HEADER TRANSFERASE 27-FEB-08 3CDJ TITLE CRYSTAL STRUCTURE OF THE E. COLI KH/S1 DOMAIN TRUNCATED PNPASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYNUCLEOTIDE PHOSPHORYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C TERMINAL S1/KH TRUNCATED PNPASE; COMPND 5 EC: 2.7.7.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: PNP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28C KEYWDS POLYNUCLEOTIDE PHOSPHORYLASE, MRNA TURNOVER, RNASE, RNA DEGRADATION, KEYWDS 2 RNASE PH DOMAIN, EXORIBONUCLEASE, KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.SHI,W.Z.YANG,S.LIN-CHAO,K.F.CHAK,H.S.YUAN REVDAT 2 01-NOV-23 3CDJ 1 REMARK REVDAT 1 09-DEC-08 3CDJ 0 JRNL AUTH Z.SHI,W.Z.YANG,S.LIN-CHAO,K.F.CHAK,H.S.YUAN JRNL TITL CRYSTAL STRUCTURE OF ESCHERICHIA COLI PNPASE: CENTRAL JRNL TITL 2 CHANNEL RESIDUES ARE INVOLVED IN PROCESSIVE RNA DEGRADATION. JRNL REF RNA V. 14 2361 2008 JRNL REFN ISSN 1355-8382 JRNL PMID 18812438 JRNL DOI 10.1261/RNA.1244308 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.3 REMARK 3 NUMBER OF REFLECTIONS : 17295 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.270 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1254 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3382 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 36 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.44 REMARK 3 ESD FROM SIGMAA (A) : 0.54 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.52 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.75 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.285 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.127 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3CDJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000046643. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-07 REMARK 200 TEMPERATURE (KELVIN) : 123 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13C1 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 : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17295 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 92.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1E3P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M AMMONIUM SULFATE AND 0.1M TRIS REMARK 280 -HCL, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 80.04250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.21256 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 51.05033 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 80.04250 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 46.21256 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 51.05033 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 80.04250 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 46.21256 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 51.05033 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 80.04250 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 46.21256 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 51.05033 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 80.04250 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 46.21256 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 51.05033 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 80.04250 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 46.21256 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 51.05033 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 92.42512 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 102.10067 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 92.42512 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 102.10067 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 92.42512 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 102.10067 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 92.42512 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 102.10067 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 92.42512 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 102.10067 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 92.42512 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 102.10067 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: 7610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 55580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 LYS A 18 REMARK 465 ARG A 19 REMARK 465 LYS A 20 REMARK 465 GLY A 98 REMARK 465 SER A 99 REMARK 465 PHE A 100 REMARK 465 PHE A 101 REMARK 465 ARG A 102 REMARK 465 ARG A 103 REMARK 465 GLU A 104 REMARK 465 GLY A 105 REMARK 465 ARG A 106 REMARK 465 PRO A 107 REMARK 465 GLY A 129 REMARK 465 VAL A 261 REMARK 465 ASN A 262 REMARK 465 GLU A 263 REMARK 465 ALA A 264 REMARK 465 LEU A 265 REMARK 465 ASN A 266 REMARK 465 ALA A 267 REMARK 465 ARG A 268 REMARK 465 VAL A 269 REMARK 465 ALA A 270 REMARK 465 ALA A 271 REMARK 465 LEU A 272 REMARK 465 ALA A 273 REMARK 465 GLU A 274 REMARK 465 ALA A 275 REMARK 465 ARG A 276 REMARK 465 LEU A 277 REMARK 465 SER A 278 REMARK 465 ASP A 279 REMARK 465 ALA A 280 REMARK 465 TYR A 281 REMARK 465 ARG A 282 REMARK 465 ILE A 283 REMARK 465 THR A 284 REMARK 465 ASP A 285 REMARK 465 LYS A 286 REMARK 465 GLN A 287 REMARK 465 GLU A 288 REMARK 465 ARG A 289 REMARK 465 TYR A 290 REMARK 465 ALA A 291 REMARK 465 GLN A 292 REMARK 465 VAL A 293 REMARK 465 ASP A 294 REMARK 465 VAL A 295 REMARK 465 ILE A 296 REMARK 465 LYS A 297 REMARK 465 SER A 298 REMARK 465 GLU A 299 REMARK 465 THR A 300 REMARK 465 ILE A 301 REMARK 465 ALA A 302 REMARK 465 THR A 303 REMARK 465 LEU A 304 REMARK 465 LEU A 305 REMARK 465 ALA A 306 REMARK 465 GLU A 307 REMARK 465 ASP A 308 REMARK 465 GLU A 309 REMARK 465 THR A 310 REMARK 465 LEU A 311 REMARK 465 ASP A 312 REMARK 465 GLU A 313 REMARK 465 ASN A 314 REMARK 465 GLU A 315 REMARK 465 LEU A 316 REMARK 465 GLY A 317 REMARK 465 GLU A 318 REMARK 465 ILE A 319 REMARK 465 LEU A 320 REMARK 465 HIS A 321 REMARK 465 ALA A 382 REMARK 465 ARG A 383 REMARK 465 ASP A 384 REMARK 465 ALA A 385 REMARK 465 GLN A 386 REMARK 465 VAL A 387 REMARK 465 LEU A 388 REMARK 465 ASP A 389 REMARK 465 GLU A 390 REMARK 465 LEU A 391 REMARK 465 MET A 392 REMARK 465 GLY A 393 REMARK 465 SER A 409 REMARK 465 VAL A 410 REMARK 465 GLY A 411 REMARK 465 GLU A 412 REMARK 465 THR A 413 REMARK 465 GLY A 414 REMARK 465 MET A 415 REMARK 465 VAL A 416 REMARK 465 GLY A 417 REMARK 465 SER A 418 REMARK 465 PRO A 419 REMARK 465 LYS A 420 REMARK 465 ARG A 421 REMARK 465 ARG A 422 REMARK 465 ILE A 564 REMARK 465 ASN A 565 REMARK 465 ALA A 566 REMARK 465 PRO A 567 REMARK 465 ARG A 568 REMARK 465 GLY A 569 REMARK 465 ASP A 570 REMARK 465 HIS A 571 REMARK 465 HIS A 572 REMARK 465 HIS A 573 REMARK 465 HIS A 574 REMARK 465 HIS A 575 REMARK 465 HIS A 576 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 OE2 GLU A 394 O HOH A 599 1.63 REMARK 500 O LYS A 325 N VAL A 327 1.76 REMARK 500 NH2 ARG A 342 O MET A 346 1.95 REMARK 500 O LYS A 539 O MET A 542 2.00 REMARK 500 O ASP A 340 N ARG A 342 2.03 REMARK 500 O ILE A 347 OD1 ASP A 503 2.12 REMARK 500 O LEU A 161 O SER A 164 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH1 ARG A 30 NH1 ARG A 30 18444 2.09 REMARK 500 NH2 ARG A 30 NH2 ARG A 30 18444 2.15 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 TYR A 91 CA TYR A 91 CB 0.205 REMARK 500 TYR A 91 CG TYR A 91 CD2 0.253 REMARK 500 TYR A 91 CE1 TYR A 91 CZ 0.194 REMARK 500 TYR A 91 CZ TYR A 91 CE2 0.103 REMARK 500 THR A 396 CA THR A 396 C -0.184 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 THR A 23 N - CA - C ANGL. DEV. = 17.1 DEGREES REMARK 500 LEU A 24 CA - CB - CG ANGL. DEV. = 19.0 DEGREES REMARK 500 LEU A 25 N - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 THR A 61 N - CA - C ANGL. DEV. = -17.1 DEGREES REMARK 500 ARG A 89 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 TYR A 91 CB - CG - CD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 TYR A 91 CB - CG - CD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 TYR A 91 CG - CD1 - CE1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ASN A 132 N - CA - C ANGL. DEV. = -18.4 DEGREES REMARK 500 SER A 164 CB - CA - C ANGL. DEV. = -12.3 DEGREES REMARK 500 SER A 164 N - CA - C ANGL. DEV. = -26.9 DEGREES REMARK 500 PRO A 171 C - N - CD ANGL. DEV. = -28.1 DEGREES REMARK 500 ASP A 199 N - CA - C ANGL. DEV. = -17.0 DEGREES REMARK 500 GLU A 215 N - CA - C ANGL. DEV. = -16.5 DEGREES REMARK 500 TRP A 256 CB - CA - C ANGL. DEV. = -14.9 DEGREES REMARK 500 TRP A 256 N - CA - C ANGL. DEV. = -27.4 DEGREES REMARK 500 GLN A 257 N - CA - CB ANGL. DEV. = 12.2 DEGREES REMARK 500 GLN A 257 N - CA - C ANGL. DEV. = -28.3 DEGREES REMARK 500 PRO A 258 C - N - CA ANGL. DEV. = 24.4 DEGREES REMARK 500 PRO A 258 C - N - CD ANGL. DEV. = -22.2 DEGREES REMARK 500 GLY A 335 N - CA - C ANGL. DEV. = -20.4 DEGREES REMARK 500 PRO A 337 C - N - CD ANGL. DEV. = -16.7 DEGREES REMARK 500 ARG A 338 C - N - CA ANGL. DEV. = 19.8 DEGREES REMARK 500 ARG A 338 N - CA - C ANGL. DEV. = 28.8 DEGREES REMARK 500 ILE A 339 N - CA - C ANGL. DEV. = -18.4 DEGREES REMARK 500 ARG A 342 N - CA - C ANGL. DEV. = -17.8 DEGREES REMARK 500 PRO A 358 C - N - CA ANGL. DEV. = 11.4 DEGREES REMARK 500 GLU A 394 CA - C - N ANGL. DEV. = -13.9 DEGREES REMARK 500 ARG A 395 N - CA - CB ANGL. DEV. = -19.1 DEGREES REMARK 500 ARG A 395 N - CA - C ANGL. DEV. = 46.1 DEGREES REMARK 500 PRO A 407 C - N - CA ANGL. DEV. = 21.0 DEGREES REMARK 500 PRO A 407 C - N - CD ANGL. DEV. = -17.8 DEGREES REMARK 500 PRO A 407 N - CA - C ANGL. DEV. = 17.4 DEGREES REMARK 500 SER A 457 N - CA - C ANGL. DEV. = 22.1 DEGREES REMARK 500 SER A 461 N - CA - C ANGL. DEV. = 24.5 DEGREES REMARK 500 MET A 463 N - CA - C ANGL. DEV. = -25.9 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 PRO A 27 125.08 -35.57 REMARK 500 GLN A 70 -122.71 43.19 REMARK 500 LYS A 71 -42.18 178.96 REMARK 500 LYS A 74 -153.52 -116.32 REMARK 500 ASP A 78 61.78 76.12 REMARK 500 GLU A 109 -136.88 46.49 REMARK 500 VAL A 131 22.27 -143.83 REMARK 500 PRO A 167 101.78 -45.05 REMARK 500 ASN A 187 61.83 32.79 REMARK 500 ALA A 249 -10.35 -144.50 REMARK 500 TRP A 256 120.02 163.76 REMARK 500 GLU A 259 177.61 -42.99 REMARK 500 ILE A 323 -58.06 -143.07 REMARK 500 GLU A 324 141.64 -5.40 REMARK 500 ASN A 326 -36.11 44.47 REMARK 500 PRO A 337 98.46 60.81 REMARK 500 ARG A 338 -122.77 19.67 REMARK 500 ASP A 340 86.10 68.87 REMARK 500 GLU A 343 -104.87 -51.26 REMARK 500 LYS A 344 15.27 -170.59 REMARK 500 ARG A 348 150.39 85.52 REMARK 500 ARG A 395 -83.21 -89.57 REMARK 500 PRO A 407 -147.93 32.35 REMARK 500 ASP A 440 -8.41 -58.15 REMARK 500 MET A 441 -12.14 72.42 REMARK 500 SER A 457 -165.05 140.84 REMARK 500 SER A 460 -33.36 -24.28 REMARK 500 SER A 462 105.01 -166.95 REMARK 500 MET A 463 -15.81 -161.45 REMARK 500 PRO A 479 63.90 -61.77 REMARK 500 ASP A 513 -71.33 75.20 REMARK 500 THR A 538 -72.64 -103.01 REMARK 500 LYS A 539 -69.09 -140.54 REMARK 500 GLN A 543 -28.09 146.34 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 GLU A 394 ARG A 395 -149.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU A 394 -11.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CDI RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY REMARK 999 EXIST IN THE UNIPROT. DBREF 3CDJ A 18 576 PDB 3CDJ 3CDJ 18 576 SEQRES 1 A 559 LYS ARG LYS ASP ILE THR LEU LEU ASN PRO ILE VAL ARG SEQRES 2 A 559 LYS PHE GLN TYR GLY GLN HIS THR VAL THR LEU GLU THR SEQRES 3 A 559 GLY MET MET ALA ARG GLN ALA THR ALA ALA VAL MET VAL SEQRES 4 A 559 SER MET ASP ASP THR ALA VAL PHE VAL THR VAL VAL GLY SEQRES 5 A 559 GLN LYS LYS ALA LYS PRO GLY GLN ASP PHE PHE PRO LEU SEQRES 6 A 559 THR VAL ASN TYR GLN GLU ARG THR TYR ALA ALA GLY ARG SEQRES 7 A 559 ILE PRO GLY SER PHE PHE ARG ARG GLU GLY ARG PRO SER SEQRES 8 A 559 GLU GLY GLU THR LEU ILE ALA ARG LEU ILE ASP ARG PRO SEQRES 9 A 559 ILE ARG PRO LEU PHE PRO GLU GLY PHE VAL ASN GLU VAL SEQRES 10 A 559 GLN VAL ILE ALA THR VAL VAL SER VAL ASN PRO GLN VAL SEQRES 11 A 559 ASN PRO ASP ILE VAL ALA MET ILE GLY ALA SER ALA ALA SEQRES 12 A 559 LEU SER LEU SER GLY ILE PRO PHE ASN GLY PRO ILE GLY SEQRES 13 A 559 ALA ALA ARG VAL GLY TYR ILE ASN ASP GLN TYR VAL LEU SEQRES 14 A 559 ASN PRO THR GLN ASP GLU LEU LYS GLU SER LYS LEU ASP SEQRES 15 A 559 LEU VAL VAL ALA GLY THR GLU ALA ALA VAL LEU MET VAL SEQRES 16 A 559 GLU SER GLU ALA GLN LEU LEU SER GLU ASP GLN MET LEU SEQRES 17 A 559 GLY ALA VAL VAL PHE GLY HIS GLU GLN GLN GLN VAL VAL SEQRES 18 A 559 ILE GLN ASN ILE ASN GLU LEU VAL LYS GLU ALA GLY LYS SEQRES 19 A 559 PRO ARG TRP ASP TRP GLN PRO GLU PRO VAL ASN GLU ALA SEQRES 20 A 559 LEU ASN ALA ARG VAL ALA ALA LEU ALA GLU ALA ARG LEU SEQRES 21 A 559 SER ASP ALA TYR ARG ILE THR ASP LYS GLN GLU ARG TYR SEQRES 22 A 559 ALA GLN VAL ASP VAL ILE LYS SER GLU THR ILE ALA THR SEQRES 23 A 559 LEU LEU ALA GLU ASP GLU THR LEU ASP GLU ASN GLU LEU SEQRES 24 A 559 GLY GLU ILE LEU HIS ALA ILE GLU LYS ASN VAL VAL ARG SEQRES 25 A 559 SER ARG VAL LEU ALA GLY GLU PRO ARG ILE ASP GLY ARG SEQRES 26 A 559 GLU LYS ASP MET ILE ARG GLY LEU ASP VAL ARG THR GLY SEQRES 27 A 559 VAL LEU PRO ARG THR HIS GLY SER ALA LEU PHE THR ARG SEQRES 28 A 559 GLY GLU THR GLN ALA LEU VAL THR ALA THR LEU GLY THR SEQRES 29 A 559 ALA ARG ASP ALA GLN VAL LEU ASP GLU LEU MET GLY GLU SEQRES 30 A 559 ARG THR ASP THR PHE LEU PHE HIS TYR ASN PHE PRO PRO SEQRES 31 A 559 TYR SER VAL GLY GLU THR GLY MET VAL GLY SER PRO LYS SEQRES 32 A 559 ARG ARG GLU ILE GLY HIS GLY ARG LEU ALA LYS ARG GLY SEQRES 33 A 559 VAL LEU ALA VAL MET PRO ASP MET ASP LYS PHE PRO TYR SEQRES 34 A 559 THR VAL ARG VAL VAL SER GLU ILE THR GLU SER ASN GLY SEQRES 35 A 559 SER SER SER MET ALA SER VAL CYS GLY ALA SER LEU ALA SEQRES 36 A 559 LEU MET ASP ALA GLY VAL PRO ILE LYS ALA ALA VAL ALA SEQRES 37 A 559 GLY ILE ALA MET GLY LEU VAL LYS GLU GLY ASP ASN TYR SEQRES 38 A 559 VAL VAL LEU SER ASP ILE LEU GLY ASP GLU ASP HIS LEU SEQRES 39 A 559 GLY ASP MET ASP PHE LYS VAL ALA GLY SER ARG ASP GLY SEQRES 40 A 559 ILE SER ALA LEU GLN MET ASP ILE LYS ILE GLU GLY ILE SEQRES 41 A 559 THR LYS GLU ILE MET GLN VAL ALA LEU ASN GLN ALA LYS SEQRES 42 A 559 GLY ALA ARG LEU HIS ILE LEU GLY VAL MET GLU GLN ALA SEQRES 43 A 559 ILE ASN ALA PRO ARG GLY ASP HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *36(H2 O) HELIX 1 1 THR A 90 GLY A 94 5 5 HELIX 2 2 GLY A 110 ARG A 123 1 14 HELIX 3 3 PRO A 124 PHE A 126 5 3 HELIX 4 4 ASN A 148 SER A 164 1 17 HELIX 5 5 ASP A 222 GLY A 250 1 29 HELIX 6 6 GLY A 427 ALA A 436 1 10 HELIX 7 7 MET A 463 ALA A 476 1 14 HELIX 8 8 LEU A 505 ASP A 509 5 5 HELIX 9 9 GLU A 540 GLU A 561 1 22 SHEET 1 A 3 ILE A 28 ARG A 30 0 SHEET 2 A 3 HIS A 37 THR A 43 -1 O THR A 43 N ILE A 28 SHEET 3 A 3 GLN A 33 TYR A 34 -1 N TYR A 34 O HIS A 37 SHEET 1 B 6 ILE A 28 ARG A 30 0 SHEET 2 B 6 HIS A 37 THR A 43 -1 O THR A 43 N ILE A 28 SHEET 3 B 6 ALA A 52 MET A 58 -1 O MET A 55 N GLU A 42 SHEET 4 B 6 THR A 61 VAL A 68 -1 O VAL A 67 N ALA A 52 SHEET 5 B 6 VAL A 134 SER A 142 -1 O VAL A 141 N ALA A 62 SHEET 6 B 6 LEU A 82 GLU A 88 1 N ASN A 85 O VAL A 136 SHEET 1 C 8 GLN A 183 LEU A 186 0 SHEET 2 C 8 GLY A 173 ILE A 180 -1 N GLY A 178 O VAL A 185 SHEET 3 C 8 LEU A 198 GLY A 204 -1 O LEU A 200 N VAL A 177 SHEET 4 C 8 VAL A 209 LEU A 219 -1 O GLU A 215 N ASP A 199 SHEET 5 C 8 ILE A 525 ILE A 532 -1 O ILE A 525 N LEU A 219 SHEET 6 C 8 MET A 514 GLY A 520 -1 N ALA A 519 O SER A 526 SHEET 7 C 8 ALA A 485 GLU A 494 -1 N LEU A 491 O MET A 514 SHEET 8 C 8 ASN A 497 LEU A 501 -1 O LEU A 501 N GLY A 490 SHEET 1 D 5 LEU A 350 THR A 354 0 SHEET 2 D 5 GLY A 362 ARG A 368 -1 O LEU A 365 N ARG A 353 SHEET 3 D 5 THR A 371 GLY A 380 -1 O ALA A 373 N PHE A 366 SHEET 4 D 5 THR A 447 GLU A 456 -1 O GLU A 453 N LEU A 374 SHEET 5 D 5 PHE A 399 ASN A 404 1 N LEU A 400 O VAL A 450 CRYST1 160.085 160.085 153.151 90.00 90.00 120.00 H 3 2 18 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 0.006247 0.003607 0.000000 0.00000 SCALE2 0.000000 0.007213 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006530 0.00000