HEADER DNA BINDING PROTEIN/DNA 17-SEP-17 5YEJ TITLE CRYSTAL STRUCTURE OF BIOQ WITH ITS NATUREL DOUBLE-STRANDED DNA TITLE 2 OPERATOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: TETR FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: BIOQ; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(*AP*CP*CP*TP*GP*AP*AP*CP*AP*CP*CP*GP*TP*TP*CP*AP*AP*GP*T)-3'); COMPND 9 CHAIN: D, G; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'- COMPND 13 D(*AP*CP*TP*TP*GP*AP*AP*CP*GP*GP*TP*GP*TP*TP*CP*AP*GP*GP*T)-3'); COMPND 14 CHAIN: F; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 STRAIN: ATCC 700084 / MC(2)155; SOURCE 5 GENE: MSMEI_3111; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS BIOQ, DNA COMPLEX, TETR FAMILY, DNA BINDING PROTEIN, DNA BINDING KEYWDS 2 PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.YAN,Z.Y.GUAN,T.T.ZOU REVDAT 4 27-MAR-24 5YEJ 1 COMPND REVDAT 3 10-OCT-18 5YEJ 1 COMPND REMARK REVDAT 2 03-OCT-18 5YEJ 1 JRNL REVDAT 1 26-SEP-18 5YEJ 0 JRNL AUTH L.YAN,Q.TANG,Z.GUAN,K.PEI,T.ZOU,J.HE JRNL TITL STRUCTURAL INSIGHTS INTO OPERATOR RECOGNITION BY BIOQ IN THE JRNL TITL 2 MYCOBACTERIUM SMEGMATIS BIOTIN SYNTHESIS PATHWAY. JRNL REF BIOCHIM BIOPHYS ACTA GEN V.1862 1843 2018 JRNL REF 2 SUBJ JRNL REFN ISSN 0304-4165 JRNL PMID 29852200 JRNL DOI 10.1016/J.BBAGEN.2018.05.015 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 29496 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 1399 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 37.6792 - 5.8059 0.98 2849 133 0.1799 0.2238 REMARK 3 2 5.8059 - 4.6109 0.99 2857 123 0.2000 0.2309 REMARK 3 3 4.6109 - 4.0288 0.99 2834 144 0.1911 0.2543 REMARK 3 4 4.0288 - 3.6608 0.98 2836 144 0.2059 0.2407 REMARK 3 5 3.6608 - 3.3986 0.95 2731 134 0.2210 0.3106 REMARK 3 6 3.3986 - 3.1983 0.95 2732 122 0.2484 0.3195 REMARK 3 7 3.1983 - 3.0382 0.99 2803 147 0.2591 0.3177 REMARK 3 8 3.0382 - 2.9060 0.99 2836 158 0.2856 0.3696 REMARK 3 9 2.9060 - 2.7942 1.00 2866 155 0.3289 0.3930 REMARK 3 10 2.7942 - 2.6978 0.96 2753 139 0.3621 0.3922 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.050 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 : 0.009 5206 REMARK 3 ANGLE : 1.074 7302 REMARK 3 CHIRALITY : 0.060 851 REMARK 3 PLANARITY : 0.005 745 REMARK 3 DIHEDRAL : 28.278 1925 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 158.9312 11.9710 189.4112 REMARK 3 T TENSOR REMARK 3 T11: 0.8032 T22: 0.6355 REMARK 3 T33: 0.6484 T12: -0.0946 REMARK 3 T13: -0.1990 T23: 0.2080 REMARK 3 L TENSOR REMARK 3 L11: 1.4131 L22: 2.7487 REMARK 3 L33: 0.3075 L12: -0.9435 REMARK 3 L13: 0.0691 L23: 0.8327 REMARK 3 S TENSOR REMARK 3 S11: -0.1166 S12: -0.1452 S13: 0.0540 REMARK 3 S21: -0.0682 S22: 0.0308 S23: 0.1838 REMARK 3 S31: -0.0773 S32: 0.0086 S33: 0.0696 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 5YEJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300005147. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29957 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.690 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.7000 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: SAD REMARK 200 SOFTWARE USED: CRANK2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, MAGNESIUM ACETATE, 1 REMARK 280 -PROPANOL, MOPS, HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.15K 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 30.34350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 106.23400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.34350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 106.23400 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, G REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 -182.06100 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 BIOMT1 2 -1.000000 0.000000 0.000000 184.99286 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 347.74044 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, F, 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 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 F 101 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 MET A -26 REMARK 465 GLY A -25 REMARK 465 SER A -24 REMARK 465 HIS A -23 REMARK 465 HIS A -22 REMARK 465 HIS A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 GLY A -15 REMARK 465 LEU A -14 REMARK 465 VAL A -13 REMARK 465 PRO A -12 REMARK 465 ARG A -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 HIS A -8 REMARK 465 SER A -7 REMARK 465 ASP A -6 REMARK 465 GLU A -5 REMARK 465 VAL A -4 REMARK 465 ASP A -3 REMARK 465 ALA A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 VAL A 1 REMARK 465 ASP A 154 REMARK 465 ALA A 155 REMARK 465 VAL A 156 REMARK 465 GLY A 157 REMARK 465 ALA A 158 REMARK 465 LEU A 159 REMARK 465 GLY A 160 REMARK 465 ASP A 161 REMARK 465 ASP A 162 REMARK 465 GLN A 163 REMARK 465 SER A 164 REMARK 465 MET A 165 REMARK 465 LEU A 166 REMARK 465 THR A 167 REMARK 465 ARG A 168 REMARK 465 ASP A 169 REMARK 465 GLY A 170 REMARK 465 THR A 171 REMARK 465 GLY A 189 REMARK 465 GLY A 190 REMARK 465 GLY A 191 REMARK 465 SER A 192 REMARK 465 GLU A 193 REMARK 465 PHE A 194 REMARK 465 THR A 195 REMARK 465 GLY A 196 REMARK 465 PHE A 197 REMARK 465 SER A 198 REMARK 465 SER A 199 REMARK 465 ALA A 200 REMARK 465 GLU A 201 REMARK 465 ARG A 202 REMARK 465 SER A 203 REMARK 465 PHE A 204 REMARK 465 GLU A 205 REMARK 465 MET B -26 REMARK 465 GLY B -25 REMARK 465 SER B -24 REMARK 465 HIS B -23 REMARK 465 HIS B -22 REMARK 465 HIS B -21 REMARK 465 HIS B -20 REMARK 465 HIS B -19 REMARK 465 HIS B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 GLY B -15 REMARK 465 LEU B -14 REMARK 465 VAL B -13 REMARK 465 PRO B -12 REMARK 465 ARG B -11 REMARK 465 GLY B -10 REMARK 465 SER B -9 REMARK 465 HIS B -8 REMARK 465 SER B -7 REMARK 465 ASP B -6 REMARK 465 GLU B -5 REMARK 465 VAL B -4 REMARK 465 ASP B -3 REMARK 465 ALA B -2 REMARK 465 HIS B -1 REMARK 465 MET B 0 REMARK 465 VAL B 1 REMARK 465 ALA B 67 REMARK 465 LEU B 151 REMARK 465 GLN B 152 REMARK 465 TRP B 153 REMARK 465 ASP B 154 REMARK 465 ALA B 155 REMARK 465 VAL B 156 REMARK 465 GLY B 157 REMARK 465 ALA B 158 REMARK 465 LEU B 159 REMARK 465 GLY B 160 REMARK 465 ASP B 161 REMARK 465 ASP B 162 REMARK 465 GLN B 163 REMARK 465 SER B 164 REMARK 465 MET B 165 REMARK 465 LEU B 166 REMARK 465 THR B 167 REMARK 465 ARG B 168 REMARK 465 ASP B 169 REMARK 465 GLY B 170 REMARK 465 THR B 171 REMARK 465 GLY B 189 REMARK 465 GLY B 190 REMARK 465 GLY B 191 REMARK 465 SER B 192 REMARK 465 GLU B 193 REMARK 465 PHE B 194 REMARK 465 THR B 195 REMARK 465 GLY B 196 REMARK 465 PHE B 197 REMARK 465 SER B 198 REMARK 465 SER B 199 REMARK 465 ALA B 200 REMARK 465 GLU B 201 REMARK 465 ARG B 202 REMARK 465 SER B 203 REMARK 465 PHE B 204 REMARK 465 GLU B 205 REMARK 465 MET C -26 REMARK 465 GLY C -25 REMARK 465 SER C -24 REMARK 465 HIS C -23 REMARK 465 HIS C -22 REMARK 465 HIS C -21 REMARK 465 HIS C -20 REMARK 465 HIS C -19 REMARK 465 HIS C -18 REMARK 465 SER C -17 REMARK 465 SER C -16 REMARK 465 GLY C -15 REMARK 465 LEU C -14 REMARK 465 VAL C -13 REMARK 465 PRO C -12 REMARK 465 ARG C -11 REMARK 465 GLY C -10 REMARK 465 SER C -9 REMARK 465 HIS C -8 REMARK 465 SER C -7 REMARK 465 ASP C -6 REMARK 465 GLU C -5 REMARK 465 VAL C -4 REMARK 465 ASP C -3 REMARK 465 ALA C -2 REMARK 465 HIS C -1 REMARK 465 MET C 0 REMARK 465 VAL C 1 REMARK 465 ASP C 154 REMARK 465 ALA C 155 REMARK 465 VAL C 156 REMARK 465 GLY C 157 REMARK 465 ALA C 158 REMARK 465 LEU C 159 REMARK 465 GLY C 160 REMARK 465 ASP C 161 REMARK 465 ASP C 162 REMARK 465 GLN C 163 REMARK 465 SER C 164 REMARK 465 MET C 165 REMARK 465 LEU C 166 REMARK 465 THR C 167 REMARK 465 ARG C 168 REMARK 465 ASP C 169 REMARK 465 GLY C 170 REMARK 465 THR C 171 REMARK 465 GLY C 189 REMARK 465 GLY C 190 REMARK 465 GLY C 191 REMARK 465 SER C 192 REMARK 465 GLU C 193 REMARK 465 PHE C 194 REMARK 465 THR C 195 REMARK 465 GLY C 196 REMARK 465 PHE C 197 REMARK 465 SER C 198 REMARK 465 SER C 199 REMARK 465 ALA C 200 REMARK 465 GLU C 201 REMARK 465 ARG C 202 REMARK 465 SER C 203 REMARK 465 PHE C 204 REMARK 465 GLU C 205 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 ASP A 68 CG OD1 OD2 REMARK 470 LEU A 69 CG CD1 CD2 REMARK 470 GLU A 73 CG CD OE1 OE2 REMARK 470 GLN B 2 CG CD OE1 NE2 REMARK 470 ASP B 65 CG OD1 OD2 REMARK 470 ARG B 120 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 175 CG CD NE CZ NH1 NH2 REMARK 470 DA D 2 O5' REMARK 470 LEU C 69 CG CD1 CD2 REMARK 470 GLN C 74 CG CD OE1 NE2 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 CG2 ILE B 58 CD2 HIS B 89 1.75 REMARK 500 O ALA B 93 OG SER B 97 2.09 REMARK 500 CG2 ILE B 58 NE2 HIS B 89 2.12 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 DA D 10 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC D 11 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DC D 11 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA F 18 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC F 19 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT F 20 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG F 26 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA G 26 O4' - C1' - N9 ANGL. DEV. = 4.4 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 THR A 66 17.02 -143.37 REMARK 500 ASP A 68 41.56 -97.61 REMARK 500 LEU A 87 4.51 -67.26 REMARK 500 ALA A 121 6.65 -58.20 REMARK 500 GLN A 173 3.68 -60.68 REMARK 500 THR B 61 49.28 -93.16 REMARK 500 ALA B 62 -5.16 -141.19 REMARK 500 ALA B 187 15.30 -69.28 REMARK 500 THR C 66 31.43 -141.72 REMARK 500 ASP C 68 31.95 -99.64 REMARK 500 LEU C 87 1.29 -68.06 REMARK 500 GLN C 173 21.38 -77.54 REMARK 500 PHE C 176 -72.36 -59.15 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 GLN C 173 PHE C 174 143.72 REMARK 500 REMARK 500 REMARK: NULL DBREF 5YEJ A 2 205 UNP I7FDJ0 I7FDJ0_MYCS2 2 205 DBREF 5YEJ B 2 205 UNP I7FDJ0 I7FDJ0_MYCS2 2 205 DBREF 5YEJ D 2 20 PDB 5YEJ 5YEJ 2 20 DBREF 5YEJ F 18 36 PDB 5YEJ 5YEJ 18 36 DBREF 5YEJ G 18 36 PDB 5YEJ 5YEJ 18 36 DBREF 5YEJ C 2 205 UNP I7FDJ0 I7FDJ0_MYCS2 2 205 SEQADV 5YEJ MET A -26 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ GLY A -25 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ SER A -24 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS A -23 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS A -22 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS A -21 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS A -20 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS A -19 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS A -18 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ SER A -17 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ SER A -16 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ GLY A -15 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ LEU A -14 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ VAL A -13 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ PRO A -12 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ ARG A -11 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ GLY A -10 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ SER A -9 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS A -8 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ SER A -7 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ ASP A -6 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ GLU A -5 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ VAL A -4 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ ASP A -3 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ ALA A -2 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS A -1 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ MET A 0 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ VAL A 1 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ MET B -26 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ GLY B -25 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ SER B -24 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS B -23 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS B -22 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS B -21 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS B -20 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS B -19 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS B -18 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ SER B -17 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ SER B -16 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ GLY B -15 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ LEU B -14 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ VAL B -13 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ PRO B -12 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ ARG B -11 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ GLY B -10 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ SER B -9 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS B -8 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ SER B -7 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ ASP B -6 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ GLU B -5 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ VAL B -4 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ ASP B -3 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ ALA B -2 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS B -1 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ MET B 0 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ VAL B 1 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ MET C -26 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ GLY C -25 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ SER C -24 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS C -23 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS C -22 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS C -21 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS C -20 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS C -19 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS C -18 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ SER C -17 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ SER C -16 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ GLY C -15 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ LEU C -14 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ VAL C -13 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ PRO C -12 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ ARG C -11 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ GLY C -10 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ SER C -9 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS C -8 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ SER C -7 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ ASP C -6 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ GLU C -5 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ VAL C -4 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ ASP C -3 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ ALA C -2 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ HIS C -1 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ MET C 0 UNP I7FDJ0 EXPRESSION TAG SEQADV 5YEJ VAL C 1 UNP I7FDJ0 EXPRESSION TAG SEQRES 1 A 232 MET GLY SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU SEQRES 2 A 232 VAL PRO ARG GLY SER HIS SER ASP GLU VAL ASP ALA HIS SEQRES 3 A 232 MET VAL GLN LEU HIS LYS PRO ASP VAL VAL ALA ALA ALA SEQRES 4 A 232 THR LYS ILE LEU ASP ASP HIS GLY ILE ALA ASP LEU THR SEQRES 5 A 232 MET ARG ARG LEU ALA ARG GLU LEU ASP VAL THR PRO GLY SEQRES 6 A 232 ALA LEU TYR TRP HIS PHE ALA ASN LYS GLN GLU LEU LEU SEQRES 7 A 232 GLY ALA VAL ALA ASP HIS ILE LEU ARG THR ALA ARG THR SEQRES 8 A 232 ASP THR ALA ASP LEU ALA TRP ARG GLU GLN ILE HIS GLU SEQRES 9 A 232 SER CYS ARG ALA LEU ARG ASP ALA LEU LEU SER HIS THR SEQRES 10 A 232 ASP GLY ALA GLU LEU VAL SER ALA SER PHE ALA SER GLY SEQRES 11 A 232 GLN SER VAL VAL ILE THR GLU ILE VAL GLU GLN LEU GLY SEQRES 12 A 232 ARG ALA ALA ARG ALA ALA GLY VAL SER ASP ALA ASP VAL SEQRES 13 A 232 ASP ALA ALA ALA ARG THR VAL ILE TYR TYR VAL LEU GLY SEQRES 14 A 232 PHE THR VAL ASP GLU GLN SER ARG LEU GLN TRP ASP ALA SEQRES 15 A 232 VAL GLY ALA LEU GLY ASP ASP GLN SER MET LEU THR ARG SEQRES 16 A 232 ASP GLY THR ARG GLN PHE ARG PHE GLY LEU GLN LEU LEU SEQRES 17 A 232 VAL ASP GLY LEU ALA ALA HIS GLY GLY GLY SER GLU PHE SEQRES 18 A 232 THR GLY PHE SER SER ALA GLU ARG SER PHE GLU SEQRES 1 B 232 MET GLY SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU SEQRES 2 B 232 VAL PRO ARG GLY SER HIS SER ASP GLU VAL ASP ALA HIS SEQRES 3 B 232 MET VAL GLN LEU HIS LYS PRO ASP VAL VAL ALA ALA ALA SEQRES 4 B 232 THR LYS ILE LEU ASP ASP HIS GLY ILE ALA ASP LEU THR SEQRES 5 B 232 MET ARG ARG LEU ALA ARG GLU LEU ASP VAL THR PRO GLY SEQRES 6 B 232 ALA LEU TYR TRP HIS PHE ALA ASN LYS GLN GLU LEU LEU SEQRES 7 B 232 GLY ALA VAL ALA ASP HIS ILE LEU ARG THR ALA ARG THR SEQRES 8 B 232 ASP THR ALA ASP LEU ALA TRP ARG GLU GLN ILE HIS GLU SEQRES 9 B 232 SER CYS ARG ALA LEU ARG ASP ALA LEU LEU SER HIS THR SEQRES 10 B 232 ASP GLY ALA GLU LEU VAL SER ALA SER PHE ALA SER GLY SEQRES 11 B 232 GLN SER VAL VAL ILE THR GLU ILE VAL GLU GLN LEU GLY SEQRES 12 B 232 ARG ALA ALA ARG ALA ALA GLY VAL SER ASP ALA ASP VAL SEQRES 13 B 232 ASP ALA ALA ALA ARG THR VAL ILE TYR TYR VAL LEU GLY SEQRES 14 B 232 PHE THR VAL ASP GLU GLN SER ARG LEU GLN TRP ASP ALA SEQRES 15 B 232 VAL GLY ALA LEU GLY ASP ASP GLN SER MET LEU THR ARG SEQRES 16 B 232 ASP GLY THR ARG GLN PHE ARG PHE GLY LEU GLN LEU LEU SEQRES 17 B 232 VAL ASP GLY LEU ALA ALA HIS GLY GLY GLY SER GLU PHE SEQRES 18 B 232 THR GLY PHE SER SER ALA GLU ARG SER PHE GLU SEQRES 1 D 19 DA DC DC DT DG DA DA DC DA DC DC DG DT SEQRES 2 D 19 DT DC DA DA DG DT SEQRES 1 F 19 DA DC DT DT DG DA DA DC DG DG DT DG DT SEQRES 2 F 19 DT DC DA DG DG DT SEQRES 1 G 19 DA DC DC DT DG DA DA DC DA DC DC DG DT SEQRES 2 G 19 DT DC DA DA DG DT SEQRES 1 C 232 MET GLY SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU SEQRES 2 C 232 VAL PRO ARG GLY SER HIS SER ASP GLU VAL ASP ALA HIS SEQRES 3 C 232 MET VAL GLN LEU HIS LYS PRO ASP VAL VAL ALA ALA ALA SEQRES 4 C 232 THR LYS ILE LEU ASP ASP HIS GLY ILE ALA ASP LEU THR SEQRES 5 C 232 MET ARG ARG LEU ALA ARG GLU LEU ASP VAL THR PRO GLY SEQRES 6 C 232 ALA LEU TYR TRP HIS PHE ALA ASN LYS GLN GLU LEU LEU SEQRES 7 C 232 GLY ALA VAL ALA ASP HIS ILE LEU ARG THR ALA ARG THR SEQRES 8 C 232 ASP THR ALA ASP LEU ALA TRP ARG GLU GLN ILE HIS GLU SEQRES 9 C 232 SER CYS ARG ALA LEU ARG ASP ALA LEU LEU SER HIS THR SEQRES 10 C 232 ASP GLY ALA GLU LEU VAL SER ALA SER PHE ALA SER GLY SEQRES 11 C 232 GLN SER VAL VAL ILE THR GLU ILE VAL GLU GLN LEU GLY SEQRES 12 C 232 ARG ALA ALA ARG ALA ALA GLY VAL SER ASP ALA ASP VAL SEQRES 13 C 232 ASP ALA ALA ALA ARG THR VAL ILE TYR TYR VAL LEU GLY SEQRES 14 C 232 PHE THR VAL ASP GLU GLN SER ARG LEU GLN TRP ASP ALA SEQRES 15 C 232 VAL GLY ALA LEU GLY ASP ASP GLN SER MET LEU THR ARG SEQRES 16 C 232 ASP GLY THR ARG GLN PHE ARG PHE GLY LEU GLN LEU LEU SEQRES 17 C 232 VAL ASP GLY LEU ALA ALA HIS GLY GLY GLY SER GLU PHE SEQRES 18 C 232 THR GLY PHE SER SER ALA GLU ARG SER PHE GLU FORMUL 7 HOH *4(H2 O) HELIX 1 AA1 HIS A 4 GLY A 20 1 17 HELIX 2 AA2 THR A 25 LEU A 33 1 9 HELIX 3 AA3 THR A 36 GLY A 38 5 3 HELIX 4 AA4 ALA A 39 PHE A 44 1 6 HELIX 5 AA5 ASN A 46 LEU A 59 1 14 HELIX 6 AA6 ARG A 60 ALA A 62 5 3 HELIX 7 AA7 ALA A 70 LEU A 87 1 18 HELIX 8 AA8 ASP A 91 GLY A 103 1 13 HELIX 9 AA9 SER A 105 ALA A 121 1 17 HELIX 10 AB1 SER A 125 ALA A 127 5 3 HELIX 11 AB2 ASP A 128 TRP A 153 1 26 HELIX 12 AB3 GLN A 173 ALA A 187 1 15 HELIX 13 AB4 HIS B 4 GLY B 20 1 17 HELIX 14 AB5 ILE B 21 LEU B 24 5 4 HELIX 15 AB6 THR B 25 ASP B 34 1 10 HELIX 16 AB7 THR B 36 PHE B 44 1 9 HELIX 17 AB8 ASN B 46 THR B 61 1 16 HELIX 18 AB9 ALA B 70 SER B 88 1 19 HELIX 19 AC1 ASP B 91 GLY B 103 1 13 HELIX 20 AC2 SER B 105 GLY B 123 1 19 HELIX 21 AC3 ASP B 128 SER B 149 1 22 HELIX 22 AC4 GLN B 173 ALA B 187 1 15 HELIX 23 AC5 HIS C 4 HIS C 19 1 16 HELIX 24 AC6 THR C 25 LEU C 33 1 9 HELIX 25 AC7 THR C 36 HIS C 43 5 8 HELIX 26 AC8 ASN C 46 ARG C 60 1 15 HELIX 27 AC9 ALA C 70 LEU C 87 1 18 HELIX 28 AD1 ASP C 91 GLY C 103 1 13 HELIX 29 AD2 SER C 105 VAL C 124 1 20 HELIX 30 AD3 ASP C 128 GLN C 152 1 25 HELIX 31 AD4 GLN C 173 ALA C 187 1 15 CRYST1 60.687 212.468 88.126 90.00 99.43 90.00 C 1 2 1 12 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 0.016478 0.000000 0.002737 0.00000 SCALE2 0.000000 0.004707 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011503 0.00000