PDB Short entry for 5KAL HEADER TRANSFERASE/RNA 01-JUN-16 5KAL TITLE TERMINAL URIDYLYL TRANSFERASE 4 FROM TRYPANOSOMA BRUCEI WITH BOUND UTP TITLE 2 AND UPU COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA URIDYLYLTRANSFERASE 4; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (5'-R(*UP*U)-3'); COMPND 7 CHAIN: Y, Z; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 3 ORGANISM_TAXID: 5691; SOURCE 4 GENE: TUT4; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 10 ORGANISM_TAXID: 5691 KEYWDS TRYPANOSOMA, RNA EDITING, TUTASE, TRANSFERASE, TRANSFERASE-RNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.R.STAGNO,H.LUECKE,R.AFASIZHEV REVDAT 3 27-SEP-23 5KAL 1 LINK REVDAT 2 28-DEC-16 5KAL 1 JRNL REVDAT 1 26-OCT-16 5KAL 0 JRNL AUTH L.RAJAPPA-TITU,T.SUEMATSU,P.MUNOZ-TELLO,M.LONG,O.DEMIR, JRNL AUTH 2 K.J.CHENG,J.R.STAGNO,H.LUECKE,R.E.AMARO,I.APHASIZHEVA, JRNL AUTH 3 R.APHASIZHEV,S.THORE JRNL TITL RNA EDITING TUTASE 1: STRUCTURAL FOUNDATION OF SUBSTRATE JRNL TITL 2 RECOGNITION, COMPLEX INTERACTIONS AND DRUG TARGETING. JRNL REF NUCLEIC ACIDS RES. V. 44 10862 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 27744351 JRNL DOI 10.1093/NAR/GKW917 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV-2447_1692: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 20345 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.260 REMARK 3 FREE R VALUE TEST SET COUNT : 1070 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 47.1356 - 5.4975 0.99 2509 137 0.2047 0.2316 REMARK 3 2 5.4975 - 4.3645 0.98 2390 125 0.1593 0.1824 REMARK 3 3 4.3645 - 3.8131 1.00 2433 133 0.1698 0.2226 REMARK 3 4 3.8131 - 3.4646 1.00 2411 129 0.2001 0.2490 REMARK 3 5 3.4646 - 3.2163 1.00 2374 145 0.2407 0.2984 REMARK 3 6 3.2163 - 3.0267 1.00 2366 142 0.2894 0.3557 REMARK 3 7 3.0267 - 2.8752 1.00 2403 125 0.3006 0.3411 REMARK 3 8 2.8752 - 2.7500 1.00 2389 134 0.3328 0.4429 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.014 5428 REMARK 3 ANGLE : 0.566 7358 REMARK 3 CHIRALITY : 0.043 827 REMARK 3 PLANARITY : 0.003 931 REMARK 3 DIHEDRAL : 10.891 3246 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 23.1549 26.5803 -69.6440 REMARK 3 T TENSOR REMARK 3 T11: 0.1661 T22: 0.1747 REMARK 3 T33: 0.2623 T12: 0.0165 REMARK 3 T13: 0.0413 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 0.5192 L22: 0.7617 REMARK 3 L33: 1.8922 L12: -0.1128 REMARK 3 L13: 0.5518 L23: -0.3190 REMARK 3 S TENSOR REMARK 3 S11: 0.0363 S12: 0.0867 S13: 0.0307 REMARK 3 S21: -0.1314 S22: -0.0301 S23: 0.0054 REMARK 3 S31: -0.0717 S32: 0.0687 S33: -0.0172 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 5KAL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000221951. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-AUG-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20369 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 47.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.520 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.48 REMARK 200 R MERGE FOR SHELL (I) : 0.37400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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: 2IKF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM CACODYLATE PH 6.5, 200MM REMARK 280 CALCIUM ACETATE, 18% PEG-8000, 5MM UTP, 5MM UPU, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 21.43800 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, Y 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 REMARK 350 BIOMOLECULE: 2 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: 2010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, Z 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 LYS A 22 REMARK 465 ASP A 23 REMARK 465 LEU A 24 REMARK 465 HIS A 25 REMARK 465 THR A 26 REMARK 465 ARG A 27 REMARK 465 VAL A 333 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 GLN B 18 REMARK 465 PHE B 19 REMARK 465 VAL B 20 REMARK 465 SER B 21 REMARK 465 LYS B 22 REMARK 465 ASP B 23 REMARK 465 LEU B 24 REMARK 465 HIS B 25 REMARK 465 THR B 26 REMARK 465 ARG B 27 REMARK 465 HIS B 28 REMARK 465 GLY B 130 REMARK 465 GLY B 131 REMARK 465 ALA B 132 REMARK 465 VAL B 133 REMARK 465 VAL B 333 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 HOH A 610 O HOH A 649 2.18 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 132 73.51 -103.83 REMARK 500 LYS A 256 -32.28 -132.43 REMARK 500 ARG A 283 91.79 -168.12 REMARK 500 ASN A 285 18.60 47.04 REMARK 500 LYS B 256 -33.75 -132.34 REMARK 500 TRP B 274 67.26 -100.34 REMARK 500 VAL B 289 143.30 -178.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 66 OD1 REMARK 620 2 ASP A 68 OD2 94.4 REMARK 620 3 UTP A 501 O1A 137.7 101.1 REMARK 620 4 UTP A 501 O1B 151.5 88.6 68.7 REMARK 620 5 UTP A 501 O3G 98.1 163.3 76.9 75.2 REMARK 620 6 HOH A 602 O 88.1 71.0 61.0 119.5 120.2 REMARK 620 7 HOH A 638 O 76.0 84.2 144.2 76.1 88.1 149.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG Y 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 UTP A 501 O1A REMARK 620 2 HOH A 602 O 63.4 REMARK 620 3 HOH A 610 O 67.6 108.1 REMARK 620 4 HOH A 613 O 94.4 148.9 79.9 REMARK 620 5 HOH A 649 O 94.9 75.6 59.8 130.8 REMARK 620 6 U Y 2 O3' 108.2 81.0 165.1 86.3 134.9 REMARK 620 7 HOH Y 205 O 138.8 150.3 75.7 60.3 81.9 102.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 66 OD1 REMARK 620 2 ASP B 68 OD2 84.9 REMARK 620 3 UTP B 401 O1A 134.4 119.3 REMARK 620 4 UTP B 401 O1B 139.9 94.4 80.2 REMARK 620 5 UTP B 401 O3G 83.2 150.2 88.0 77.8 REMARK 620 6 HOH B 507 O 79.0 71.4 74.4 138.6 132.2 REMARK 620 7 HOH B 508 O 59.8 69.5 161.0 82.4 80.9 124.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 66 OD2 REMARK 620 2 ASP B 136 OD1 107.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG Z 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 UTP B 401 O1A REMARK 620 2 HOH B 505 O 68.3 REMARK 620 3 HOH B 506 O 87.9 80.3 REMARK 620 4 HOH B 507 O 73.7 118.5 144.2 REMARK 620 5 HOH B 527 O 106.8 71.5 139.8 75.7 REMARK 620 6 U Z 2 O3' 121.6 153.8 76.2 87.6 121.4 REMARK 620 7 HOH Z 202 O 140.6 73.6 76.0 136.4 69.0 89.5 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UTP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UTP B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG Y 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG Z 101 DBREF 5KAL A 1 333 UNP A4UBD5 A4UBD5_9TRYP 1 333 DBREF 5KAL B 1 333 UNP A4UBD5 A4UBD5_9TRYP 1 333 DBREF 5KAL Y 1 2 PDB 5KAL 5KAL 1 2 DBREF 5KAL Z 1 2 PDB 5KAL 5KAL 1 2 SEQADV 5KAL MET A -19 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL GLY A -18 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL SER A -17 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL SER A -16 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL HIS A -15 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL HIS A -14 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL HIS A -13 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL HIS A -12 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL HIS A -11 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL HIS A -10 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL SER A -9 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL SER A -8 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL GLY A -7 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL LEU A -6 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL VAL A -5 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL PRO A -4 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL ARG A -3 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL GLY A -2 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL SER A -1 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL HIS A 0 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL MET B -19 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL GLY B -18 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL SER B -17 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL SER B -16 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL HIS B -15 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL HIS B -14 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL HIS B -13 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL HIS B -12 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL HIS B -11 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL HIS B -10 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL SER B -9 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL SER B -8 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL GLY B -7 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL LEU B -6 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL VAL B -5 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL PRO B -4 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL ARG B -3 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL GLY B -2 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL SER B -1 UNP A4UBD5 EXPRESSION TAG SEQADV 5KAL HIS B 0 UNP A4UBD5 EXPRESSION TAG SEQRES 1 A 353 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 353 LEU VAL PRO ARG GLY SER HIS MET PRO PRO SER PRO ALA SEQRES 3 A 353 VAL VAL GLY ARG SER LEU VAL ASN SER PHE LYS GLN PHE SEQRES 4 A 353 VAL SER LYS ASP LEU HIS THR ARG HIS VAL ASP ALA THR SEQRES 5 A 353 TYR ARG LEU VAL LEU ASP CYS VAL ALA ALA VAL ASP PRO SEQRES 6 A 353 LEU MET ARG LEU TYR THR PHE GLY SER THR VAL VAL TYR SEQRES 7 A 353 GLY VAL HIS GLU LYS GLY SER ASP VAL ASP PHE VAL VAL SEQRES 8 A 353 LEU ASN LYS THR ASP VAL GLU ASP GLY LYS GLY GLY ASP SEQRES 9 A 353 ALA ALA THR GLN VAL ALA LYS GLY LEU GLN ALA ASP ILE SEQRES 10 A 353 LEU ALA LYS LEU ALA ARG VAL ILE ARG GLN LYS HIS LEU SEQRES 11 A 353 SER TRP ASN VAL GLU GLU VAL ARG ARG THR ARG VAL PRO SEQRES 12 A 353 VAL VAL ARG VAL LYS GLY GLY GLY ALA VAL ASP PHE ASP SEQRES 13 A 353 ILE THR ALA TYR ARG ARG ASN GLY VAL ARG ASN SER ALA SEQRES 14 A 353 LEU LEU ARG ALA TYR PHE GLU GLN ASN PRO PRO CYS ARG SEQRES 15 A 353 TRP LEU SER MET SER ILE LYS ARG TRP SER LYS GLN THR SEQRES 16 A 353 GLY LEU ASN ALA SER VAL ILE GLY GLY SER ILE THR SER SEQRES 17 A 353 TYR GLY PHE ASN LEU MET VAL VAL TYR TYR LEU LEU GLN SEQRES 18 A 353 ARG ASN HIS LEU GLN PHE VAL PRO PRO SER THR ILE ASP SEQRES 19 A 353 VAL SER ARG VAL GLU PRO LEU PRO PRO HIS LEU PRO LEU SEQRES 20 A 353 GLU GLU PRO ALA ASP GLU GLY LEU GLU LEU GLY THR GLN SEQRES 21 A 353 VAL LEU ASP PHE LEU HIS PHE PHE LEU HIS GLU PHE ASP SEQRES 22 A 353 SER ASP LYS GLN VAL ILE SER LEU ASN ARG PRO GLY ILE SEQRES 23 A 353 THR THR LYS GLU GLU LEU ASP TRP THR LYS SER ALA GLU SEQRES 24 A 353 ASP PHE ALA ARG MET ASN GLY GLU LYS VAL HIS TYR GLN SEQRES 25 A 353 TRP CYS ILE GLU ASP PRO TYR GLU LEU ASN LEU ASN VAL SEQRES 26 A 353 GLY ARG ASN VAL THR PRO LEU LYS ARG ASP PHE LEU ARG SEQRES 27 A 353 ARG HIS LEU GLU LYS ALA ARG ASP THR ALA LEU LEU THR SEQRES 28 A 353 ILE VAL SEQRES 1 B 353 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 353 LEU VAL PRO ARG GLY SER HIS MET PRO PRO SER PRO ALA SEQRES 3 B 353 VAL VAL GLY ARG SER LEU VAL ASN SER PHE LYS GLN PHE SEQRES 4 B 353 VAL SER LYS ASP LEU HIS THR ARG HIS VAL ASP ALA THR SEQRES 5 B 353 TYR ARG LEU VAL LEU ASP CYS VAL ALA ALA VAL ASP PRO SEQRES 6 B 353 LEU MET ARG LEU TYR THR PHE GLY SER THR VAL VAL TYR SEQRES 7 B 353 GLY VAL HIS GLU LYS GLY SER ASP VAL ASP PHE VAL VAL SEQRES 8 B 353 LEU ASN LYS THR ASP VAL GLU ASP GLY LYS GLY GLY ASP SEQRES 9 B 353 ALA ALA THR GLN VAL ALA LYS GLY LEU GLN ALA ASP ILE SEQRES 10 B 353 LEU ALA LYS LEU ALA ARG VAL ILE ARG GLN LYS HIS LEU SEQRES 11 B 353 SER TRP ASN VAL GLU GLU VAL ARG ARG THR ARG VAL PRO SEQRES 12 B 353 VAL VAL ARG VAL LYS GLY GLY GLY ALA VAL ASP PHE ASP SEQRES 13 B 353 ILE THR ALA TYR ARG ARG ASN GLY VAL ARG ASN SER ALA SEQRES 14 B 353 LEU LEU ARG ALA TYR PHE GLU GLN ASN PRO PRO CYS ARG SEQRES 15 B 353 TRP LEU SER MET SER ILE LYS ARG TRP SER LYS GLN THR SEQRES 16 B 353 GLY LEU ASN ALA SER VAL ILE GLY GLY SER ILE THR SER SEQRES 17 B 353 TYR GLY PHE ASN LEU MET VAL VAL TYR TYR LEU LEU GLN SEQRES 18 B 353 ARG ASN HIS LEU GLN PHE VAL PRO PRO SER THR ILE ASP SEQRES 19 B 353 VAL SER ARG VAL GLU PRO LEU PRO PRO HIS LEU PRO LEU SEQRES 20 B 353 GLU GLU PRO ALA ASP GLU GLY LEU GLU LEU GLY THR GLN SEQRES 21 B 353 VAL LEU ASP PHE LEU HIS PHE PHE LEU HIS GLU PHE ASP SEQRES 22 B 353 SER ASP LYS GLN VAL ILE SER LEU ASN ARG PRO GLY ILE SEQRES 23 B 353 THR THR LYS GLU GLU LEU ASP TRP THR LYS SER ALA GLU SEQRES 24 B 353 ASP PHE ALA ARG MET ASN GLY GLU LYS VAL HIS TYR GLN SEQRES 25 B 353 TRP CYS ILE GLU ASP PRO TYR GLU LEU ASN LEU ASN VAL SEQRES 26 B 353 GLY ARG ASN VAL THR PRO LEU LYS ARG ASP PHE LEU ARG SEQRES 27 B 353 ARG HIS LEU GLU LYS ALA ARG ASP THR ALA LEU LEU THR SEQRES 28 B 353 ILE VAL SEQRES 1 Y 2 U U SEQRES 1 Z 2 U U HET UTP A 501 40 HET MG A 502 1 HET UTP B 401 40 HET MG B 402 1 HET MG B 403 1 HET MG Y 101 1 HET MG Z 101 1 HETNAM UTP URIDINE 5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 5 UTP 2(C9 H15 N2 O15 P3) FORMUL 6 MG 5(MG 2+) FORMUL 12 HOH *190(H2 O) HELIX 1 AA1 SER A 4 PHE A 16 1 13 HELIX 2 AA2 VAL A 29 ASP A 44 1 16 HELIX 3 AA3 GLY A 53 GLY A 59 1 7 HELIX 4 AA4 ASN A 73 ASP A 79 1 7 HELIX 5 AA5 THR A 87 HIS A 109 1 23 HELIX 6 AA6 ARG A 142 ASN A 158 1 17 HELIX 7 AA7 PRO A 160 THR A 175 1 16 HELIX 8 AA8 THR A 187 ARG A 202 1 16 HELIX 9 AA9 PRO A 209 ILE A 213 5 5 HELIX 10 AB1 ASP A 214 VAL A 218 5 5 HELIX 11 AB2 GLY A 234 GLU A 251 1 18 HELIX 12 AB3 GLU A 270 ASP A 273 5 4 HELIX 13 AB4 THR A 275 ALA A 282 1 8 HELIX 14 AB5 THR A 310 ALA A 328 1 19 HELIX 15 AB6 SER B 4 PHE B 16 1 13 HELIX 16 AB7 ASP B 30 ASP B 44 1 15 HELIX 17 AB8 GLY B 53 GLY B 59 1 7 HELIX 18 AB9 ASN B 73 ASP B 79 1 7 HELIX 19 AC1 THR B 87 HIS B 109 1 23 HELIX 20 AC2 ARG B 142 ASN B 158 1 17 HELIX 21 AC3 CYS B 161 THR B 175 1 15 HELIX 22 AC4 THR B 187 ARG B 202 1 16 HELIX 23 AC5 PRO B 209 ILE B 213 5 5 HELIX 24 AC6 ASP B 214 VAL B 218 5 5 HELIX 25 AC7 GLY B 234 GLU B 251 1 18 HELIX 26 AC8 GLU B 270 ASP B 273 5 4 HELIX 27 AC9 THR B 275 ASN B 285 1 11 HELIX 28 AD1 THR B 310 ALA B 328 1 19 SHEET 1 AA1 5 ARG A 48 PHE A 52 0 SHEET 2 AA1 5 VAL A 67 LEU A 72 -1 O LEU A 72 N ARG A 48 SHEET 3 AA1 5 VAL A 133 ALA A 139 1 O ASP A 136 N PHE A 69 SHEET 4 AA1 5 VAL A 124 GLY A 129 -1 N VAL A 127 O PHE A 135 SHEET 5 AA1 5 ASN A 113 VAL A 117 -1 N ASN A 113 O LYS A 128 SHEET 1 AA2 2 GLN A 257 VAL A 258 0 SHEET 2 AA2 2 THR A 267 THR A 268 -1 O THR A 267 N VAL A 258 SHEET 1 AA3 5 ARG B 48 PHE B 52 0 SHEET 2 AA3 5 VAL B 67 LEU B 72 -1 O VAL B 70 N TYR B 50 SHEET 3 AA3 5 PHE B 135 ALA B 139 1 O ASP B 136 N PHE B 69 SHEET 4 AA3 5 VAL B 124 LYS B 128 -1 N VAL B 127 O PHE B 135 SHEET 5 AA3 5 ASN B 113 VAL B 117 -1 N GLU B 115 O ARG B 126 SHEET 1 AA4 2 GLN B 257 VAL B 258 0 SHEET 2 AA4 2 THR B 267 THR B 268 -1 O THR B 267 N VAL B 258 LINK OD1 ASP A 66 MG MG A 502 1555 1555 2.25 LINK OD2 ASP A 68 MG MG A 502 1555 1555 2.75 LINK O1A UTP A 501 MG MG A 502 1555 1555 2.62 LINK O1B UTP A 501 MG MG A 502 1555 1555 2.54 LINK O3G UTP A 501 MG MG A 502 1555 1555 2.21 LINK O1A UTP A 501 MG MG Y 101 1555 1555 2.45 LINK MG MG A 502 O HOH A 602 1555 1555 2.21 LINK MG MG A 502 O HOH A 638 1555 1555 2.30 LINK O HOH A 602 MG MG Y 101 1555 1555 2.25 LINK O HOH A 610 MG MG Y 101 1555 1555 2.21 LINK O HOH A 613 MG MG Y 101 1555 1555 2.18 LINK O HOH A 649 MG MG Y 101 1555 1555 2.16 LINK OD1 ASP B 66 MG MG B 402 1555 1555 2.83 LINK OD2 ASP B 66 MG MG B 403 1555 1555 2.10 LINK OD2 ASP B 68 MG MG B 402 1555 1555 2.81 LINK OD1 ASP B 136 MG MG B 403 1555 1555 2.10 LINK O1A UTP B 401 MG MG B 402 1555 1555 2.33 LINK O1B UTP B 401 MG MG B 402 1555 1555 2.26 LINK O3G UTP B 401 MG MG B 402 1555 1555 2.16 LINK O1A UTP B 401 MG MG Z 101 1555 1555 2.33 LINK MG MG B 402 O HOH B 507 1555 1555 2.17 LINK MG MG B 402 O HOH B 508 1555 1555 2.20 LINK O HOH B 505 MG MG Z 101 1555 1555 2.18 LINK O HOH B 506 MG MG Z 101 1555 1555 2.16 LINK O HOH B 507 MG MG Z 101 1555 1555 2.20 LINK O HOH B 527 MG MG Z 101 1555 1555 2.20 LINK O3' U Y 2 MG MG Y 101 1555 1555 2.24 LINK MG MG Y 101 O HOH Y 205 1555 1555 2.27 LINK O3' U Z 2 MG MG Z 101 1555 1555 2.34 LINK MG MG Z 101 O HOH Z 202 1555 1555 2.21 SITE 1 AC1 22 PHE A 52 SER A 54 SER A 65 ASP A 66 SITE 2 AC1 22 ASP A 68 GLY A 144 ASN A 147 SER A 148 SITE 3 AC1 22 LYS A 169 LYS A 173 SER A 188 TYR A 189 SITE 4 AC1 22 MG A 502 HOH A 602 HOH A 603 HOH A 610 SITE 5 AC1 22 HOH A 613 HOH A 624 HOH A 636 HOH A 638 SITE 6 AC1 22 U Y 2 MG Y 101 SITE 1 AC2 5 ASP A 66 ASP A 68 UTP A 501 HOH A 602 SITE 2 AC2 5 HOH A 638 SITE 1 AC3 21 PHE B 52 SER B 54 SER B 65 ASP B 66 SITE 2 AC3 21 ASP B 68 GLY B 144 ASN B 147 SER B 148 SITE 3 AC3 21 LYS B 169 LYS B 173 SER B 188 TYR B 189 SITE 4 AC3 21 MG B 402 HOH B 505 HOH B 506 HOH B 507 SITE 5 AC3 21 HOH B 508 HOH B 524 HOH B 526 U Z 2 SITE 6 AC3 21 MG Z 101 SITE 1 AC4 6 ASP B 66 ASP B 68 UTP B 401 HOH B 507 SITE 2 AC4 6 HOH B 508 MG Z 101 SITE 1 AC5 3 ASP B 66 ARG B 126 ASP B 136 SITE 1 AC6 7 UTP A 501 HOH A 602 HOH A 610 HOH A 613 SITE 2 AC6 7 HOH A 649 U Y 2 HOH Y 205 SITE 1 AC7 8 UTP B 401 MG B 402 HOH B 505 HOH B 506 SITE 2 AC7 8 HOH B 507 HOH B 527 U Z 2 HOH Z 202 CRYST1 82.688 42.876 109.618 90.00 94.05 90.00 P 1 21 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 0.012094 0.000000 0.000856 0.00000 SCALE2 0.000000 0.023323 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009145 0.00000