN REGULATION 2,TRANSCRIPTION FACTOR ATR2,TRANSCRIPTION COMPND 7 FACTOR EN 36,BHLH TRANSCRIPTION FACTOR BHLH005; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PROTEIN TIFY 7; COMPND 11 CHAIN: C, D; COMPND 12 FRAGMENT: UNP RESIDUES 194-215; COMPND 13 SYNONYM: JASMONATE ZIM DOMAIN-CONTAINING PROTEIN 9; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: MYC3, ATR2, BHLH5, EN36, AT5G46760, MZA15.18; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSUMO; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 14 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 15 ORGANISM_TAXID: 3702 KEYWDS HELIX-SHEET-HELIX SANDWICH FOLD, JASMONATE SIGNALING, MYC KEYWDS 2 TRANSCRIPTION FACTOR, MYC-JAZ COMPLEX, TRANSCRIPTION REGULATOR EXPDTA X-RAY DIFFRACTION AUTHOR J.KE,F.ZHANG,J.S.BRUNZELLE,H.E.XU,K.MELCHER,S.Y.HE REVDAT 6 27-SEP-23 4YWC 1 REMARK REVDAT 5 11-DEC-19 4YWC 1 REMARK REVDAT 4 06-SEP-17 4YWC 1 JRNL REMARK REVDAT 3 23-SEP-15 4YWC 1 JRNL REVDAT 2 26-AUG-15 4YWC 1 JRNL REVDAT 1 05-AUG-15 4YWC 0 JRNL AUTH F.ZHANG,J.YAO,J.KE,L.ZHANG,V.Q.LAM,X.F.XIN,X.E.ZHOU,J.CHEN, JRNL AUTH 2 J.BRUNZELLE,P.R.GRIFFIN,M.ZHOU,H.E.XU,K.MELCHER,S.Y.HE JRNL TITL STRUCTURAL BASIS OF JAZ REPRESSION OF MYC TRANSCRIPTION JRNL TITL 2 FACTORS IN JASMONATE SIGNALLING. JRNL REF NATURE V. 525 269 2015 JRNL REFN ESSN 1476-4687 JRNL PMID 26258305 JRNL DOI 10.1038/NATURE14661 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 21103 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 1022 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 49.6311 - 4.5901 1.00 2994 170 0.1987 0.2554 REMARK 3 2 4.5901 - 3.6437 1.00 2912 133 0.1985 0.2285 REMARK 3 3 3.6437 - 3.1832 1.00 2876 128 0.2200 0.2860 REMARK 3 4 3.1832 - 2.8922 1.00 2825 166 0.2829 0.3410 REMARK 3 5 2.8922 - 2.6849 0.99 2827 143 0.3057 0.3820 REMARK 3 6 2.6849 - 2.5266 0.99 2822 135 0.3395 0.4297 REMARK 3 7 2.5266 - 2.4000 1.00 2825 147 0.3565 0.4213 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.040 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 : 0.008 3132 REMARK 3 ANGLE : 1.244 4219 REMARK 3 CHIRALITY : 0.049 466 REMARK 3 PLANARITY : 0.005 547 REMARK 3 DIHEDRAL : 17.363 1107 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 4YWC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000208123. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9787 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21208 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.13900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.30 REMARK 200 R MERGE FOR SHELL (I) : 1.07000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 4RRU REMARK 200 REMARK 200 REMARK: PLATE SHAPED CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE PURIFIED PROTEINS AT A REMARK 280 CONCENTRATION OF 15 MG/ML ARE MIXED WITH 0.2 M MAGNESIUM NITRATE, REMARK 280 20% (W/V) POLYETHYLENE GLYCOL 3,350. CRYSTALS OF ABOUT 100 UM REMARK 280 IN LENGTH APPEARED IN 3 DAYS, PH 5.9, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 80.92300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 80.92300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 29.55250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.31350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.55250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.31350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 80.92300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.55250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 55.31350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 80.92300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.55250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 55.31350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 THR A 5 REMARK 465 SER A 6 REMARK 465 SER A 7 REMARK 465 ILE A 8 REMARK 465 ASN A 9 REMARK 465 PHE A 10 REMARK 465 LEU A 11 REMARK 465 THR A 12 REMARK 465 SER A 13 REMARK 465 ASP A 14 REMARK 465 ASP A 15 REMARK 465 ASP A 16 REMARK 465 ALA A 17 REMARK 465 MET A 22 REMARK 465 GLU A 23 REMARK 465 ALA A 24 REMARK 465 PHE A 25 REMARK 465 ILE A 26 REMARK 465 GLY A 27 REMARK 465 THR A 28 REMARK 465 ASN A 29 REMARK 465 HIS A 30 REMARK 465 HIS A 31 REMARK 465 SER A 32 REMARK 465 SER A 33 REMARK 465 LEU A 34 REMARK 465 PHE A 35 REMARK 465 PRO A 36 REMARK 465 PRO A 37 REMARK 465 PRO A 38 REMARK 465 PRO A 39 REMARK 465 GLN A 40 REMARK 465 GLN A 41 REMARK 465 PRO A 42 REMARK 465 PRO A 43 REMARK 465 GLN A 44 REMARK 465 GLU A 101 REMARK 465 ASP A 102 REMARK 465 LYS A 103 REMARK 465 GLU A 104 REMARK 465 LYS A 105 REMARK 465 LYS A 106 REMARK 465 LYS A 107 REMARK 465 ASN A 108 REMARK 465 ASN A 109 REMARK 465 THR A 110 REMARK 465 GLY A 132 REMARK 465 ILE A 133 REMARK 465 GLY A 134 REMARK 465 VAL A 135 REMARK 465 SER A 136 REMARK 465 ASP A 137 REMARK 465 GLU A 138 REMARK 465 SER A 139 REMARK 465 ASN A 238 REMARK 465 ASN A 239 REMARK 465 GLY A 240 REMARK 465 GLY A 241 REMARK 465 GLY A 242 REMARK 465 THR B 5 REMARK 465 SER B 6 REMARK 465 SER B 7 REMARK 465 ILE B 8 REMARK 465 ASN B 9 REMARK 465 PHE B 10 REMARK 465 LEU B 11 REMARK 465 THR B 12 REMARK 465 SER B 13 REMARK 465 ASP B 14 REMARK 465 ASP B 15 REMARK 465 ASP B 16 REMARK 465 ALA B 17 REMARK 465 MET B 22 REMARK 465 GLU B 23 REMARK 465 ALA B 24 REMARK 465 PHE B 25 REMARK 465 ILE B 26 REMARK 465 GLY B 27 REMARK 465 THR B 28 REMARK 465 ASN B 29 REMARK 465 HIS B 30 REMARK 465 HIS B 31 REMARK 465 SER B 32 REMARK 465 SER B 33 REMARK 465 LEU B 34 REMARK 465 PHE B 35 REMARK 465 PRO B 36 REMARK 465 PRO B 37 REMARK 465 PRO B 38 REMARK 465 PRO B 39 REMARK 465 GLN B 40 REMARK 465 GLN B 41 REMARK 465 PRO B 42 REMARK 465 PRO B 43 REMARK 465 GLN B 44 REMARK 465 PRO B 45 REMARK 465 ASP B 102 REMARK 465 LYS B 103 REMARK 465 GLU B 104 REMARK 465 LYS B 105 REMARK 465 LYS B 106 REMARK 465 LYS B 107 REMARK 465 ASN B 108 REMARK 465 ASN B 109 REMARK 465 THR B 110 REMARK 465 GLY B 132 REMARK 465 ILE B 133 REMARK 465 GLY B 134 REMARK 465 VAL B 135 REMARK 465 SER B 136 REMARK 465 ASP B 137 REMARK 465 GLU B 138 REMARK 465 SER B 139 REMARK 465 ASN B 238 REMARK 465 ASN B 239 REMARK 465 GLY B 240 REMARK 465 GLY B 241 REMARK 465 GLY B 242 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 PRO A 45 CG CD REMARK 470 PHE A 79 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 85 CG OD1 OD2 REMARK 470 ASN A 86 CG OD1 ND2 REMARK 470 GLU A 124 CG CD OE1 OE2 REMARK 470 LEU A 128 CG CD1 CD2 REMARK 470 GLU A 142 CG CD OE1 OE2 REMARK 470 LYS C 224 CG CD CE NZ REMARK 470 ASP B 78 CG OD1 OD2 REMARK 470 PHE B 79 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP B 80 CG OD1 OD2 REMARK 470 ASP B 85 CG OD1 OD2 REMARK 470 ASN B 86 CG OD1 ND2 REMARK 470 LEU D 238 CG CD1 CD2 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 GLN A 46 CB GLN A 46 CG -0.163 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 GLN A 46 CB - CA - C ANGL. DEV. = -12.2 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 ALA A 20 -73.46 -109.23 REMARK 500 PHE B 47 -72.20 -134.98 REMARK 500 SER B 130 -69.94 -122.10 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 LEU C 238 MET C 239 -44.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RRU RELATED DB: PDB REMARK 900 RELATED ID: 4RQW RELATED DB: PDB REMARK 900 RELATED ID: 4RS9 RELATED DB: PDB DBREF 4YWC A 5 242 UNP Q9FIP9 MYC3_ARATH 5 242 DBREF 4YWC C 218 239 UNP Q8W4J8 TIF7_ARATH 194 215 DBREF 4YWC B 5 242 UNP Q9FIP9 MYC3_ARATH 5 242 DBREF 4YWC D 218 239 UNP Q8W4J8 TIF7_ARATH 194 215 SEQRES 1 A 238 THR SER SER ILE ASN PHE LEU THR SER ASP ASP ASP ALA SEQRES 2 A 238 SER ALA ALA ALA MET GLU ALA PHE ILE GLY THR ASN HIS SEQRES 3 A 238 HIS SER SER LEU PHE PRO PRO PRO PRO GLN GLN PRO PRO SEQRES 4 A 238 GLN PRO GLN PHE ASN GLU ASP THR LEU GLN GLN ARG LEU SEQRES 5 A 238 GLN ALA LEU ILE GLU SER ALA GLY GLU ASN TRP THR TYR SEQRES 6 A 238 ALA ILE PHE TRP GLN ILE SER HIS ASP PHE ASP SER SER SEQRES 7 A 238 THR GLY ASP ASN THR VAL ILE LEU GLY TRP GLY ASP GLY SEQRES 8 A 238 TYR TYR LYS GLY GLU GLU ASP LYS GLU LYS LYS LYS ASN SEQRES 9 A 238 ASN THR ASN THR ALA GLU GLN GLU HIS ARG LYS ARG VAL SEQRES 10 A 238 ILE ARG GLU LEU ASN SER LEU ILE SER GLY GLY ILE GLY SEQRES 11 A 238 VAL SER ASP GLU SER ASN ASP GLU GLU VAL THR ASP THR SEQRES 12 A 238 GLU TRP PHE PHE LEU VAL SER MET THR GLN SER PHE VAL SEQRES 13 A 238 ASN GLY VAL GLY LEU PRO GLY GLU SER PHE LEU ASN SER SEQRES 14 A 238 ARG VAL ILE TRP LEU SER GLY SER GLY ALA LEU THR GLY SEQRES 15 A 238 SER GLY CYS GLU ARG ALA GLY GLN GLY GLN ILE TYR GLY SEQRES 16 A 238 LEU LYS THR MET VAL CYS ILE ALA THR GLN ASN GLY VAL SEQRES 17 A 238 VAL GLU LEU GLY SER SER GLU VAL ILE SER GLN SER SER SEQRES 18 A 238 ASP LEU MET HIS LYS VAL ASN ASN LEU PHE ASN PHE ASN SEQRES 19 A 238 ASN GLY GLY GLY SEQRES 1 C 22 SER VAL PRO GLN ALA ARG LYS ALA SER LEU ALA ARG PHE SEQRES 2 C 22 LEU GLU LYS ARG LYS GLU ARG LEU MET SEQRES 1 B 238 THR SER SER ILE ASN PHE LEU THR SER ASP ASP ASP ALA SEQRES 2 B 238 SER ALA ALA ALA MET GLU ALA PHE ILE GLY THR ASN HIS SEQRES 3 B 238 HIS SER SER LEU PHE PRO PRO PRO PRO GLN GLN PRO PRO SEQRES 4 B 238 GLN PRO GLN PHE ASN GLU ASP THR LEU GLN GLN ARG LEU SEQRES 5 B 238 GLN ALA LEU ILE GLU SER ALA GLY GLU ASN TRP THR TYR SEQRES 6 B 238 ALA ILE PHE TRP GLN ILE SER HIS ASP PHE ASP SER SER SEQRES 7 B 238 THR GLY ASP ASN THR VAL ILE LEU GLY TRP GLY ASP GLY SEQRES 8 B 238 TYR TYR LYS GLY GLU GLU ASP LYS GLU LYS LYS LYS ASN SEQRES 9 B 238 ASN THR ASN THR ALA GLU GLN GLU HIS ARG LYS ARG VAL SEQRES 10 B 238 ILE ARG GLU LEU ASN SER LEU ILE SER GLY GLY ILE GLY SEQRES 11 B 238 VAL SER ASP GLU SER ASN ASP GLU GLU VAL THR ASP THR SEQRES 12 B 238 GLU TRP PHE PHE LEU VAL SER MET THR GLN SER PHE VAL SEQRES 13 B 238 ASN GLY VAL GLY LEU PRO GLY GLU SER PHE LEU ASN SER SEQRES 14 B 238 ARG VAL ILE TRP LEU SER GLY SER GLY ALA LEU THR GLY SEQRES 15 B 238 SER GLY CYS GLU ARG ALA GLY GLN GLY GLN ILE TYR GLY SEQRES 16 B 238 LEU LYS THR MET VAL CYS ILE ALA THR GLN ASN GLY VAL SEQRES 17 B 238 VAL GLU LEU GLY SER SER GLU VAL ILE SER GLN SER SER SEQRES 18 B 238 ASP LEU MET HIS LYS VAL ASN ASN LEU PHE ASN PHE ASN SEQRES 19 B 238 ASN GLY GLY GLY SEQRES 1 D 22 SER VAL PRO GLN ALA ARG LYS ALA SER LEU ALA ARG PHE SEQRES 2 D 22 LEU GLU LYS ARG LYS GLU ARG LEU MET FORMUL 5 HOH *100(H2 O) HELIX 1 AA1 GLN A 46 THR A 51 1 6 HELIX 2 AA2 THR A 51 SER A 62 1 12 HELIX 3 AA3 THR A 112 SER A 130 1 19 HELIX 4 AA4 THR A 145 SER A 154 1 10 HELIX 5 AA5 MET A 155 GLN A 157 5 3 HELIX 6 AA6 VAL A 163 ASN A 172 1 10 HELIX 7 AA7 GLY A 180 GLY A 188 1 9 HELIX 8 AA8 CYS A 189 TYR A 198 1 10 HELIX 9 AA9 SER A 224 ASN A 236 1 13 HELIX 10 AB1 VAL C 219 GLU C 236 1 18 HELIX 11 AB2 THR B 51 SER B 62 1 12 HELIX 12 AB3 THR B 112 SER B 130 1 19 HELIX 13 AB4 THR B 145 SER B 154 1 10 HELIX 14 AB5 MET B 155 GLN B 157 5 3 HELIX 15 AB6 VAL B 163 ASN B 172 1 10 HELIX 16 AB7 GLY B 180 GLY B 188 1 9 HELIX 17 AB8 CYS B 189 TYR B 198 1 10 HELIX 18 AB9 SER B 224 ASN B 236 1 13 HELIX 19 AC1 VAL D 219 MET D 239 1 21 SHEET 1 AA1 6 PHE A 159 VAL A 160 0 SHEET 2 AA1 6 THR A 87 TYR A 97 -1 N LEU A 90 O PHE A 159 SHEET 3 AA1 6 TYR A 69 ASP A 78 -1 N PHE A 72 O ASP A 94 SHEET 4 AA1 6 GLY A 211 SER A 217 -1 O GLU A 214 N ILE A 71 SHEET 5 AA1 6 THR A 202 THR A 208 -1 N THR A 208 O GLY A 211 SHEET 6 AA1 6 VAL A 175 SER A 179 -1 N LEU A 178 O MET A 203 SHEET 1 AA2 6 PHE B 159 VAL B 160 0 SHEET 2 AA2 6 ASN B 86 TYR B 97 -1 N LEU B 90 O PHE B 159 SHEET 3 AA2 6 TYR B 69 PHE B 79 -1 N SER B 76 O ILE B 89 SHEET 4 AA2 6 GLY B 211 SER B 217 -1 O GLU B 214 N ILE B 71 SHEET 5 AA2 6 THR B 202 THR B 208 -1 N THR B 208 O GLY B 211 SHEET 6 AA2 6 VAL B 175 SER B 179 -1 N LEU B 178 O MET B 203 CISPEP 1 ALA A 19 ALA A 20 0 -0.17 CISPEP 2 SER A 130 GLY A 131 0 -25.55 CISPEP 3 ASN A 236 PHE A 237 0 7.40 CISPEP 4 ALA B 20 ALA B 21 0 -12.14 CISPEP 5 ASN B 236 PHE B 237 0 1.90 CRYST1 59.105 110.627 161.846 90.00 90.00 90.00 C 2 2 21 16 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 0.016919 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009039 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006179 0.00000