HEADER TRANSFERASE 30-JUN-19 6KD3 TITLE STRUCTURAL AND CATALYTIC ANALYSIS OF TWO DIVERSE URIDINE TITLE 2 PHOSPHORYLASES IN THE OOMYCETE PHYTOPHTHORA CAPSICI. COMPND MOL_ID: 1; COMPND 2 MOLECULE: URIDINE PHOSPHORYLASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.4.2.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYTOPHTHORA CAPSICI LT1534; SOURCE 3 ORGANISM_TAXID: 763924; SOURCE 4 STRAIN: LT1534; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS URIDINE PHOSPHORYLASE, PHYTOPHTHORA CAPSICI, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.C.YANG,X.G.ZHANG REVDAT 2 27-MAR-24 6KD3 1 REMARK REVDAT 1 25-DEC-19 6KD3 0 JRNL AUTH C.C.YANG,X.G.ZHANG JRNL TITL STRUCTURAL AND CATALYTIC ANALYSIS OF TWO DIVERSE URIDINE JRNL TITL 2 PHOSPHORYLASES IN THE OOMYCETE PHYTOPHTHORA CAPSICI. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 2.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 67.8 REMARK 3 NUMBER OF REFLECTIONS : 31606 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.388 REMARK 3 R VALUE (WORKING SET) : 0.386 REMARK 3 FREE R VALUE : 0.428 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1585 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 47.4000 - 6.1423 0.78 3278 154 0.4599 0.4710 REMARK 3 2 6.1423 - 4.8769 0.78 3157 190 0.4153 0.4506 REMARK 3 3 4.8769 - 4.2609 0.77 3137 142 0.3702 0.4296 REMARK 3 4 4.2609 - 3.8715 0.79 3164 185 0.3697 0.3952 REMARK 3 5 3.8715 - 3.5941 0.79 3236 160 0.3578 0.4298 REMARK 3 6 3.5941 - 3.3823 0.81 3225 175 0.3580 0.4275 REMARK 3 7 3.3823 - 3.2129 0.76 3040 164 0.3627 0.3993 REMARK 3 8 3.2129 - 3.0731 0.68 2706 149 0.3693 0.4309 REMARK 3 9 3.0731 - 2.9548 0.57 2249 121 0.3760 0.4139 REMARK 3 10 2.9548 - 2.8529 0.45 1791 95 0.3500 0.3743 REMARK 3 11 2.8529 - 2.7680 0.26 1038 50 0.3121 0.3386 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) : 0.730 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 54.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.16 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 6KD3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300012761. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-19 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 : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31606 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.760 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.23500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.4 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 : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM IODIDE, 20% PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K 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 52.91800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.19300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.91800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.19300 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -1 REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 PRO A 3 REMARK 465 ASN A 4 REMARK 465 MET A 5 REMARK 465 ASP A 6 REMARK 465 ALA A 7 REMARK 465 VAL A 8 REMARK 465 ALA A 9 REMARK 465 ASP A 10 REMARK 465 ALA A 11 REMARK 465 GLN A 39 REMARK 465 GLU A 40 REMARK 465 GLU A 41 REMARK 465 ALA A 309 REMARK 465 ALA A 310 REMARK 465 ALA A 311 REMARK 465 ALA A 312 REMARK 465 LEU A 313 REMARK 465 GLU A 314 REMARK 465 HIS A 315 REMARK 465 HIS A 316 REMARK 465 HIS A 317 REMARK 465 HIS A 318 REMARK 465 HIS A 319 REMARK 465 HIS A 320 REMARK 465 MET B -1 REMARK 465 GLY B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 PRO B 3 REMARK 465 ASN B 4 REMARK 465 MET B 5 REMARK 465 ASP B 6 REMARK 465 ALA B 7 REMARK 465 VAL B 8 REMARK 465 ALA B 9 REMARK 465 ASP B 10 REMARK 465 ALA B 11 REMARK 465 GLN B 39 REMARK 465 GLU B 40 REMARK 465 GLU B 41 REMARK 465 ALA B 309 REMARK 465 ALA B 310 REMARK 465 ALA B 311 REMARK 465 ALA B 312 REMARK 465 LEU B 313 REMARK 465 GLU B 314 REMARK 465 HIS B 315 REMARK 465 HIS B 316 REMARK 465 HIS B 317 REMARK 465 HIS B 318 REMARK 465 HIS B 319 REMARK 465 HIS B 320 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 THR A 12 CG2 REMARK 470 GLN A 14 CD OE1 NE2 REMARK 470 HIS A 16 ND1 CD2 CE1 NE2 REMARK 470 VAL A 17 CG2 REMARK 470 ARG A 18 CD NE CZ NH1 NH2 REMARK 470 HIS A 21 ND1 CD2 CE1 NE2 REMARK 470 LEU A 23 CG CD1 CD2 REMARK 470 GLU A 24 CD OE1 OE2 REMARK 470 HIS A 26 ND1 CD2 CE1 NE2 REMARK 470 VAL A 29 CG2 REMARK 470 PHE A 31 CD1 CD2 CE1 CE2 CZ REMARK 470 ILE A 33 CG2 CD1 REMARK 470 GLN A 43 CD OE1 NE2 REMARK 470 GLN A 44 CD OE1 NE2 REMARK 470 VAL A 45 CG1 REMARK 470 ASN A 47 CG OD1 ND2 REMARK 470 THR A 48 CG2 REMARK 470 PHE A 55 CD1 CD2 CE1 CE2 CZ REMARK 470 ILE A 56 CG2 CD1 REMARK 470 THR A 57 CG2 REMARK 470 GLU A 62 CD OE1 OE2 REMARK 470 THR A 65 CG2 REMARK 470 HIS A 66 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 69 CD OE1 NE2 REMARK 470 LYS A 73 CG CD CE NZ REMARK 470 ILE A 77 CG2 CD1 REMARK 470 THR A 78 CG2 REMARK 470 THR A 79 CG2 REMARK 470 TYR A 81 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR A 83 CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 84 CD OE1 NE2 REMARK 470 LEU A 85 CD1 CD2 REMARK 470 PRO A 87 CD REMARK 470 ILE A 88 CG2 CD1 REMARK 470 SER A 90 OG REMARK 470 THR A 95 OG1 CG2 REMARK 470 LEU A 96 CD1 CD2 REMARK 470 PHE A 97 CD1 CD2 CE1 CE2 CZ REMARK 470 VAL A 104 CG2 REMARK 470 ASN A 106 OD1 ND2 REMARK 470 ILE A 109 CG2 CD1 REMARK 470 MET A 111 SD CE REMARK 470 LEU A 117 CD1 CD2 REMARK 470 VAL A 121 CG2 REMARK 470 THR A 122 CG2 REMARK 470 GLU A 126 CD OE1 OE2 REMARK 470 HIS A 131 ND1 CD2 CE1 NE2 REMARK 470 TYR A 135 CD1 CD2 CE1 CE2 CZ OH REMARK 470 MET A 138 SD CE REMARK 470 VAL A 146 CG2 REMARK 470 GLU A 156 CD OE1 OE2 REMARK 470 ASN A 159 OD1 ND2 REMARK 470 ASN A 160 OD1 ND2 REMARK 470 LYS A 161 CD CE NZ REMARK 470 LEU A 162 CD1 CD2 REMARK 470 GLU A 163 CD OE1 OE2 REMARK 470 SER A 164 OG REMARK 470 VAL A 165 CG2 REMARK 470 ASP A 166 OD1 OD2 REMARK 470 VAL A 168 CG2 REMARK 470 THR A 174 CG2 REMARK 470 VAL A 175 CG2 REMARK 470 ARG A 177 CD NE CZ NH1 NH2 REMARK 470 PRO A 178 CD REMARK 470 ILE A 180 CG2 CD1 REMARK 470 PRO A 183 CD REMARK 470 GLU A 184 CD OE1 OE2 REMARK 470 ARG A 186 CD NE CZ NH1 NH2 REMARK 470 GLU A 188 CD OE1 OE2 REMARK 470 ILE A 189 CG2 CD1 REMARK 470 ILE A 190 CG2 CD1 REMARK 470 THR A 191 CG2 REMARK 470 LYS A 194 CD CE NZ REMARK 470 GLU A 195 CD OE1 OE2 REMARK 470 VAL A 196 CG2 REMARK 470 LEU A 198 CD1 CD2 REMARK 470 PRO A 199 CD REMARK 470 TYR A 200 CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 204 CD CE NZ REMARK 470 LEU A 206 CD1 CD2 REMARK 470 ASN A 209 OD1 ND2 REMARK 470 ILE A 222 CG2 CD1 REMARK 470 GLU A 224 CD OE1 OE2 REMARK 470 LEU A 227 CD1 CD2 REMARK 470 GLU A 228 CD OE1 OE2 REMARK 470 MET A 231 SD CE REMARK 470 PHE A 233 CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 235 CD OE1 NE2 REMARK 470 LYS A 236 CG CD CE NZ REMARK 470 LEU A 237 CG CD1 CD2 REMARK 470 ASP A 239 CG OD1 OD2 REMARK 470 ARG A 250 CD NE CZ NH1 NH2 REMARK 470 LEU A 251 CD1 CD2 REMARK 470 MET A 252 SD CE REMARK 470 PHE A 255 CD1 CD2 CE1 CE2 CZ REMARK 470 HIS A 257 ND1 CD2 CE1 NE2 REMARK 470 LYS A 258 CG CD CE NZ REMARK 470 LEU A 259 CD1 CD2 REMARK 470 ASN A 260 CG OD1 ND2 REMARK 470 ILE A 261 CG2 CD1 REMARK 470 PRO A 262 CD REMARK 470 VAL A 263 CG1 CG2 REMARK 470 ASN A 275 OD1 ND2 REMARK 470 VAL A 279 CG1 REMARK 470 LEU A 280 CD1 CD2 REMARK 470 HIS A 283 ND1 CD2 CE1 NE2 REMARK 470 GLU A 284 CD OE1 OE2 REMARK 470 THR A 285 CG2 REMARK 470 GLN A 287 CD OE1 NE2 REMARK 470 ASP A 288 OD1 OD2 REMARK 470 PHE A 289 CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 290 CD OE1 OE2 REMARK 470 ARG A 291 CD NE CZ NH1 NH2 REMARK 470 VAL A 296 CG2 REMARK 470 LEU A 297 CD1 CD2 REMARK 470 LEU A 298 CD1 CD2 REMARK 470 HIS A 299 ND1 CD2 CE1 NE2 REMARK 470 TYR A 300 CD1 CD2 CE1 CE2 CZ OH REMARK 470 VAL A 305 CG1 REMARK 470 ASN A 306 OD1 ND2 REMARK 470 SER A 308 OG REMARK 470 THR B 12 CG2 REMARK 470 GLN B 14 CD OE1 NE2 REMARK 470 HIS B 16 ND1 CD2 CE1 NE2 REMARK 470 VAL B 17 CG2 REMARK 470 ARG B 18 CD NE CZ NH1 NH2 REMARK 470 HIS B 21 ND1 CD2 CE1 NE2 REMARK 470 LEU B 23 CG CD1 CD2 REMARK 470 GLU B 24 CD OE1 OE2 REMARK 470 HIS B 26 ND1 CD2 CE1 NE2 REMARK 470 VAL B 29 CG2 REMARK 470 PHE B 31 CD1 CD2 CE1 CE2 CZ REMARK 470 ILE B 33 CG2 CD1 REMARK 470 GLN B 43 CD OE1 NE2 REMARK 470 GLN B 44 CD OE1 NE2 REMARK 470 VAL B 45 CG1 REMARK 470 ASN B 47 CG OD1 ND2 REMARK 470 THR B 48 CG2 REMARK 470 PHE B 55 CD1 CD2 CE1 CE2 CZ REMARK 470 ILE B 56 CG2 CD1 REMARK 470 THR B 57 CG2 REMARK 470 GLU B 62 CD OE1 OE2 REMARK 470 THR B 65 CG2 REMARK 470 HIS B 66 CG ND1 CD2 CE1 NE2 REMARK 470 GLN B 69 CD OE1 NE2 REMARK 470 LYS B 73 CG CD CE NZ REMARK 470 ILE B 77 CG2 CD1 REMARK 470 THR B 78 CG2 REMARK 470 THR B 79 CG2 REMARK 470 TYR B 81 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR B 83 CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN B 84 CD OE1 NE2 REMARK 470 LEU B 85 CD1 CD2 REMARK 470 PRO B 87 CD REMARK 470 ILE B 88 CG2 CD1 REMARK 470 SER B 90 OG REMARK 470 THR B 95 OG1 CG2 REMARK 470 LEU B 96 CD1 CD2 REMARK 470 PHE B 97 CD1 CD2 CE1 CE2 CZ REMARK 470 VAL B 104 CG1 REMARK 470 ASN B 106 OD1 ND2 REMARK 470 ILE B 109 CG2 CD1 REMARK 470 MET B 111 SD CE REMARK 470 LEU B 117 CD1 CD2 REMARK 470 VAL B 121 CG2 REMARK 470 THR B 122 CG2 REMARK 470 GLU B 126 CD OE1 OE2 REMARK 470 HIS B 131 ND1 CD2 CE1 NE2 REMARK 470 TYR B 135 CD1 CD2 CE1 CE2 CZ OH REMARK 470 MET B 138 SD CE REMARK 470 VAL B 146 CG1 REMARK 470 GLU B 156 CD OE1 OE2 REMARK 470 ASN B 159 OD1 ND2 REMARK 470 ASN B 160 OD1 ND2 REMARK 470 LYS B 161 CD CE NZ REMARK 470 LEU B 162 CD1 CD2 REMARK 470 GLU B 163 CD OE1 OE2 REMARK 470 SER B 164 OG REMARK 470 VAL B 165 CG2 REMARK 470 ASP B 166 OD1 OD2 REMARK 470 VAL B 168 CG2 REMARK 470 THR B 174 CG2 REMARK 470 VAL B 175 CG1 REMARK 470 ARG B 177 CD NE CZ NH1 NH2 REMARK 470 PRO B 178 CD REMARK 470 ILE B 180 CG2 CD1 REMARK 470 PRO B 183 CD REMARK 470 GLU B 184 CD OE1 OE2 REMARK 470 ARG B 186 CD NE CZ NH1 NH2 REMARK 470 GLU B 188 CD OE1 OE2 REMARK 470 ILE B 189 CG2 CD1 REMARK 470 ILE B 190 CG2 CD1 REMARK 470 THR B 191 CG2 REMARK 470 LYS B 194 CD CE NZ REMARK 470 GLU B 195 CD OE1 OE2 REMARK 470 VAL B 196 CG2 REMARK 470 LEU B 198 CD1 CD2 REMARK 470 PRO B 199 CD REMARK 470 TYR B 200 CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 204 CD CE NZ REMARK 470 LEU B 206 CD1 CD2 REMARK 470 ASN B 209 OD1 ND2 REMARK 470 ILE B 222 CG2 CD1 REMARK 470 GLU B 224 CD OE1 OE2 REMARK 470 LEU B 227 CD1 CD2 REMARK 470 GLU B 228 CD OE1 OE2 REMARK 470 MET B 231 SD CE REMARK 470 PHE B 233 CD1 CD2 CE1 CE2 CZ REMARK 470 GLN B 235 CD OE1 NE2 REMARK 470 LYS B 236 CG CD CE NZ REMARK 470 LEU B 237 CG CD1 CD2 REMARK 470 ASP B 239 CG OD1 OD2 REMARK 470 ARG B 250 CD NE CZ NH1 NH2 REMARK 470 LEU B 251 CD1 CD2 REMARK 470 MET B 252 SD CE REMARK 470 PHE B 255 CD1 CD2 CE1 CE2 CZ REMARK 470 HIS B 257 ND1 CD2 CE1 NE2 REMARK 470 LYS B 258 CG CD CE NZ REMARK 470 LEU B 259 CD1 CD2 REMARK 470 ASN B 260 CG OD1 ND2 REMARK 470 ILE B 261 CG2 CD1 REMARK 470 PRO B 262 CD REMARK 470 VAL B 263 CG1 CG2 REMARK 470 ASN B 275 OD1 ND2 REMARK 470 VAL B 279 CG1 REMARK 470 LEU B 280 CD1 CD2 REMARK 470 HIS B 283 ND1 CD2 CE1 NE2 REMARK 470 GLU B 284 CD OE1 OE2 REMARK 470 THR B 285 CG2 REMARK 470 GLN B 287 CD OE1 NE2 REMARK 470 ASP B 288 OD1 OD2 REMARK 470 PHE B 289 CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 290 CD OE1 OE2 REMARK 470 ARG B 291 CD NE CZ NH1 NH2 REMARK 470 VAL B 296 CG2 REMARK 470 LEU B 297 CD1 CD2 REMARK 470 LEU B 298 CD1 CD2 REMARK 470 HIS B 299 ND1 CD2 CE1 NE2 REMARK 470 TYR B 300 CD1 CD2 CE1 CE2 CZ OH REMARK 470 VAL B 305 CG1 REMARK 470 ASN B 306 OD1 ND2 REMARK 470 SER B 308 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 VAL A 263 O HOH A 401 1.91 REMARK 500 O CYS A 256 O HOH A 402 1.91 REMARK 500 O GLU A 213 O HOH A 403 1.93 REMARK 500 O ASP A 51 O HOH A 404 1.98 REMARK 500 OE1 GLU B 147 O HOH B 401 1.98 REMARK 500 OG1 THR B 269 O HOH B 402 1.98 REMARK 500 O TYR A 127 O HOH A 405 2.00 REMARK 500 O SER A 155 O HOH A 406 2.00 REMARK 500 O GLU A 195 O HOH A 407 2.00 REMARK 500 OH TYR A 94 O SER A 113 2.00 REMARK 500 OE1 GLN A 215 O HOH A 408 2.01 REMARK 500 O HOH B 424 O HOH B 428 2.01 REMARK 500 O SER B 90 O HOH B 403 2.02 REMARK 500 O GLU B 147 O HOH B 404 2.04 REMARK 500 O VAL A 168 O SER A 173 2.04 REMARK 500 O SER A 179 O HOH A 409 2.05 REMARK 500 NH1 ARG A 42 O HOH A 410 2.07 REMARK 500 O ALA A 192 O HOH A 411 2.07 REMARK 500 N ASN A 47 O HOH A 412 2.08 REMARK 500 OG1 THR A 226 OD2 ASP A 229 2.08 REMARK 500 OG SER A 179 O HOH A 413 2.09 REMARK 500 O THR A 48 O HOH A 414 2.09 REMARK 500 OG1 THR B 205 OD1 ASN B 244 2.09 REMARK 500 O GLN B 84 O HOH B 405 2.10 REMARK 500 O VAL A 170 N GLY A 172 2.12 REMARK 500 N CYS A 181 O HOH A 401 2.13 REMARK 500 O LEU B 271 O HOH B 402 2.13 REMARK 500 O CYS A 37 N ARG A 42 2.14 REMARK 500 O ALA B 192 O HOH B 406 2.14 REMARK 500 OD2 ASP A 210 O HOH A 415 2.15 REMARK 500 OE1 GLU A 213 O HOH A 415 2.16 REMARK 500 N VAL A 196 O HOH A 411 2.16 REMARK 500 O VAL B 146 O HOH B 404 2.17 REMARK 500 O HIS B 107 OG SER B 113 2.19 REMARK 500 NE2 HIS B 119 O HOH B 407 2.19 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 LEU B 171 CA - CB - CG ANGL. DEV. = 17.2 DEGREES REMARK 500 SER B 173 N - CA - C ANGL. DEV. = 23.2 DEGREES REMARK 500 THR B 174 N - CA - C ANGL. DEV. = 22.2 DEGREES REMARK 500 LEU B 271 CA - CB - CG ANGL. DEV. = 15.0 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 VAL A 15 93.02 -55.86 REMARK 500 ARG A 18 61.33 -67.96 REMARK 500 CYS A 37 -83.46 -111.55 REMARK 500 ALA A 61 -1.51 -52.15 REMARK 500 ARG A 63 -63.32 -96.95 REMARK 500 GLN A 84 60.41 38.04 REMARK 500 SER A 90 -72.63 59.24 REMARK 500 HIS A 107 23.13 -165.54 REMARK 500 SER A 141 -179.99 -179.50 REMARK 500 GLU A 147 152.78 -47.99 REMARK 500 VAL A 151 58.64 -91.48 REMARK 500 VAL A 152 93.29 -50.11 REMARK 500 SER A 155 -60.19 -92.30 REMARK 500 ASN A 159 -147.22 -117.93 REMARK 500 LEU A 171 -20.69 57.88 REMARK 500 SER A 173 -117.37 -71.44 REMARK 500 THR A 174 59.50 82.83 REMARK 500 PRO A 178 56.87 -146.87 REMARK 500 SER A 182 -82.32 -29.57 REMARK 500 GLU A 195 -62.14 -125.61 REMARK 500 VAL A 196 93.81 70.84 REMARK 500 TYR A 212 -61.30 -97.93 REMARK 500 GLN A 215 15.37 -62.42 REMARK 500 ASP A 219 49.26 -146.91 REMARK 500 THR A 226 -139.94 -116.38 REMARK 500 PHE A 233 -73.50 -51.94 REMARK 500 ASN A 244 133.47 179.76 REMARK 500 GLU A 246 -150.80 -151.10 REMARK 500 ARG A 250 -73.93 -56.41 REMARK 500 LEU A 251 -56.05 -18.97 REMARK 500 MET A 252 0.67 -69.63 REMARK 500 LEU A 271 167.56 164.19 REMARK 500 ARG A 273 4.62 -69.03 REMARK 500 ASP A 277 -15.56 -148.45 REMARK 500 SER A 282 -170.66 -67.93 REMARK 500 TYR B 83 -155.02 -86.25 REMARK 500 SER B 90 -66.70 62.79 REMARK 500 ALA B 133 83.87 -59.00 REMARK 500 SER B 155 -66.73 -92.85 REMARK 500 SER B 173 -69.23 -152.66 REMARK 500 PRO B 178 44.80 -152.80 REMARK 500 GLU B 187 -6.09 -59.60 REMARK 500 VAL B 196 78.17 -47.54 REMARK 500 LEU B 198 136.65 -173.55 REMARK 500 TYR B 212 -72.36 -93.03 REMARK 500 LEU B 218 38.79 -92.40 REMARK 500 ASP B 219 36.35 -155.23 REMARK 500 LYS B 258 -81.35 -45.86 REMARK 500 LEU B 259 25.73 -66.88 REMARK 500 ASN B 260 -11.21 81.34 REMARK 500 REMARK 500 THIS ENTRY HAS 53 RAMACHANDRAN OUTLIERS. 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 GLY A 216 ARG A 217 -148.67 REMARK 500 ALA B 192 ALA B 193 149.21 REMARK 500 REMARK 500 REMARK: NULL DBREF 6KD3 A -1 320 PDB 6KD3 6KD3 -1 320 DBREF 6KD3 B -1 320 PDB 6KD3 6KD3 -1 320 SEQRES 1 A 322 MET GLY MET ALA PRO ASN MET ASP ALA VAL ALA ASP ALA SEQRES 2 A 322 THR ALA GLN VAL HIS VAL ARG ASN SER HIS ILE LEU GLU SEQRES 3 A 322 MET HIS SER ASP VAL LEU PHE HIS ILE GLY LEU THR CYS SEQRES 4 A 322 SER GLN GLU GLU ARG GLN GLN VAL ALA ASN THR PHE GLY SEQRES 5 A 322 ASP VAL LYS PHE PHE ILE THR GLY GLY SER ALA GLU ARG SEQRES 6 A 322 MET THR HIS PHE ALA GLN SER VAL ALA LYS GLU LEU GLY SEQRES 7 A 322 ILE THR THR PRO TYR GLY TYR GLN LEU ALA PRO ILE GLY SEQRES 8 A 322 SER THR SER ARG TYR THR LEU PHE LYS VAL GLY PRO VAL SEQRES 9 A 322 LEU VAL ALA ASN HIS GLY ILE GLY MET PRO SER ILE SER SEQRES 10 A 322 ILE LEU LEU HIS GLU VAL THR LYS LEU LEU GLU TYR ALA SEQRES 11 A 322 GLY ALA HIS GLY ALA THR TYR ILE ARG MET GLY THR SER SEQRES 12 A 322 GLY GLY ILE GLY VAL GLU PRO GLY THR VAL VAL ILE THR SEQRES 13 A 322 SER GLU GLY VAL ASN ASN LYS LEU GLU SER VAL ASP GLU SEQRES 14 A 322 VAL ALA VAL LEU GLY SER THR VAL ARG ARG PRO SER ILE SEQRES 15 A 322 CYS SER PRO GLU VAL ARG GLU GLU ILE ILE THR ALA ALA SEQRES 16 A 322 LYS GLU VAL GLY LEU PRO TYR ALA VAL GLY LYS THR LEU SEQRES 17 A 322 SER CYS ASN ASP PHE TYR GLU GLY GLN GLY ARG LEU ASP SEQRES 18 A 322 GLY ALA ILE CYS GLU TYR THR LEU GLU ASP LYS MET ALA SEQRES 19 A 322 PHE LEU GLN LYS LEU ALA ASP ALA GLY VAL ARG ASN ILE SEQRES 20 A 322 GLU MET GLU ALA ARG LEU MET ALA GLY PHE CYS HIS LYS SEQRES 21 A 322 LEU ASN ILE PRO VAL ALA VAL VAL CYS VAL THR LEU LEU SEQRES 22 A 322 ASN ARG LEU ASN GLY ASP GLN VAL LEU SER SER HIS GLU SEQRES 23 A 322 THR LEU GLN ASP PHE GLU ARG ARG PRO GLY ALA VAL LEU SEQRES 24 A 322 LEU HIS TYR ILE LYS SER LYS VAL ASN ALA SER ALA ALA SEQRES 25 A 322 ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 322 MET GLY MET ALA PRO ASN MET ASP ALA VAL ALA ASP ALA SEQRES 2 B 322 THR ALA GLN VAL HIS VAL ARG ASN SER HIS ILE LEU GLU SEQRES 3 B 322 MET HIS SER ASP VAL LEU PHE HIS ILE GLY LEU THR CYS SEQRES 4 B 322 SER GLN GLU GLU ARG GLN GLN VAL ALA ASN THR PHE GLY SEQRES 5 B 322 ASP VAL LYS PHE PHE ILE THR GLY GLY SER ALA GLU ARG SEQRES 6 B 322 MET THR HIS PHE ALA GLN SER VAL ALA LYS GLU LEU GLY SEQRES 7 B 322 ILE THR THR PRO TYR GLY TYR GLN LEU ALA PRO ILE GLY SEQRES 8 B 322 SER THR SER ARG TYR THR LEU PHE LYS VAL GLY PRO VAL SEQRES 9 B 322 LEU VAL ALA ASN HIS GLY ILE GLY MET PRO SER ILE SER SEQRES 10 B 322 ILE LEU LEU HIS GLU VAL THR LYS LEU LEU GLU TYR ALA SEQRES 11 B 322 GLY ALA HIS GLY ALA THR TYR ILE ARG MET GLY THR SER SEQRES 12 B 322 GLY GLY ILE GLY VAL GLU PRO GLY THR VAL VAL ILE THR SEQRES 13 B 322 SER GLU GLY VAL ASN ASN LYS LEU GLU SER VAL ASP GLU SEQRES 14 B 322 VAL ALA VAL LEU GLY SER THR VAL ARG ARG PRO SER ILE SEQRES 15 B 322 CYS SER PRO GLU VAL ARG GLU GLU ILE ILE THR ALA ALA SEQRES 16 B 322 LYS GLU VAL GLY LEU PRO TYR ALA VAL GLY LYS THR LEU SEQRES 17 B 322 SER CYS ASN ASP PHE TYR GLU GLY GLN GLY ARG LEU ASP SEQRES 18 B 322 GLY ALA ILE CYS GLU TYR THR LEU GLU ASP LYS MET ALA SEQRES 19 B 322 PHE LEU GLN LYS LEU ALA ASP ALA GLY VAL ARG ASN ILE SEQRES 20 B 322 GLU MET GLU ALA ARG LEU MET ALA GLY PHE CYS HIS LYS SEQRES 21 B 322 LEU ASN ILE PRO VAL ALA VAL VAL CYS VAL THR LEU LEU SEQRES 22 B 322 ASN ARG LEU ASN GLY ASP GLN VAL LEU SER SER HIS GLU SEQRES 23 B 322 THR LEU GLN ASP PHE GLU ARG ARG PRO GLY ALA VAL LEU SEQRES 24 B 322 LEU HIS TYR ILE LYS SER LYS VAL ASN ALA SER ALA ALA SEQRES 25 B 322 ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *62(H2 O) HELIX 1 AA1 GLN A 44 GLY A 50 1 7 HELIX 2 AA2 ARG A 63 GLY A 76 1 14 HELIX 3 AA3 ILE A 109 GLY A 129 1 21 HELIX 4 AA4 CYS A 181 ALA A 193 1 13 HELIX 5 AA5 LEU A 227 GLY A 241 1 15 HELIX 6 AA6 ARG A 250 LYS A 258 1 9 HELIX 7 AA7 SER A 282 GLU A 290 1 9 HELIX 8 AA8 ARG A 291 ALA A 307 1 17 HELIX 9 AA9 GLN B 44 GLY B 50 1 7 HELIX 10 AB1 SER B 60 LEU B 75 1 16 HELIX 11 AB2 ILE B 109 ALA B 128 1 20 HELIX 12 AB3 CYS B 181 ILE B 190 1 10 HELIX 13 AB4 THR B 226 ASP B 239 1 14 HELIX 14 AB5 GLU B 248 LEU B 259 1 12 HELIX 15 AB6 ASN B 272 GLY B 276 5 5 HELIX 16 AB7 SER B 282 ARG B 291 1 10 HELIX 17 AB8 ARG B 291 ASN B 306 1 16 SHEET 1 AA1 2 VAL A 29 LEU A 30 0 SHEET 2 AA1 2 LEU A 35 THR A 36 -1 O LEU A 35 N LEU A 30 SHEET 1 AA2 4 VAL A 102 ASN A 106 0 SHEET 2 AA2 4 PHE A 54 GLY A 58 1 N PHE A 54 O LEU A 103 SHEET 3 AA2 4 THR A 134 GLY A 139 1 O MET A 138 N THR A 57 SHEET 4 AA2 4 VAL A 263 CYS A 267 1 O VAL A 266 N ARG A 137 SHEET 1 AA3 3 GLY A 157 VAL A 158 0 SHEET 2 AA3 3 LYS A 204 SER A 207 1 O THR A 205 N VAL A 158 SHEET 3 AA3 3 VAL A 242 GLU A 246 1 O ARG A 243 N LYS A 204 SHEET 1 AA4 9 THR B 95 VAL B 99 0 SHEET 2 AA4 9 VAL B 102 ASN B 106 -1 O ASN B 106 N THR B 95 SHEET 3 AA4 9 PHE B 54 GLY B 58 1 N ILE B 56 O LEU B 103 SHEET 4 AA4 9 THR B 134 GLY B 142 1 O ILE B 136 N PHE B 55 SHEET 5 AA4 9 VAL B 263 LEU B 271 1 O ALA B 264 N ARG B 137 SHEET 6 AA4 9 VAL B 152 VAL B 158 -1 N THR B 154 O VAL B 265 SHEET 7 AA4 9 VAL B 202 SER B 207 1 O GLY B 203 N SER B 155 SHEET 8 AA4 9 VAL B 242 GLU B 246 1 O ARG B 243 N LYS B 204 SHEET 9 AA4 9 THR B 134 GLY B 142 -1 N GLY B 142 O ILE B 245 SHEET 1 AA5 2 ASP B 166 GLU B 167 0 SHEET 2 AA5 2 VAL B 175 ARG B 176 -1 O ARG B 176 N ASP B 166 CRYST1 105.836 66.386 261.061 90.00 96.77 90.00 C 1 2 1 8 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 0.009449 0.000000 0.001122 0.00000 SCALE2 0.000000 0.015063 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003857 0.00000