PDB Short entry for 3AF6 HEADER HYDROLASE/RNA 24-FEB-10 3AF6 TITLE THE CRYSTAL STRUCTURE OF AN ARCHAEAL CPSF SUBUNIT, PH1404 FROM TITLE 2 PYROCOCCUS HORIKOSHII COMPLEXED WITH RNA-ANALOG COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN PH1404; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3'; COMPND 7 CHAIN: B, C; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: RNA-ANALOG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: OT3; SOURCE 5 GENE: PH1404; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-11A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS ARCHAEAL CPSF, BETA-CASP FAMILY, KH DOMAIN, RIBONUCLEASE, METALLO- KEYWDS 2 BETA-LACTAMASE SUPERFAMILY, PYROCOCCUS HORIKOSHII, ARCHAEA, RNA- KEYWDS 3 ANALOG, HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.NISHIDA,H.ISHIKAWA,N.NAKAGAWA,R.MASUI,S.KURAMITSU REVDAT 3 01-NOV-23 3AF6 1 REMARK LINK REVDAT 2 30-JUN-10 3AF6 1 JRNL REVDAT 1 21-APR-10 3AF6 0 JRNL AUTH Y.NISHIDA,H.ISHIKAWA,S.BABA,N.NAKAGAWA,S.KURAMITSU,R.MASUI JRNL TITL CRYSTAL STRUCTURE OF AN ARCHAEAL CLEAVAGE AND JRNL TITL 2 POLYADENYLATION SPECIFICITY FACTOR SUBUNIT FROM PYROCOCCUS JRNL TITL 3 HORIKOSHII JRNL REF PROTEINS V. 78 2395 2010 JRNL REFN ISSN 0887-3585 JRNL PMID 20544974 JRNL DOI 10.1002/PROT.22748 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 97464.100 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 50924 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) : 0.220 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 5026 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6977 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE : 0.3350 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 815 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5099 REMARK 3 NUCLEIC ACID ATOMS : 106 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 37 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 59.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.54000 REMARK 3 B22 (A**2) : 1.54000 REMARK 3 B33 (A**2) : -3.08000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.36 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) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.41 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.900 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) : 1.380 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.370 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.990 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.030 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 46.11 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_PH1404.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : LIGAND.PARAM REMARK 3 PARAMETER FILE 5 : DNA-RNA_REP_SSU.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : LIGAND.TOP REMARK 3 TOPOLOGY FILE 5 : DNA-RNA_SSU.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED; THE FRIEDEL REMARK 3 PAIRS WERE USED FOR PHASING. REMARK 4 REMARK 4 3AF6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000029176. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.8 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) : 1.0000 REMARK 200 MONOCHROMATOR : SI DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52847 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.1200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.060 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: PDB ENTRY 3AF5 REMARK 200 REMARK 200 REMARK: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, 0.1M SODIUM REMARK 280 CHLORIDE, 8% (V/V) PEG 6000, PH 4.8, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 118.75050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 43.21900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 43.21900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 178.12575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 43.21900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 43.21900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 59.37525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 43.21900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.21900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 178.12575 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 43.21900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.21900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 59.37525 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 118.75050 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 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH C 35 LIES ON A SPECIAL POSITION. 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 THR A 2 REMARK 465 PHE A 3 REMARK 465 LEU A 4 REMARK 465 ILE A 5 REMARK 465 LYS A 6 REMARK 465 ARG A 7 REMARK 465 GLU A 8 REMARK 465 ALA A 51 REMARK 465 ILE A 52 REMARK 465 MET A 53 REMARK 465 LYS A 54 REMARK 465 ASP A 55 REMARK 465 GLY A 56 REMARK 465 SSU C 3 REMARK 465 SSU C 4 REMARK 465 SSU C 5 REMARK 465 SSU C 6 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 SSU B 1 S1P REMARK 470 SSU B 6 O2' C2' C1' O4' C4' C5' C3' REMARK 470 SSU B 6 O3' N1 C6 C5 C4 O4 N3 REMARK 470 SSU B 6 C2 O2 REMARK 470 SSU C 1 S1P REMARK 470 SSU C 2 O2' C2' C1' O4' C4' C5' C3' REMARK 470 SSU C 2 O3' N1 C6 C5 C4 O4 N3 REMARK 470 SSU C 2 C2 O2 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 SSU B 1 O3' SSU B 2 P -0.086 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 GLN A 10 37.48 -155.01 REMARK 500 ASN A 23 22.83 -72.21 REMARK 500 LYS A 31 59.05 39.75 REMARK 500 ILE A 32 106.17 -54.04 REMARK 500 LYS A 47 56.01 -102.12 REMARK 500 ASN A 48 146.47 172.99 REMARK 500 VAL A 78 38.74 -76.92 REMARK 500 ILE A 92 40.58 -71.74 REMARK 500 PRO A 94 90.61 -54.03 REMARK 500 LYS A 95 0.28 -43.97 REMARK 500 ALA A 97 86.50 -60.13 REMARK 500 GLU A 98 99.99 -36.44 REMARK 500 ILE A 102 88.71 177.46 REMARK 500 GLU A 110 109.97 -175.18 REMARK 500 LYS A 135 -22.97 -34.86 REMARK 500 LYS A 137 42.44 72.76 REMARK 500 THR A 145 103.54 -31.94 REMARK 500 GLU A 163 15.50 -140.63 REMARK 500 GLU A 183 128.64 -37.21 REMARK 500 ALA A 204 114.09 -169.39 REMARK 500 ASP A 217 159.41 67.93 REMARK 500 PHE A 218 79.95 -163.87 REMARK 500 MET A 224 43.59 -150.05 REMARK 500 HIS A 234 92.02 -66.04 REMARK 500 HIS A 261 -23.27 -140.40 REMARK 500 PHE A 274 143.73 -170.05 REMARK 500 ASP A 275 42.47 -149.17 REMARK 500 ASN A 357 63.56 -107.60 REMARK 500 LEU A 386 95.12 -164.97 REMARK 500 ARG A 422 20.29 -75.17 REMARK 500 GLU A 453 -74.72 -78.92 REMARK 500 ILE A 484 -89.17 -99.01 REMARK 500 ASN A 490 110.59 -170.55 REMARK 500 SER A 494 123.82 -31.24 REMARK 500 GLU A 495 19.26 -69.97 REMARK 500 SER A 512 168.52 -48.60 REMARK 500 MET A 583 159.08 -47.19 REMARK 500 ALA A 641 79.59 -116.61 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 ZN A 657 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 256 NE2 REMARK 620 2 HIS A 258 ND1 105.8 REMARK 620 3 HIS A 344 NE2 100.6 110.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 658 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 260 OD1 REMARK 620 2 HIS A 261 NE2 114.9 REMARK 620 3 ASP A 367 OD1 137.2 92.0 REMARK 620 4 HIS A 618 NE2 115.0 94.5 94.0 REMARK 620 5 SO4 A 655 O2 78.2 162.1 70.4 90.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 652 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 653 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 654 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 655 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 656 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 657 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 658 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3AF5 RELATED DB: PDB REMARK 900 SAME PROTEIN, FREE STRUCTURE DBREF 3AF6 A 1 651 UNP O50112 O50112_PYRHO 1 651 DBREF 3AF6 B 1 6 PDB 3AF6 3AF6 1 6 DBREF 3AF6 C 1 6 PDB 3AF6 3AF6 1 6 SEQRES 1 A 651 MET THR PHE LEU ILE LYS ARG GLU THR GLN VAL ASP GLN SEQRES 2 A 651 ILE LEU ARG ASP ILE ARG ALA VAL VAL ASN GLN MET VAL SEQRES 3 A 651 PRO LYS GLU ALA LYS ILE THR GLU ILE GLU PHE GLU GLY SEQRES 4 A 651 PRO GLU LEU VAL ILE TYR VAL LYS ASN PRO GLU ALA ILE SEQRES 5 A 651 MET LYS ASP GLY GLU LEU ILE LYS ASP LEU ALA LYS VAL SEQRES 6 A 651 LEU LYS LYS ARG ILE SER VAL ARG PRO ASP PRO GLU VAL SEQRES 7 A 651 LEU LEU PRO PRO GLU GLU ALA GLU LYS LEU ILE PHE GLU SEQRES 8 A 651 ILE VAL PRO LYS GLU ALA GLU ILE THR ASN ILE ALA PHE SEQRES 9 A 651 ASP PRO SER VAL GLY GLU VAL LEU ILE GLU ALA LYS LYS SEQRES 10 A 651 PRO GLY LEU VAL ILE GLY LYS ASN GLY GLU THR LEU ARG SEQRES 11 A 651 LEU ILE THR GLN LYS VAL LYS TRP ALA PRO LYS VAL VAL SEQRES 12 A 651 ARG THR PRO PRO LEU GLN SER GLN THR ILE TYR SER ILE SEQRES 13 A 651 ARG GLN ILE LEU GLN THR GLU SER LYS ASP ARG ARG LYS SEQRES 14 A 651 PHE LEU ARG GLN VAL GLY ARG ASN ILE TYR ARG LYS PRO SEQRES 15 A 651 GLU TYR LYS SER ARG TRP ILE ARG ILE THR GLY LEU GLY SEQRES 16 A 651 GLY PHE ARG GLU VAL GLY ARG SER ALA LEU LEU VAL GLN SEQRES 17 A 651 THR ASP GLU SER PHE VAL LEU VAL ASP PHE GLY VAL ASN SEQRES 18 A 651 VAL ALA MET LEU ASN ASP PRO TYR LYS ALA PHE PRO HIS SEQRES 19 A 651 PHE ASP ALA PRO GLU PHE GLN TYR VAL LEU ARG GLU GLY SEQRES 20 A 651 LEU LEU ASP ALA ILE ILE ILE THR HIS ALA HIS LEU ASP SEQRES 21 A 651 HIS CYS GLY MET LEU PRO TYR LEU PHE ARG TYR ASN LEU SEQRES 22 A 651 PHE ASP GLY PRO ILE TYR THR THR PRO PRO THR ARG ASP SEQRES 23 A 651 LEU MET VAL LEU LEU GLN LYS ASP PHE ILE GLU ILE GLN SEQRES 24 A 651 GLN SER ASN GLY GLN ASP PRO LEU TYR ARG PRO ARG ASP SEQRES 25 A 651 ILE LYS GLU VAL ILE LYS HIS THR ILE THR LEU ASP TYR SEQRES 26 A 651 GLY GLU VAL ARG ASP ILE SER PRO ASP ILE ARG LEU THR SEQRES 27 A 651 LEU HIS ASN ALA GLY HIS ILE LEU GLY SER ALA ILE VAL SEQRES 28 A 651 HIS LEU HIS ILE GLY ASN GLY LEU HIS ASN ILE ALA ILE SEQRES 29 A 651 THR GLY ASP PHE LYS PHE ILE PRO THR ARG LEU LEU GLU SEQRES 30 A 651 PRO ALA ASN ALA LYS PHE PRO ARG LEU GLU THR LEU VAL SEQRES 31 A 651 MET GLU SER THR TYR GLY GLY ALA ASN ASP ILE GLN MET SEQRES 32 A 651 PRO ARG GLU GLU ALA GLU LYS ARG LEU ILE GLU VAL ILE SEQRES 33 A 651 HIS ASN THR ILE LYS ARG GLY GLY LYS VAL LEU ILE PRO SEQRES 34 A 651 ALA MET ALA VAL GLY ARG ALA GLN GLU VAL MET MET VAL SEQRES 35 A 651 LEU GLU GLU TYR ALA ARG ILE GLY GLY ILE GLU VAL PRO SEQRES 36 A 651 ILE TYR LEU ASP GLY MET ILE TRP GLU ALA THR ALA ILE SEQRES 37 A 651 HIS THR ALA TYR PRO GLU TYR LEU SER ARG ARG LEU ARG SEQRES 38 A 651 GLU GLN ILE PHE LYS GLU GLY TYR ASN PRO PHE LEU SER SEQRES 39 A 651 GLU ILE PHE HIS PRO VAL ALA ASN SER ARG GLU ARG GLN SEQRES 40 A 651 ASP ILE ILE ASP SER ASN GLU PRO ALA ILE ILE ILE ALA SEQRES 41 A 651 SER SER GLY MET LEU VAL GLY GLY PRO SER VAL GLU TYR SEQRES 42 A 651 PHE LYS GLN LEU ALA PRO ASP PRO LYS ASN SER ILE ILE SEQRES 43 A 651 PHE VAL SER TYR GLN ALA GLU GLY THR LEU GLY ARG GLN SEQRES 44 A 651 VAL GLN SER GLY ILE ARG GLU ILE PRO MET VAL GLY GLU SEQRES 45 A 651 GLU GLY ARG THR GLU VAL ILE LYS VAL ASN MET GLU VAL SEQRES 46 A 651 HIS THR ILE ASP GLY PHE SER GLY HIS ALA ASP ARG ARG SEQRES 47 A 651 GLU LEU MET ASN TYR VAL ALA LYS VAL ARG PRO ARG PRO SEQRES 48 A 651 GLU ARG ILE ILE THR VAL HIS GLY GLU PRO GLN LYS CYS SEQRES 49 A 651 LEU ASP LEU ALA THR SER ILE HIS ARG LYS PHE GLY ILE SEQRES 50 A 651 SER THR ARG ALA PRO ASN ASN LEU ASP THR ILE ARG LEU SEQRES 51 A 651 ARG SEQRES 1 B 6 SSU SSU SSU SSU SSU SSU SEQRES 1 C 6 SSU SSU SSU SSU SSU SSU MODRES 3AF6 SSU B 1 U URIDINE-5'-PHOSPHOROTHIOATE MODRES 3AF6 SSU B 2 U URIDINE-5'-PHOSPHOROTHIOATE MODRES 3AF6 SSU B 3 U URIDINE-5'-PHOSPHOROTHIOATE MODRES 3AF6 SSU B 4 U URIDINE-5'-PHOSPHOROTHIOATE MODRES 3AF6 SSU B 5 U URIDINE-5'-PHOSPHOROTHIOATE MODRES 3AF6 SSU B 6 U URIDINE-5'-PHOSPHOROTHIOATE MODRES 3AF6 SSU C 1 U URIDINE-5'-PHOSPHOROTHIOATE MODRES 3AF6 SSU C 2 U URIDINE-5'-PHOSPHOROTHIOATE HET SSU B 1 1 HET SSU B 2 20 HET SSU B 3 20 HET SSU B 4 20 HET SSU B 5 20 HET SSU B 6 4 HET SSU C 1 17 HET SSU C 2 4 HET SO4 A 652 5 HET SO4 A 653 5 HET SO4 A 654 5 HET SO4 A 655 5 HET SO4 A 656 5 HET ZN A 657 1 HET ZN A 658 1 HETNAM SSU URIDINE-5'-PHOSPHOROTHIOATE HETNAM SO4 SULFATE ION HETNAM ZN ZINC ION HETSYN SSU SP-SULFUR-SUBSTITUTED URIDINE FORMUL 2 SSU 8(C9 H13 N2 O8 P S) FORMUL 4 SO4 5(O4 S 2-) FORMUL 9 ZN 2(ZN 2+) FORMUL 11 HOH *37(H2 O) HELIX 1 1 GLN A 10 ASN A 23 1 14 HELIX 2 2 PRO A 27 ALA A 30 5 4 HELIX 3 3 LEU A 58 LYS A 67 1 10 HELIX 4 4 LYS A 117 VAL A 121 5 5 HELIX 5 5 LEU A 129 LYS A 135 1 7 HELIX 6 6 SER A 150 THR A 162 1 13 HELIX 7 7 GLU A 163 TYR A 179 1 17 HELIX 8 8 ASN A 221 LEU A 225 5 5 HELIX 9 9 ASP A 227 PHE A 232 1 6 HELIX 10 10 ALA A 237 GLU A 246 1 10 HELIX 11 11 HIS A 258 GLY A 263 1 6 HELIX 12 12 PRO A 266 TYR A 271 1 6 HELIX 13 13 THR A 281 ASN A 302 1 22 HELIX 14 14 ARG A 309 HIS A 319 1 11 HELIX 15 15 PRO A 404 LYS A 421 1 18 HELIX 16 16 GLY A 434 ARG A 448 1 15 HELIX 17 17 MET A 461 TYR A 472 1 12 HELIX 18 18 PRO A 473 LEU A 476 5 4 HELIX 19 19 SER A 477 GLN A 483 1 7 HELIX 20 20 ASN A 502 SER A 512 1 11 HELIX 21 21 GLY A 528 ALA A 538 1 11 HELIX 22 22 THR A 555 SER A 562 1 8 HELIX 23 23 GLU A 572 GLY A 574 5 3 HELIX 24 24 ASP A 596 VAL A 607 1 12 HELIX 25 25 GLU A 620 GLY A 636 1 17 SHEET 1 A 3 ILE A 32 GLU A 38 0 SHEET 2 A 3 GLU A 41 VAL A 46 -1 O VAL A 43 N GLU A 36 SHEET 3 A 3 ILE A 70 PRO A 74 1 O SER A 71 N LEU A 42 SHEET 1 B 3 ALA A 103 ASP A 105 0 SHEET 2 B 3 GLU A 110 ALA A 115 -1 N GLU A 110 O ASP A 105 SHEET 3 B 3 PRO A 140 ARG A 144 1 O LYS A 141 N ILE A 113 SHEET 1 C 7 THR A 320 THR A 322 0 SHEET 2 C 7 ILE A 278 THR A 280 1 N ILE A 278 O ILE A 321 SHEET 3 C 7 ALA A 251 ILE A 253 1 N ILE A 252 O TYR A 279 SHEET 4 C 7 PHE A 213 VAL A 216 1 N LEU A 215 O ILE A 253 SHEET 5 C 7 ALA A 204 THR A 209 -1 N LEU A 205 O VAL A 216 SHEET 6 C 7 ILE A 189 GLY A 195 -1 N ARG A 190 O GLN A 208 SHEET 7 C 7 THR A 647 ARG A 649 -1 O ILE A 648 N ILE A 191 SHEET 1 D 7 ARG A 329 SER A 332 0 SHEET 2 D 7 ILE A 335 ASN A 341 -1 O LEU A 337 N ARG A 329 SHEET 3 D 7 ALA A 349 ILE A 355 -1 O ILE A 350 N HIS A 340 SHEET 4 D 7 HIS A 360 ILE A 364 -1 O ILE A 364 N VAL A 351 SHEET 5 D 7 THR A 388 GLU A 392 1 O VAL A 390 N ALA A 363 SHEET 6 D 7 ARG A 613 VAL A 617 1 O ILE A 615 N LEU A 389 SHEET 7 D 7 SER A 638 ARG A 640 1 O SER A 638 N ILE A 614 SHEET 1 E 6 PHE A 497 PRO A 499 0 SHEET 2 E 6 ILE A 456 ASP A 459 1 N ILE A 456 O HIS A 498 SHEET 3 E 6 ALA A 516 ALA A 520 1 O ILE A 517 N TYR A 457 SHEET 4 E 6 LYS A 425 PRO A 429 1 N ILE A 428 O ILE A 518 SHEET 5 E 6 SER A 544 PHE A 547 1 O SER A 544 N LEU A 427 SHEET 6 E 6 GLU A 584 THR A 587 1 O HIS A 586 N ILE A 545 SHEET 1 F 2 GLU A 566 VAL A 570 0 SHEET 2 F 2 THR A 576 LYS A 580 -1 O GLU A 577 N MET A 569 LINK O3' SSU B 1 P SSU B 2 1555 1555 1.52 LINK O3' SSU B 2 P SSU B 3 1555 1555 1.61 LINK O3' SSU B 3 P SSU B 4 1555 1555 1.61 LINK O3' SSU B 4 P SSU B 5 1555 1555 1.61 LINK O3' SSU B 5 P SSU B 6 1555 1555 1.64 LINK O3' SSU C 1 P SSU C 2 1555 1555 1.63 LINK NE2 HIS A 256 ZN ZN A 657 1555 1555 2.25 LINK ND1 HIS A 258 ZN ZN A 657 1555 1555 2.54 LINK OD1 ASP A 260 ZN ZN A 658 1555 1555 2.54 LINK NE2 HIS A 261 ZN ZN A 658 1555 1555 2.16 LINK NE2 HIS A 344 ZN ZN A 657 1555 1555 2.50 LINK OD1 ASP A 367 ZN ZN A 658 1555 1555 2.53 LINK NE2 HIS A 618 ZN ZN A 658 1555 1555 2.50 LINK O2 SO4 A 655 ZN ZN A 658 1555 1555 2.56 CISPEP 1 SER A 521 SER A 522 0 -0.02 CISPEP 2 ARG A 608 PRO A 609 0 -0.23 SITE 1 AC1 5 ARG A 202 TYR A 229 HIS A 234 ASN A 644 SITE 2 AC1 5 ARG A 649 SITE 1 AC2 5 THR A 209 PHE A 213 ASP A 236 PRO A 238 SITE 2 AC2 5 TYR A 242 SITE 1 AC3 7 TYR A 325 ASN A 341 GLU A 377 GLU A 474 SITE 2 AC3 7 TYR A 475 LEU A 476 GLU A 573 SITE 1 AC4 6 ASP A 260 ASP A 367 TYR A 550 HIS A 594 SITE 2 AC4 6 HIS A 618 ZN A 658 SITE 1 AC5 6 ASP A 324 TYR A 325 GLU A 474 GLU A 573 SITE 2 AC5 6 GLY A 574 ARG A 575 SITE 1 AC6 4 HIS A 256 HIS A 258 HIS A 344 ASP A 367 SITE 1 AC7 5 ASP A 260 HIS A 261 ASP A 367 HIS A 618 SITE 2 AC7 5 SO4 A 655 CRYST1 86.438 86.438 237.501 90.00 90.00 90.00 P 43 21 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 0.011569 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011569 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004211 0.00000