HEADER HYDROLASE/RNA 13-FEB-13 4J7M TITLE CRYSTAL STRUCTURE OF MOUSE DXO IN COMPLEX WITH SUBSTRATE MIMIC RNA AND TITLE 2 CALCIUM ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN DOM3Z; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DOM-3 HOMOLOG Z, DXO; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(P*UP*(U37)P*(U37)P*UP*U)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: 5'-END MONOPHOSPHORYLATED OLIGO RNA WITH COMPND 11 PHOSPHOROTHIOATE LINK BETWEEN 1-2 U AND 2-3 U SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: DOM3Z, NG6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS DECAPPING, 5'-3' EXORIBONUCLEASE, HYDROLASE, HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.H.CHANG,L.TONG REVDAT 3 28-FEB-24 4J7M 1 REMARK SEQADV LINK REVDAT 2 12-MAR-14 4J7M 1 JRNL REVDAT 1 27-MAR-13 4J7M 0 JRNL AUTH X.JIAO,J.H.CHANG,T.KILIC,L.TONG,M.KILEDJIAN JRNL TITL A MAMMALIAN PRE-MRNA 5' END CAPPING QUALITY CONTROL JRNL TITL 2 MECHANISM AND AN UNEXPECTED LINK OF CAPPING TO PRE-MRNA JRNL TITL 3 PROCESSING. JRNL REF MOL.CELL V. 50 104 2013 JRNL REFN ISSN 1097-2765 JRNL PMID 23523372 JRNL DOI 10.1016/J.MOLCEL.2013.02.017 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 380977.460 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.6 REMARK 3 NUMBER OF REFLECTIONS : 43982 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2175 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3267 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 169 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2889 REMARK 3 NUCLEIC ACID ATOMS : 85 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 461 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.93000 REMARK 3 B22 (A**2) : -2.01000 REMARK 3 B33 (A**2) : 6.95000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.90000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.21 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.960 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.100 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.910 ; 4.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.880 ; 3.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.440 ; 5.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 52.70 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : PUS.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 PARAMETER FILE 7 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : PUS.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : U3DP.TOP REMARK 3 TOPOLOGY FILE 7 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 4J7M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000077697. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46383 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% W/V PEG3350, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 43.91850 REMARK 290 SMTRY3 2 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 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 7 REMARK 465 GLY A 8 REMARK 465 SER A 9 REMARK 465 SER A 10 REMARK 465 HIS A 11 REMARK 465 HIS A 12 REMARK 465 HIS A 13 REMARK 465 HIS A 14 REMARK 465 HIS A 15 REMARK 465 HIS A 16 REMARK 465 SER A 17 REMARK 465 SER A 18 REMARK 465 GLY A 19 REMARK 465 LEU A 20 REMARK 465 VAL A 21 REMARK 465 PRO A 22 REMARK 465 ARG A 23 REMARK 465 GLY A 24 REMARK 465 SER A 25 REMARK 465 HIS A 26 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 U B 5 C5' C4' O4' C3' O3' C2' O2' REMARK 470 U B 5 C1' N1 C2 O2 N3 C4 O4 REMARK 470 U B 5 C5 C6 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 U B 1 P U B 1 OP3 -0.088 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 64 31.54 -99.10 REMARK 500 ASP A 81 53.85 -154.84 REMARK 500 ARG A 91 41.68 -107.81 REMARK 500 ARG A 102 -129.50 51.39 REMARK 500 ASP A 346 116.55 -164.86 REMARK 500 ASP A 368 -151.91 49.29 REMARK 500 ASP A 368 -151.91 48.01 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 CA A 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 236 OD2 REMARK 620 2 GLU A 253 OE2 78.4 REMARK 620 3 LEU A 254 O 89.9 89.7 REMARK 620 4 HOH A 785 O 100.7 169.8 80.1 REMARK 620 5 U37 B 2 O1P 155.0 79.4 101.4 103.2 REMARK 620 6 HOH B 104 O 84.5 90.4 174.3 99.7 84.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UBD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UBD A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4J7L RELATED DB: PDB REMARK 900 RELATED ID: 4J7N RELATED DB: PDB REMARK 900 RELATED ID: 3FQI RELATED DB: PDB REMARK 900 RELATED ID: 3FQJ RELATED DB: PDB DBREF 4J7M A 27 384 UNP O70348 DOM3Z_MOUSE 27 384 DBREF 4J7M B 1 5 PDB 4J7M 4J7M 1 5 SEQADV 4J7M MET A 7 UNP O70348 EXPRESSION TAG SEQADV 4J7M GLY A 8 UNP O70348 EXPRESSION TAG SEQADV 4J7M SER A 9 UNP O70348 EXPRESSION TAG SEQADV 4J7M SER A 10 UNP O70348 EXPRESSION TAG SEQADV 4J7M HIS A 11 UNP O70348 EXPRESSION TAG SEQADV 4J7M HIS A 12 UNP O70348 EXPRESSION TAG SEQADV 4J7M HIS A 13 UNP O70348 EXPRESSION TAG SEQADV 4J7M HIS A 14 UNP O70348 EXPRESSION TAG SEQADV 4J7M HIS A 15 UNP O70348 EXPRESSION TAG SEQADV 4J7M HIS A 16 UNP O70348 EXPRESSION TAG SEQADV 4J7M SER A 17 UNP O70348 EXPRESSION TAG SEQADV 4J7M SER A 18 UNP O70348 EXPRESSION TAG SEQADV 4J7M GLY A 19 UNP O70348 EXPRESSION TAG SEQADV 4J7M LEU A 20 UNP O70348 EXPRESSION TAG SEQADV 4J7M VAL A 21 UNP O70348 EXPRESSION TAG SEQADV 4J7M PRO A 22 UNP O70348 EXPRESSION TAG SEQADV 4J7M ARG A 23 UNP O70348 EXPRESSION TAG SEQADV 4J7M GLY A 24 UNP O70348 EXPRESSION TAG SEQADV 4J7M SER A 25 UNP O70348 EXPRESSION TAG SEQADV 4J7M HIS A 26 UNP O70348 EXPRESSION TAG SEQRES 1 A 378 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 378 LEU VAL PRO ARG GLY SER HIS PRO SER LEU ARG THR GLN SEQRES 3 A 378 PRO SER LEU TYR SER GLY PRO PHE PRO PHE TYR ARG ARG SEQRES 4 A 378 PRO SER GLU LEU GLY CYS PHE SER LEU ASP ALA GLN ARG SEQRES 5 A 378 GLN TYR HIS GLY ASP ALA ARG ALA LEU ARG TYR TYR SER SEQRES 6 A 378 PRO PRO PRO ILE ASN GLY PRO GLY PRO ASP PHE ASP LEU SEQRES 7 A 378 ARG ASP GLY TYR PRO ASP ARG TYR GLN PRO ARG ASP GLU SEQRES 8 A 378 GLU VAL GLN GLU ARG LEU ASP HIS LEU LEU ARG TRP VAL SEQRES 9 A 378 LEU GLU HIS ARG ASN GLN LEU GLU GLY GLY PRO GLY TRP SEQRES 10 A 378 LEU ALA GLY ALA THR VAL THR TRP ARG GLY HIS LEU THR SEQRES 11 A 378 LYS LEU LEU THR THR PRO TYR GLU ARG GLN GLU GLY TRP SEQRES 12 A 378 GLN LEU ALA ALA SER ARG PHE GLN GLY THR LEU TYR LEU SEQRES 13 A 378 SER GLU VAL GLU THR PRO ALA ALA ARG ALA GLN ARG LEU SEQRES 14 A 378 ALA ARG PRO PRO LEU LEU ARG GLU LEU MET TYR MET GLY SEQRES 15 A 378 TYR LYS PHE GLU GLN TYR MET CYS ALA ASP LYS PRO GLY SEQRES 16 A 378 GLY SER PRO ASP PRO SER GLY GLU VAL ASN THR ASN VAL SEQRES 17 A 378 ALA TYR CYS SER VAL LEU ARG SER ARG LEU GLY ASN HIS SEQRES 18 A 378 PRO LEU LEU PHE SER GLY GLU VAL ASP CYS LEU ASN PRO SEQRES 19 A 378 GLN ALA PRO CYS THR GLN PRO PRO SER CYS TYR VAL GLU SEQRES 20 A 378 LEU LYS THR SER LYS GLU MET HIS SER PRO GLY GLN TRP SEQRES 21 A 378 ARG SER PHE TYR ARG HIS LYS LEU LEU LYS TRP TRP ALA SEQRES 22 A 378 GLN SER PHE LEU PRO GLY VAL PRO HIS VAL VAL ALA GLY SEQRES 23 A 378 PHE ARG ASN PRO GLU GLY PHE VAL CYS SER LEU LYS THR SEQRES 24 A 378 PHE PRO THR MET GLU MET PHE GLU ASN VAL ARG ASN ASP SEQRES 25 A 378 ARG GLU GLY TRP ASN PRO SER VAL CYS MET ASN PHE CYS SEQRES 26 A 378 ALA ALA PHE LEU SER PHE ALA GLN SER THR VAL VAL GLN SEQRES 27 A 378 ASP ASP PRO ARG LEU VAL HIS LEU PHE SER TRP GLU PRO SEQRES 28 A 378 GLY GLY PRO VAL THR VAL SER VAL HIS ARG ASP ALA PRO SEQRES 29 A 378 TYR ALA PHE LEU PRO SER TRP TYR VAL GLU THR MET THR SEQRES 30 A 378 GLN SEQRES 1 B 5 U U37 U37 U U MODRES 4J7M U37 B 2 U URIDINE 5'-MONOTHIOPHOSPHATE MODRES 4J7M U37 B 3 U URIDINE 5'-MONOTHIOPHOSPHATE HET U37 B 2 20 HET U37 B 3 20 HET UBD A 401 25 HET UBD A 402 25 HET CA A 403 1 HETNAM U37 URIDINE 5'-MONOTHIOPHOSPHATE HETNAM UBD URIDINE 3',5'-BIS(DIHYDROGEN PHOSPHATE) HETNAM CA CALCIUM ION FORMUL 2 U37 2(C9 H13 N2 O8 P S) FORMUL 3 UBD 2(C9 H14 N2 O12 P2) FORMUL 5 CA CA 2+ FORMUL 6 HOH *461(H2 O) HELIX 1 1 GLN A 32 SER A 37 5 6 HELIX 2 2 LEU A 103 GLU A 112 1 10 HELIX 3 3 TRP A 123 GLY A 126 5 4 HELIX 4 4 ARG A 132 THR A 141 1 10 HELIX 5 5 THR A 167 ALA A 176 1 10 HELIX 6 6 PRO A 178 MET A 195 1 18 HELIX 7 7 SER A 262 HIS A 272 1 11 HELIX 8 8 HIS A 272 LEU A 283 1 12 HELIX 9 9 MET A 309 VAL A 315 5 7 HELIX 10 10 ASN A 323 VAL A 342 1 20 HELIX 11 11 PRO A 375 GLN A 384 1 10 SHEET 1 A 9 TYR A 60 HIS A 61 0 SHEET 2 A 9 SER A 47 LEU A 54 -1 N SER A 53 O HIS A 61 SHEET 3 A 9 ALA A 215 LEU A 224 -1 O VAL A 219 N LEU A 49 SHEET 4 A 9 HIS A 227 GLU A 234 -1 O PHE A 231 N LEU A 220 SHEET 5 A 9 THR A 128 TRP A 131 1 N THR A 128 O LEU A 230 SHEET 6 A 9 THR A 159 GLU A 164 1 O LEU A 160 N VAL A 129 SHEET 7 A 9 TRP A 149 PHE A 156 -1 N ALA A 152 O SER A 163 SHEET 8 A 9 LEU A 349 TRP A 355 -1 O PHE A 353 N LEU A 151 SHEET 9 A 9 THR A 362 ARG A 367 -1 O SER A 364 N LEU A 352 SHEET 1 B 2 TYR A 69 TYR A 70 0 SHEET 2 B 2 CYS A 196 ALA A 197 -1 O ALA A 197 N TYR A 69 SHEET 1 C 5 PHE A 82 ASP A 83 0 SHEET 2 C 5 PHE A 299 PRO A 307 -1 O VAL A 300 N PHE A 82 SHEET 3 C 5 HIS A 288 ARG A 294 -1 N VAL A 289 O PHE A 306 SHEET 4 C 5 TYR A 251 LYS A 258 1 N GLU A 253 O VAL A 290 SHEET 5 C 5 CYS A 237 LEU A 238 -1 N CYS A 237 O VAL A 252 SHEET 1 D 2 TYR A 92 GLN A 93 0 SHEET 2 D 2 VAL A 210 ASN A 211 1 O VAL A 210 N GLN A 93 LINK O3' U B 1 P U37 B 2 1555 1555 1.61 LINK OD2 ASP A 236 CA CA A 403 1555 1555 2.51 LINK OE2 GLU A 253 CA CA A 403 1555 1555 2.47 LINK O LEU A 254 CA CA A 403 1555 1555 2.46 LINK CA CA A 403 O HOH A 785 1555 1555 2.53 LINK CA CA A 403 O1P U37 B 2 1555 1555 2.42 LINK CA CA A 403 O HOH B 104 1555 1555 2.66 CISPEP 1 TYR A 88 PRO A 89 0 -0.12 CISPEP 2 PRO A 247 PRO A 248 0 0.13 CISPEP 3 ALA A 369 PRO A 370 0 0.24 SITE 1 AC1 9 ARG A 30 THR A 31 GLN A 32 GLY A 358 SITE 2 AC1 9 GLY A 359 PRO A 360 HOH A 778 HOH A 852 SITE 3 AC1 9 HOH A 881 SITE 1 AC2 9 LEU A 111 GLU A 112 HIS A 113 ARG A 114 SITE 2 AC2 9 ASN A 115 GLN A 116 ARG A 316 HOH A 576 SITE 3 AC2 9 HOH A 632 SITE 1 AC3 7 ASP A 236 GLU A 253 LEU A 254 HOH A 785 SITE 2 AC3 7 U B 1 U37 B 2 HOH B 104 CRYST1 49.985 87.837 54.356 90.00 111.69 90.00 P 1 21 1 2 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 0.020006 0.000000 0.007956 0.00000 SCALE2 0.000000 0.011385 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019799 0.00000