HEADER DNA BINDING PROTEIN/DNA 30-OCT-12 2YPF TITLE STRUCTURE OF THE AVRBS3-DNA COMPLEX PROVIDES NEW INSIGHTS INTO TITLE 2 THE INITIAL THYMINE-RECOGNITION MECHANISM COMPND MOL_ID: 1; COMPND 2 MOLECULE: AVRBS3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AVIRULENCE PROTEIN AVRBS3; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*TP*TP*TP*AP*TP*AP*TP*AP*AP*AP*CP*CP*TP*AP COMPND 8 *AP*CP*CP*CP*TP*CP*TP*AP)-3'; COMPND 9 CHAIN: B; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-D(*TP*AP*GP*AP*GP*GP*GP*TP*TP*AP*GP*GP*TP*TP COMPND 12 *TP*AP*TP*AP*TP*AP*AP)-3'; COMPND 13 CHAIN: C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XANTHOMONAS CAMPESTRIS; SOURCE 3 ORGANISM_TAXID: 339; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET24A; 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 DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.STELLA,R.MOLINA,I.YEFIMENKO,J.PRIETO,G.H.SILVA,C.BERTONATI, AUTHOR 2 A.JUILLERAT,P.DUCHATEAU,G.MONTOYA REVDAT 2 11-SEP-13 2YPF 1 TITLE SOURCE REVDAT 1 28-AUG-13 2YPF 0 JRNL AUTH S.STELLA,R.MOLINA,I.YEFIMENKO,J.PRIETO,G.H.SILVA, JRNL AUTH 2 C.BERTONATI,A.JUILLERAT,P.DUCHATEAU,G.MONTOYA JRNL TITL STRUCTURE OF THE AVRBS3-DNA COMPLEX PROVIDES NEW INSIGHTS JRNL TITL 2 INTO THE INITIAL THYMINE-RECOGNITION MECHANISM JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 1707 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 23999294 JRNL DOI 10.1107/S0907444913016429 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 93.27 REMARK 3 NUMBER OF REFLECTIONS : 25764 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) : 0.23857 REMARK 3 R VALUE (WORKING SET) : 0.23578 REMARK 3 FREE R VALUE : 0.28983 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 1373 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) : 2.553 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.619 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1896 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.284 REMARK 3 BIN FREE R VALUE SET COUNT : 100 REMARK 3 BIN FREE R VALUE : 0.331 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4777 REMARK 3 NUCLEIC ACID ATOMS : 874 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.161 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.72 REMARK 3 B22 (A**2) : -1.27 REMARK 3 B33 (A**2) : 0.51 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : -0.08 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.970 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.367 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.284 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 25.211 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5816 ; 0.012 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8126 ; 1.897 ; 1.829 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 674 ; 7.588 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 165 ;44.084 ;26.727 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 758 ;21.737 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;22.616 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 973 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4021 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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 : NULL 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 REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2YPF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-SEP-12. REMARK 100 THE PDBE ID CODE IS EBI-53955. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL (PILATUS 6M) REMARK 200 DETECTOR MANUFACTURER : DECTRIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25764 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.55 REMARK 200 RESOLUTION RANGE LOW (A) : 32.29 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.3 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 2.2 REMARK 200 R MERGE (I) : 0.04 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.79 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.07 REMARK 200 R MERGE FOR SHELL (I) : 0.62 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.31 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 3V6T REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH=6.5, 5-15% PEG3350, REMARK 280 5-15% 2-PROPANOL 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 75.55500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.12500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 75.55500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 50.12500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 VAL A 151 REMARK 465 ASP A 152 REMARK 465 LEU A 153 REMARK 465 ARG A 154 REMARK 465 THR A 155 REMARK 465 LEU A 156 REMARK 465 ALA A 157 REMARK 465 TYR A 158 REMARK 465 SER A 159 REMARK 465 GLN A 160 REMARK 465 GLN A 161 REMARK 465 GLN A 162 REMARK 465 GLN A 163 REMARK 465 GLU A 164 REMARK 465 LYS A 165 REMARK 465 ILE A 166 REMARK 465 LYS A 167 REMARK 465 PRO A 168 REMARK 465 LYS A 169 REMARK 465 VAL A 170 REMARK 465 ARG A 171 REMARK 465 SER A 172 REMARK 465 THR A 173 REMARK 465 VAL A 174 REMARK 465 ALA A 175 REMARK 465 GLN A 176 REMARK 465 HIS A 177 REMARK 465 HIS A 178 REMARK 465 GLU A 179 REMARK 465 ALA A 180 REMARK 465 LEU A 181 REMARK 465 VAL A 182 REMARK 465 ALA A 183 REMARK 465 HIS A 184 REMARK 465 CYS A 862 REMARK 465 GLN A 863 REMARK 465 ALA A 864 REMARK 465 HIS A 865 REMARK 465 GLY A 866 REMARK 465 LEU A 867 REMARK 465 THR A 868 REMARK 465 PRO A 869 REMARK 465 GLN A 870 REMARK 465 GLN A 871 REMARK 465 VAL A 872 REMARK 465 VAL A 873 REMARK 465 ALA A 874 REMARK 465 ILE A 875 REMARK 465 ALA A 876 REMARK 465 SER A 877 REMARK 465 ASN A 878 REMARK 465 GLY A 879 REMARK 465 GLY A 880 REMARK 465 GLY A 881 REMARK 465 ARG A 882 REMARK 465 PRO A 883 REMARK 465 ALA A 884 REMARK 465 LEU A 885 REMARK 465 GLU A 886 REMARK 465 SER A 887 REMARK 465 ILE A 888 REMARK 465 VAL A 889 REMARK 465 ALA A 890 REMARK 465 GLN A 891 REMARK 465 LEU A 892 REMARK 465 SER A 893 REMARK 465 ARG A 894 REMARK 465 PRO A 895 REMARK 465 ASP A 896 REMARK 465 PRO A 897 REMARK 465 GLY A 898 REMARK 465 SER A 899 REMARK 465 SER A 900 REMARK 465 ALA A 901 REMARK 465 ALA A 902 REMARK 465 LEU A 903 REMARK 465 GLU A 904 REMARK 465 HIS A 905 REMARK 465 HIS A 906 REMARK 465 HIS A 907 REMARK 465 HIS A 908 REMARK 465 HIS A 909 REMARK 465 HIS A 910 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 PHE A 186 CG CD1 CD2 CE1 CE2 CZ REMARK 470 THR A 187 OG1 CG2 REMARK 470 HIS A 188 CG ND1 CD2 CE1 NE2 REMARK 470 HIS A 190 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 191 CG1 CG2 CD1 REMARK 470 VAL A 192 CG1 CG2 REMARK 470 LEU A 195 CG CD1 CD2 REMARK 470 SER A 197 OG REMARK 470 GLN A 198 CG CD OE1 NE2 REMARK 470 HIS A 199 CG ND1 CD2 CE1 NE2 REMARK 470 PRO A 200 CG CD REMARK 470 LEU A 203 CG CD1 CD2 REMARK 470 THR A 205 OG1 CG2 REMARK 470 VAL A 206 CG1 CG2 REMARK 470 VAL A 208 CG1 CG2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 TYR A 210 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 211 CG CD OE1 NE2 REMARK 470 ASP A 212 CG OD1 OD2 REMARK 470 MET A 213 CG SD CE REMARK 470 ILE A 214 CG1 CG2 CD1 REMARK 470 LEU A 217 CG CD1 CD2 REMARK 470 PRO A 218 CG CD REMARK 470 GLU A 219 CG CD OE1 OE2 REMARK 470 THR A 221 OG1 CG2 REMARK 470 HIS A 222 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 223 CG CD OE1 OE2 REMARK 470 ILE A 225 CG1 CG2 CD1 REMARK 470 VAL A 226 CG1 CG2 REMARK 470 VAL A 228 CG1 CG2 REMARK 470 LYS A 230 CG CD CE NZ REMARK 470 GLN A 231 CG CD OE1 NE2 REMARK 470 TRP A 232 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 232 CZ3 CH2 REMARK 470 SER A 233 OG 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 ARG A 236 O LYS A 265 2.13 REMARK 500 O ARG A 279 O LEU A 282 2.17 REMARK 500 O VAL A 295 OG SER A 299 1.85 REMARK 500 O ALA A 772 OG SER A 809 2.04 REMARK 500 NE2 GLN A 815 OP1 DC B 15 2.14 REMARK 500 N1 DA B 19 O4 DT C -19 2.18 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 DA B 3 O3' DT B 4 P -0.085 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 PRO A 200 N - CA - CB ANGL. DEV. = 7.6 DEGREES REMARK 500 PRO A 218 N - CA - CB ANGL. DEV. = 7.4 DEGREES REMARK 500 LEU A 314 CA - CB - CG ANGL. DEV. = 16.7 DEGREES REMARK 500 PRO A 655 C - N - CA ANGL. DEV. = 9.0 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 189 -48.31 54.46 REMARK 500 ILE A 191 -151.71 51.10 REMARK 500 HIS A 199 54.29 89.84 REMARK 500 ALA A 202 99.65 6.41 REMARK 500 ALA A 207 60.04 83.03 REMARK 500 LYS A 209 -155.55 -154.00 REMARK 500 GLN A 211 -162.65 64.56 REMARK 500 LEU A 217 41.85 74.14 REMARK 500 VAL A 228 -4.06 -51.47 REMARK 500 ALA A 235 68.96 -53.25 REMARK 500 ARG A 236 130.55 39.90 REMARK 500 ALA A 237 -123.10 -128.95 REMARK 500 GLU A 239 27.05 46.28 REMARK 500 ALA A 240 37.95 -99.69 REMARK 500 THR A 257 -6.36 -53.11 REMARK 500 LYS A 265 -43.02 -167.14 REMARK 500 ARG A 266 102.04 -177.18 REMARK 500 TRP A 278 95.96 -65.09 REMARK 500 ARG A 279 -78.83 -133.92 REMARK 500 LEU A 282 -153.81 176.43 REMARK 500 THR A 283 -53.11 66.35 REMARK 500 LEU A 287 52.04 -143.46 REMARK 500 ASN A 288 -19.80 170.12 REMARK 500 SER A 299 56.18 -101.68 REMARK 500 CYS A 420 -71.86 -84.51 REMARK 500 ALA A 468 -10.40 76.18 REMARK 500 GLN A 523 -72.86 -80.71 REMARK 500 GLN A 543 -35.40 -39.36 REMARK 500 GLU A 546 5.04 -67.14 REMARK 500 GLU A 564 -34.18 -34.76 REMARK 500 VAL A 588 -3.56 -59.53 REMARK 500 SER A 605 48.16 -93.23 REMARK 500 GLN A 617 -70.14 -85.00 REMARK 500 PRO A 631 -59.07 -29.89 REMARK 500 GLU A 648 1.06 -68.13 REMARK 500 PRO A 733 -35.51 -33.82 REMARK 500 PRO A 767 -22.57 -39.91 REMARK 500 PRO A 801 49.12 -87.63 REMARK 500 GLN A 802 -41.56 -134.75 REMARK 500 ASN A 810 159.20 110.41 REMARK 500 ALA A 830 43.27 -150.94 REMARK 500 VAL A 860 -76.58 -90.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ALA A 202 24.3 L L OUTSIDE RANGE REMARK 500 THR A 221 24.4 L L OUTSIDE RANGE REMARK 500 SER A 333 24.7 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL DBREF 2YPF A 151 910 PDB 2YPF 2YPF 151 910 DBREF 2YPF B -2 19 PDB 2YPF 2YPF -2 19 DBREF 2YPF C -19 1 PDB 2YPF 2YPF -19 1 SEQRES 1 A 758 VAL ASP LEU ARG THR LEU ALA TYR SER GLN GLN GLN GLN SEQRES 2 A 758 GLU LYS ILE LYS PRO LYS VAL ARG SER THR VAL ALA GLN SEQRES 3 A 758 HIS HIS GLU ALA LEU VAL ALA HIS ALA PHE THR HIS ALA SEQRES 4 A 758 HIS ILE VAL ALA LEU SER GLN HIS PRO ALA ALA LEU ALA SEQRES 5 A 758 THR VAL ALA VAL LYS TYR GLN ASP MET ILE ALA ALA LEU SEQRES 6 A 758 PRO GLU ALA THR HIS GLU ALA ILE VAL ALA VAL ALA LYS SEQRES 7 A 758 GLN TRP SER GLY ALA ARG ALA LEU GLU ALA LEU LEU THR SEQRES 8 A 758 VAL ALA GLY GLU LEU ARG GLY PRO PRO LEU GLN LEU ASP SEQRES 9 A 758 THR GLY GLN LEU LEU LYS ILE ALA LYS ARG GLY GLY VAL SEQRES 10 A 758 THR ALA VAL GLU ALA VAL HIS ALA TRP ARG ASN ALA LEU SEQRES 11 A 758 THR GLY ALA PRO LEU ASN LEU THR PRO GLU GLN VAL VAL SEQRES 12 A 758 ALA ILE ALA SER HIS ASP GLY GLY LYS GLN ALA LEU GLU SEQRES 13 A 758 THR VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA HIS SEQRES 14 A 758 GLY LEU THR PRO GLN GLN VAL VAL ALA ILE ALA SER ASN SEQRES 15 A 758 GLY GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG LEU SEQRES 16 A 758 LEU PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO GLU SEQRES 17 A 758 GLN VAL VAL ALA ILE ALA SER ASN ILE GLY GLY LYS GLN SEQRES 18 A 758 ALA LEU GLU THR VAL GLN ALA LEU LEU PRO VAL LEU CYS SEQRES 19 A 758 GLN ALA HIS GLY LEU THR PRO GLN GLN VAL VAL ALA ILE SEQRES 20 A 758 ALA SER ASN GLY GLY GLY LYS GLN ALA LEU GLU THR VAL SEQRES 21 A 758 GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY LEU SEQRES 22 A 758 THR PRO GLU GLN VAL VAL ALA ILE ALA SER ASN ILE GLY SEQRES 23 A 758 GLY LYS GLN ALA LEU GLU THR VAL GLN ALA LEU LEU PRO SEQRES 24 A 758 VAL LEU CYS GLN ALA HIS GLY LEU THR PRO GLU GLN VAL SEQRES 25 A 758 VAL ALA ILE ALA SER ASN ILE GLY GLY LYS GLN ALA LEU SEQRES 26 A 758 GLU THR VAL GLN ALA LEU LEU PRO VAL LEU CYS GLN ALA SEQRES 27 A 758 HIS GLY LEU THR PRO GLU GLN VAL VAL ALA ILE ALA SER SEQRES 28 A 758 ASN ILE GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ALA SEQRES 29 A 758 LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO SEQRES 30 A 758 GLU GLN VAL VAL ALA ILE ALA SER HIS ASP GLY GLY LYS SEQRES 31 A 758 GLN ALA LEU GLU THR VAL GLN ARG LEU LEU PRO VAL LEU SEQRES 32 A 758 CYS GLN ALA HIS GLY LEU THR PRO GLU GLN VAL VAL ALA SEQRES 33 A 758 ILE ALA SER HIS ASP GLY GLY LYS GLN ALA LEU GLU THR SEQRES 34 A 758 VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY SEQRES 35 A 758 LEU THR PRO GLN GLN VAL VAL ALA ILE ALA SER ASN GLY SEQRES 36 A 758 GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG LEU LEU SEQRES 37 A 758 PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO GLU GLN SEQRES 38 A 758 VAL VAL ALA ILE ALA SER ASN ILE GLY GLY LYS GLN ALA SEQRES 39 A 758 LEU GLU THR VAL GLN ALA LEU LEU PRO VAL LEU CYS GLN SEQRES 40 A 758 ALA HIS GLY LEU THR PRO GLU GLN VAL VAL ALA ILE ALA SEQRES 41 A 758 SER ASN ILE GLY GLY LYS GLN ALA LEU GLU THR VAL GLN SEQRES 42 A 758 ALA LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY LEU THR SEQRES 43 A 758 PRO GLU GLN VAL VAL ALA ILE ALA SER HIS ASP GLY GLY SEQRES 44 A 758 LYS GLN ALA LEU GLU THR VAL GLN ARG LEU LEU PRO VAL SEQRES 45 A 758 LEU CYS GLN ALA HIS GLY LEU THR PRO GLU GLN VAL VAL SEQRES 46 A 758 ALA ILE ALA SER HIS ASP GLY GLY LYS GLN ALA LEU GLU SEQRES 47 A 758 THR VAL GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA HIS SEQRES 48 A 758 GLY LEU THR PRO GLU GLN VAL VAL ALA ILE ALA SER HIS SEQRES 49 A 758 ASP GLY GLY LYS GLN ALA LEU GLU THR VAL GLN ARG LEU SEQRES 50 A 758 LEU PRO VAL LEU CYS GLN ALA HIS GLY LEU THR PRO GLN SEQRES 51 A 758 GLN VAL VAL ALA ILE ALA SER ASN GLY GLY GLY LYS GLN SEQRES 52 A 758 ALA LEU GLU THR VAL GLN ARG LEU LEU PRO VAL LEU CYS SEQRES 53 A 758 GLN ALA ALA GLY LEU THR PRO GLU GLN VAL VAL ALA ILE SEQRES 54 A 758 ALA SER HIS ASP GLY GLY LYS GLN ALA LEU GLU THR VAL SEQRES 55 A 758 GLN ARG LEU LEU PRO VAL LEU CYS GLN ALA HIS GLY LEU SEQRES 56 A 758 THR PRO GLN GLN VAL VAL ALA ILE ALA SER ASN GLY GLY SEQRES 57 A 758 GLY ARG PRO ALA LEU GLU SER ILE VAL ALA GLN LEU SER SEQRES 58 A 758 ARG PRO ASP PRO GLY SER SER ALA ALA LEU GLU HIS HIS SEQRES 59 A 758 HIS HIS HIS HIS SEQRES 1 B 22 DT DT DT DA DT DA DT DA DA DA DC DC DT SEQRES 2 B 22 DA DA DC DC DC DT DC DT DA SEQRES 1 C 21 DT DA DG DA DG DG DG DT DT DA DG DG DT SEQRES 2 C 21 DT DT DA DT DA DT DA DA FORMUL 4 HOH *175(H2 O) HELIX 1 1 ALA A 229 ALA A 235 1 7 HELIX 2 2 ALA A 240 THR A 243 5 4 HELIX 3 3 VAL A 244 GLY A 250 1 7 HELIX 4 4 GLY A 258 ILE A 263 1 6 HELIX 5 5 GLY A 267 TRP A 278 1 12 HELIX 6 6 GLU A 292 SER A 299 1 8 HELIX 7 7 GLY A 302 LEU A 314 1 13 HELIX 8 8 LEU A 314 GLN A 319 1 6 HELIX 9 9 THR A 324 SER A 333 1 10 HELIX 10 10 GLY A 336 ALA A 354 1 19 HELIX 11 11 THR A 358 SER A 367 1 10 HELIX 12 12 GLY A 370 GLN A 387 1 18 HELIX 13 13 THR A 392 SER A 401 1 10 HELIX 14 14 GLY A 404 GLN A 421 1 18 HELIX 15 15 THR A 426 SER A 435 1 10 HELIX 16 16 GLY A 438 GLY A 458 1 21 HELIX 17 17 THR A 460 VAL A 465 1 6 HELIX 18 18 GLY A 472 LEU A 484 1 13 HELIX 19 19 LEU A 484 GLN A 489 1 6 HELIX 20 20 THR A 494 SER A 503 1 10 HELIX 21 21 GLY A 506 ALA A 524 1 19 HELIX 22 22 THR A 528 SER A 537 1 10 HELIX 23 23 GLY A 540 ALA A 558 1 19 HELIX 24 24 THR A 562 ALA A 570 1 9 HELIX 25 25 GLY A 574 GLN A 591 1 18 HELIX 26 26 THR A 596 SER A 605 1 10 HELIX 27 27 GLY A 608 ARG A 618 1 11 HELIX 28 28 LEU A 619 ALA A 626 1 8 HELIX 29 29 THR A 630 SER A 639 1 10 HELIX 30 30 GLY A 642 GLU A 648 1 7 HELIX 31 31 LEU A 654 GLN A 659 1 6 HELIX 32 32 THR A 664 SER A 673 1 10 HELIX 33 33 GLY A 676 ALA A 686 1 11 HELIX 34 34 LEU A 687 GLY A 696 1 10 HELIX 35 35 THR A 698 VAL A 702 5 5 HELIX 36 36 GLY A 710 ARG A 720 1 11 HELIX 37 37 LEU A 722 GLN A 727 1 6 HELIX 38 38 THR A 732 SER A 741 1 10 HELIX 39 39 GLY A 744 LEU A 755 1 12 HELIX 40 40 PRO A 757 ALA A 762 1 6 HELIX 41 41 THR A 766 SER A 775 1 10 HELIX 42 42 GLY A 778 LEU A 790 1 13 HELIX 43 43 GLN A 802 SER A 809 1 8 HELIX 44 44 GLY A 812 VAL A 820 1 9 HELIX 45 45 THR A 834 SER A 843 1 10 HELIX 46 46 LYS A 848 ARG A 856 1 9 CISPEP 1 ALA A 201 ALA A 202 0 4.10 CISPEP 2 ALA A 216 LEU A 217 0 -3.56 CISPEP 3 ALA A 220 THR A 221 0 -10.83 CISPEP 4 ARG A 236 ALA A 237 0 10.31 CISPEP 5 PRO A 251 PRO A 252 0 -13.28 CISPEP 6 LEU A 287 ASN A 288 0 26.98 CRYST1 151.110 100.250 61.370 90.00 102.55 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 0.006618 0.000000 0.001473 0.00000 SCALE2 0.000000 0.009975 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016693 0.00000 MASTER 499 0 0 46 0 0 0 6 0 0 0 63 END