HEADER OXIDOREDUCTASE 03-MAR-17 5X8O OBSLTE 18-MAR-20 5X8O 6LK4 TITLE CRYSTAL STRUCTURE OF GMP REDUCTASE FROM TRYPANOSOMA BRUCEI WITH TITLE 2 GUANOSINE 5'-TRIPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.205; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI BRUCEI (STRAIN 927/4 SOURCE 3 GUTAT10.1); SOURCE 4 ORGANISM_TAXID: 185431; SOURCE 5 STRAIN: 927/4 GUTAT10.1; SOURCE 6 GENE: TB927.5.2080; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS TRYPANOSOMA BRUCEI, COMPLEX, GTP, GUANOSINE 5'-TRIPHOSPHATE, KEYWDS 2 CYSTATHIONINE BETA SYNTHASE DOMAIN, GMP REDUCTASE, GUANOSINE 5'- KEYWDS 3 MONOPHOSPHATE REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.OTANI,A.IMAMURA,S.SUGIYAMA,S.NISHIMURA,T.INUI REVDAT 2 18-MAR-20 5X8O 1 OBSLTE REVDAT 1 07-MAR-18 5X8O 0 JRNL AUTH T.OTANI,A.IMAMURA,S.SUGIYAMA,S.NISHIMURA,T.INUI JRNL TITL CRYSTAL STRUCTURE OF GMP REDUCTASE FROM TRYPANOSOMA BRUCEI JRNL TITL 2 WITH GUANOSINE 5'-TRIPHOSPHATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 16778 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400 REMARK 3 FREE R VALUE TEST SET COUNT : 771 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1185 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 55 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3098 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 29 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.459 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.300 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.209 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.541 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.888 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3163 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3125 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4288 ; 1.881 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7141 ; 1.051 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 425 ; 7.035 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;36.252 ;22.679 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 543 ;17.544 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;18.368 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 524 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3572 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 660 ; 0.002 ; 0.020 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): 1706 ; 3.131 ; 4.181 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1705 ; 3.122 ; 4.180 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2129 ; 4.793 ; 6.264 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2130 ; 4.793 ; 6.267 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1457 ; 3.971 ; 4.628 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1441 ; 3.841 ; 4.611 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2134 ; 5.810 ; 6.736 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3346 ; 7.722 ;32.755 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3338 ; 7.555 ;32.686 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 : NULL 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5X8O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1300002961. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : OSCILLATION CAMERA REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 504783 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 28.70 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.0000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4DQW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES (PH 7.5), 0.4 M NAH2PO4, REMARK 280 0.4 M KH2PO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 71.78250 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 71.78250 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 67.29000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 71.78250 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 71.78250 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 67.29000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 71.78250 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 71.78250 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 67.29000 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 71.78250 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 71.78250 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 67.29000 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 71.78250 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 71.78250 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 67.29000 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 71.78250 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 71.78250 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 67.29000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 71.78250 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 71.78250 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 67.29000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 71.78250 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 71.78250 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 67.29000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 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 SER A 2 REMARK 465 ARG A 386 REMARK 465 VAL A 387 REMARK 465 LEU A 388 REMARK 465 VAL A 389 REMARK 465 LYS A 390 REMARK 465 ASP A 391 REMARK 465 GLY A 392 REMARK 465 GLN A 393 REMARK 465 LYS A 394 REMARK 465 VAL A 395 REMARK 465 LYS A 396 REMARK 465 ILE A 397 REMARK 465 ILE A 398 REMARK 465 ARG A 399 REMARK 465 GLY A 400 REMARK 465 MET A 401 REMARK 465 ALA A 402 REMARK 465 GLY A 403 REMARK 465 PHE A 404 REMARK 465 GLY A 405 REMARK 465 ALA A 406 REMARK 465 ASN A 407 REMARK 465 LEU A 408 REMARK 465 SER A 409 REMARK 465 LYS A 410 REMARK 465 ALA A 411 REMARK 465 GLU A 412 REMARK 465 ARG A 413 REMARK 465 GLU A 414 REMARK 465 ARG A 415 REMARK 465 THR A 416 REMARK 465 GLN A 417 REMARK 465 ASP A 418 REMARK 465 GLU A 419 REMARK 465 ASP A 420 REMARK 465 VAL A 421 REMARK 465 PHE A 422 REMARK 465 SER A 423 REMARK 465 SER A 424 REMARK 465 LEU A 425 REMARK 465 VAL A 426 REMARK 465 PRO A 427 REMARK 465 GLU A 428 REMARK 465 GLY A 429 REMARK 465 VAL A 430 REMARK 465 GLU A 431 REMARK 465 GLY A 432 REMARK 465 SER A 433 REMARK 465 VAL A 434 REMARK 465 GLY A 479 REMARK 465 LEU A 480 REMARK 465 ARG A 481 REMARK 465 GLU A 482 REMARK 465 SER A 483 REMARK 465 GLY A 484 REMARK 465 SER A 485 REMARK 465 HIS A 486 REMARK 465 GLY A 487 REMARK 465 VAL A 488 REMARK 465 ALA A 489 REMARK 465 LYS A 490 REMARK 465 LEU A 491 REMARK 465 LYS A 492 REMARK 465 LEU A 493 REMARK 465 ALA A 494 REMARK 465 ALA A 495 REMARK 465 ALA A 496 REMARK 465 LEU A 497 REMARK 465 GLU A 498 REMARK 465 HIS A 499 REMARK 465 HIS A 500 REMARK 465 HIS A 501 REMARK 465 HIS A 502 REMARK 465 HIS A 503 REMARK 465 HIS A 504 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 3 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 4 CG OD1 ND2 REMARK 470 LYS A 31 CG CD CE NZ REMARK 470 LYS A 44 CE NZ REMARK 470 GLU A 82 OE1 OE2 REMARK 470 LYS A 121 CG CD CE NZ REMARK 470 LYS A 136 CG CD CE NZ REMARK 470 LYS A 140 CD CE NZ REMARK 470 LYS A 151 CE NZ REMARK 470 GLU A 155 OE1 OE2 REMARK 470 LYS A 168 CE NZ REMARK 470 LYS A 188 CG CD CE NZ REMARK 470 LYS A 217 CG CD CE NZ REMARK 470 ASN A 218 CG OD1 ND2 REMARK 470 LYS A 219 CG CD CE NZ REMARK 470 LYS A 238 NZ REMARK 470 LYS A 239 CG CD CE NZ REMARK 470 ILE A 317 CG1 CD1 REMARK 470 ARG A 355 NE CZ NH1 NH2 REMARK 470 LYS A 461 CE NZ REMARK 470 ARG A 468 CG CD NE CZ NH1 NH2 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 ARG A 139 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 280 NE - CZ - NH1 ANGL. DEV. = 3.3 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 SER A 29 124.44 179.85 REMARK 500 PRO A 48 38.81 -82.48 REMARK 500 VAL A 57 -58.17 -123.79 REMARK 500 GLU A 59 -153.49 -119.54 REMARK 500 PHE A 78 60.99 -110.63 REMARK 500 GLU A 113 -48.78 88.87 REMARK 500 ASN A 119 48.37 -94.98 REMARK 500 ASN A 137 -73.89 -55.80 REMARK 500 ALA A 292 20.20 -146.32 REMARK 500 ILE A 317 51.58 -116.51 REMARK 500 CYS A 436 92.07 -163.62 REMARK 500 THR A 476 -60.12 -100.68 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 477 ALA A 478 -142.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 602 DBREF 5X8O A 1 491 UNP Q57ZS7 Q57ZS7_TRYB2 1 491 SEQADV 5X8O ARG A 115 UNP Q57ZS7 TRP 115 CONFLICT SEQADV 5X8O LYS A 492 UNP Q57ZS7 EXPRESSION TAG SEQADV 5X8O LEU A 493 UNP Q57ZS7 EXPRESSION TAG SEQADV 5X8O ALA A 494 UNP Q57ZS7 EXPRESSION TAG SEQADV 5X8O ALA A 495 UNP Q57ZS7 EXPRESSION TAG SEQADV 5X8O ALA A 496 UNP Q57ZS7 EXPRESSION TAG SEQADV 5X8O LEU A 497 UNP Q57ZS7 EXPRESSION TAG SEQADV 5X8O GLU A 498 UNP Q57ZS7 EXPRESSION TAG SEQADV 5X8O HIS A 499 UNP Q57ZS7 EXPRESSION TAG SEQADV 5X8O HIS A 500 UNP Q57ZS7 EXPRESSION TAG SEQADV 5X8O HIS A 501 UNP Q57ZS7 EXPRESSION TAG SEQADV 5X8O HIS A 502 UNP Q57ZS7 EXPRESSION TAG SEQADV 5X8O HIS A 503 UNP Q57ZS7 EXPRESSION TAG SEQADV 5X8O HIS A 504 UNP Q57ZS7 EXPRESSION TAG SEQRES 1 A 504 MET SER PHE ASN GLU SER ALA SER ILE PRO THR GLY LEU SEQRES 2 A 504 THR TYR ASP ASP VAL LEU ILE ILE PRO GLN HIS SER ARG SEQRES 3 A 504 VAL THR SER ARG LYS GLU VAL ASN THR THR THR ARG LEU SEQRES 4 A 504 SER ARG ASN VAL LYS LEU SER ILE PRO ILE VAL ALA SER SEQRES 5 A 504 ASN MET ASP THR VAL CYS GLU GLN ARG MET ALA VAL ALA SEQRES 6 A 504 MET ALA ARG GLU GLY GLY ILE GLY ILE LEU HIS ARG PHE SEQRES 7 A 504 CYS SER ILE GLU GLU GLN CYS ALA MET LEU ARG GLU VAL SEQRES 8 A 504 LYS ARG ALA GLN SER PHE LEU ILE GLU SER PRO ARG ILE SEQRES 9 A 504 ILE LEU PRO HIS GLU THR ALA ARG GLU ALA ARG GLU GLY SEQRES 10 A 504 LEU ASN TRP LYS GLY ARG VAL GLY GLY VAL GLY CYS LEU SEQRES 11 A 504 LEU VAL VAL ASN CYS LYS ASN GLU ARG LYS LEU LEU GLY SEQRES 12 A 504 ILE ILE THR ARG HIS ASP LEU LYS LEU ALA ASP GLU SER SEQRES 13 A 504 THR THR VAL GLU SER LEU MET THR PRO VAL ASP LYS MET SEQRES 14 A 504 VAL VAL SER THR ASN THR SER ILE SER LEU GLU GLU VAL SEQRES 15 A 504 THR HIS LEU MET ARG LYS GLY ARG THR ALA ASN VAL PRO SEQRES 16 A 504 ILE VAL GLY GLN ASN GLY GLN LEU LEU TYR LEU VAL THR SEQRES 17 A 504 LEU SER ASP VAL VAL LYS LEU ARG LYS ASN LYS GLN ALA SEQRES 18 A 504 SER LEU ASP SER ARG GLY ARG LEU LEU VAL GLY ALA ALA SEQRES 19 A 504 VAL GLY VAL LYS LYS ASP ASP MET ASN ARG ALA ILE ARG SEQRES 20 A 504 LEU VAL GLU ALA GLY ALA ASP VAL LEU VAL VAL ASP ILE SEQRES 21 A 504 ALA HIS GLY HIS SER ASP LEU CYS ILE ASN MET VAL LYS SEQRES 22 A 504 ARG LEU LYS GLY ASP PRO ARG THR ALA SER VAL ASP ILE SEQRES 23 A 504 ILE ALA GLY ASN ILE ALA SER ALA GLU ALA ALA GLU ALA SEQRES 24 A 504 LEU ILE ASP ALA GLY ALA ASP GLY LEU LYS ILE GLY VAL SEQRES 25 A 504 GLY PRO GLY SER ILE CYS ILE THR ARG LEU VAL ALA GLY SEQRES 26 A 504 ALA GLY VAL PRO GLN LEU SER ALA VAL LEU ALA CYS THR SEQRES 27 A 504 ARG VAL ALA ARG ARG ARG GLY VAL PRO CYS ILE ALA ASP SEQRES 28 A 504 GLY GLY LEU ARG THR SER GLY ASP ILE SER LYS ALA ILE SEQRES 29 A 504 GLY ALA GLY ALA ASP THR VAL MET LEU GLY ASN MET LEU SEQRES 30 A 504 ALA GLY THR ASP GLU ALA PRO GLY ARG VAL LEU VAL LYS SEQRES 31 A 504 ASP GLY GLN LYS VAL LYS ILE ILE ARG GLY MET ALA GLY SEQRES 32 A 504 PHE GLY ALA ASN LEU SER LYS ALA GLU ARG GLU ARG THR SEQRES 33 A 504 GLN ASP GLU ASP VAL PHE SER SER LEU VAL PRO GLU GLY SEQRES 34 A 504 VAL GLU GLY SER VAL ALA CYS LYS GLY PRO VAL GLY PRO SEQRES 35 A 504 ILE VAL ARG GLN LEU VAL GLY GLY LEU ARG SER GLY MET SEQRES 36 A 504 SER TYR SER GLY ALA LYS SER ILE GLU GLU MET GLN ARG SEQRES 37 A 504 ARG THR ARG PHE VAL ARG MET THR GLY ALA GLY LEU ARG SEQRES 38 A 504 GLU SER GLY SER HIS GLY VAL ALA LYS LEU LYS LEU ALA SEQRES 39 A 504 ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS HET GTP A 601 32 HET PO4 A 602 5 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM PO4 PHOSPHATE ION FORMUL 2 GTP C10 H16 N5 O14 P3 FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *29(H2 O) HELIX 1 AA1 GLU A 5 ILE A 9 5 5 HELIX 2 AA2 THR A 14 ASP A 16 5 3 HELIX 3 AA3 SER A 29 VAL A 33 5 5 HELIX 4 AA4 GLU A 59 GLU A 69 1 11 HELIX 5 AA5 SER A 80 ALA A 94 1 15 HELIX 6 AA6 THR A 110 ASN A 119 1 10 HELIX 7 AA7 HIS A 148 LYS A 151 5 4 HELIX 8 AA8 THR A 158 MET A 163 1 6 HELIX 9 AA9 ASP A 167 MET A 169 5 3 HELIX 10 AB1 SER A 178 ARG A 190 1 13 HELIX 11 AB2 LEU A 209 ASN A 218 1 10 HELIX 12 AB3 LYS A 238 ALA A 251 1 14 HELIX 13 AB4 SER A 265 GLY A 277 1 13 HELIX 14 AB5 SER A 293 ALA A 303 1 11 HELIX 15 AB6 CYS A 318 ALA A 324 1 7 HELIX 16 AB7 PRO A 329 GLY A 345 1 17 HELIX 17 AB8 THR A 356 ALA A 366 1 11 HELIX 18 AB9 PRO A 439 GLY A 459 1 21 HELIX 19 AC1 SER A 462 THR A 470 1 9 SHEET 1 AA1 2 VAL A 18 ILE A 20 0 SHEET 2 AA1 2 PHE A 472 ARG A 474 -1 O VAL A 473 N LEU A 19 SHEET 1 AA2 2 THR A 37 SER A 40 0 SHEET 2 AA2 2 VAL A 43 LEU A 45 -1 O VAL A 43 N SER A 40 SHEET 1 AA3 9 ILE A 49 ALA A 51 0 SHEET 2 AA3 9 ILE A 72 LEU A 75 1 O ILE A 72 N ALA A 51 SHEET 3 AA3 9 GLY A 232 VAL A 235 1 O ALA A 234 N LEU A 75 SHEET 4 AA3 9 VAL A 255 ASP A 259 1 O VAL A 257 N VAL A 235 SHEET 5 AA3 9 ASP A 285 ILE A 291 1 O ILE A 287 N VAL A 258 SHEET 6 AA3 9 GLY A 307 ILE A 310 1 O LYS A 309 N ALA A 288 SHEET 7 AA3 9 CYS A 348 ASP A 351 1 O ILE A 349 N ILE A 310 SHEET 8 AA3 9 THR A 370 LEU A 373 1 O THR A 370 N ALA A 350 SHEET 9 AA3 9 ILE A 49 ALA A 51 1 N VAL A 50 O LEU A 373 SHEET 1 AA4 3 ILE A 99 GLU A 100 0 SHEET 2 AA4 3 LEU A 203 THR A 208 -1 O LEU A 206 N ILE A 99 SHEET 3 AA4 3 ASN A 193 VAL A 197 -1 N ILE A 196 O LEU A 204 SHEET 1 AA5 4 ILE A 104 ILE A 105 0 SHEET 2 AA5 4 CYS A 129 VAL A 133 1 O VAL A 133 N ILE A 105 SHEET 3 AA5 4 LEU A 141 THR A 146 -1 O ILE A 145 N LEU A 130 SHEET 4 AA5 4 THR A 164 PRO A 165 -1 O THR A 164 N ILE A 144 CISPEP 1 GLY A 289 ASN A 290 0 13.06 SITE 1 AC1 16 ARG A 93 ALA A 94 GLN A 95 SER A 96 SITE 2 AC1 16 PRO A 102 ARG A 103 ARG A 123 VAL A 127 SITE 3 AC1 16 GLY A 128 CYS A 129 LEU A 206 THR A 208 SITE 4 AC1 16 SER A 210 ASP A 211 LYS A 214 HOH A 715 SITE 1 AC2 4 GLY A 352 GLY A 353 GLY A 374 ASN A 375 CRYST1 143.565 143.565 134.580 90.00 90.00 90.00 I 4 2 2 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006965 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006965 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007431 0.00000