HEADER HYDROLASE, GENE REGULATION 14-JUN-06 2HBM TITLE STRUCTURE OF THE YEAST NUCLEAR EXOSOME COMPONENT, RRP6P, REVEALS AN TITLE 2 INTERPLAY BETWEEN THE ACTIVE SITE AND THE HRDC DOMAIN; PROTEIN IN TITLE 3 COMPLEX WITH MN, ZN, AND UMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXOSOME COMPLEX EXONUCLEASE RRP6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RRP6P CENTRAL FRAGMENT, RESIDUES 129-536; COMPND 5 SYNONYM: RIBOSOMAL RNA- PROCESSING PROTEIN 6; COMPND 6 EC: 3.1.13.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: RRP6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30 EK/LIC KEYWDS EXOSOME, RNA METABOLISM, RNA SURVEILLANCE, RNA PROCESSING, HYDROLASE, KEYWDS 2 GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR S.F.MIDTGAARD,J.ASSENHOLT,A.T.JONSTRUP,L.B.VAN,T.H.JENSEN, AUTHOR 2 D.E.BRODERSEN REVDAT 4 18-OCT-17 2HBM 1 REMARK REVDAT 3 24-FEB-09 2HBM 1 VERSN REVDAT 2 22-AUG-06 2HBM 1 JRNL REVDAT 1 25-JUL-06 2HBM 0 JRNL AUTH S.F.MIDTGAARD,J.ASSENHOLT,A.T.JONSTRUP,L.B.VAN,T.H.JENSEN, JRNL AUTH 2 D.E.BRODERSEN JRNL TITL STRUCTURE OF THE NUCLEAR EXOSOME COMPONENT RRP6P REVEALS AN JRNL TITL 2 INTERPLAY BETWEEN THE ACTIVE SITE AND THE HRDC DOMAIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 11898 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16882719 JRNL DOI 10.1073/PNAS.0604731103 REMARK 2 REMARK 2 RESOLUTION. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 14609 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 : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1465 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 29 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.73 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 369 REMARK 3 BIN R VALUE (WORKING SET) : 0.3320 REMARK 3 BIN FREE R VALUE : 0.3740 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 39 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3216 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 135 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 71.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.83400 REMARK 3 B22 (A**2) : 3.83400 REMARK 3 B33 (A**2) : -7.66700 REMARK 3 B12 (A**2) : -3.25000 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) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.46 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) : 0.45 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.52 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.340 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.56 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.905 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : NULL REMARK 3 BSOL : 34.90 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2HBM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000038165. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JAN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54179 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15522 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 29.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.66600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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: PDB ENTRY 2HBJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12-14% PEG 20000, 0.1M MES OR HEPES, REMARK 280 PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.44333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 52.88667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 52.88667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.44333 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS THE MONOMER PRESENT IN THE REMARK 300 ASYMMETRIC UNIT. 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 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 GLU A 517 REMARK 465 GLU A 518 REMARK 465 ALA A 519 REMARK 465 THR A 520 REMARK 465 PRO A 521 REMARK 465 ILE A 522 REMARK 465 PRO A 523 REMARK 465 SER A 524 REMARK 465 SER A 525 REMARK 465 GLU A 526 REMARK 465 THR A 527 REMARK 465 LYS A 528 REMARK 465 ALA A 529 REMARK 465 ASP A 530 REMARK 465 GLY A 531 REMARK 465 ILE A 532 REMARK 465 LEU A 533 REMARK 465 LEU A 534 REMARK 465 GLU A 535 REMARK 465 THR A 536 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CE MET A 429 CE MET A 429 5555 2.17 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 VAL A 129 84.62 49.00 REMARK 500 LYS A 155 86.03 -160.64 REMARK 500 PRO A 161 143.53 -29.97 REMARK 500 SER A 163 -76.92 -47.30 REMARK 500 ARG A 167 -100.95 -146.91 REMARK 500 LEU A 168 175.16 168.41 REMARK 500 ASP A 170 142.36 -28.84 REMARK 500 ASP A 171 139.65 -15.68 REMARK 500 ASN A 175 122.39 171.61 REMARK 500 PRO A 182 -10.02 -49.94 REMARK 500 TYR A 185 -72.39 -59.22 REMARK 500 GLU A 195 7.83 -67.97 REMARK 500 ASP A 217 22.84 -145.75 REMARK 500 ASN A 231 32.53 -94.89 REMARK 500 ASP A 243 34.42 -140.43 REMARK 500 LEU A 274 2.23 -56.28 REMARK 500 ALA A 336 13.35 -146.14 REMARK 500 ASN A 337 71.92 33.65 REMARK 500 LEU A 346 -1.38 -140.69 REMARK 500 TRP A 349 7.97 -67.34 REMARK 500 PRO A 418 130.14 -39.69 REMARK 500 GLU A 422 -134.74 -135.46 REMARK 500 LYS A 426 -131.51 -106.06 REMARK 500 TYR A 430 9.89 -58.23 REMARK 500 GLN A 431 87.25 -1.05 REMARK 500 TYR A 432 35.65 -78.49 REMARK 500 ILE A 434 98.58 -69.29 REMARK 500 PRO A 435 166.95 -39.45 REMARK 500 PRO A 436 -74.24 -55.18 REMARK 500 ARG A 438 15.90 -59.60 REMARK 500 MET A 464 110.12 -173.95 REMARK 500 THR A 476 61.32 37.90 REMARK 500 THR A 487 -51.61 -9.86 REMARK 500 ASN A 514 -97.17 -63.59 REMARK 500 THR A 515 -79.70 -2.35 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 MN A1002 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 238 OD1 REMARK 620 2 HOH A3006 O 87.7 REMARK 620 3 U A3001 OP1 150.2 98.3 REMARK 620 4 HOH A3005 O 87.7 85.8 121.8 REMARK 620 5 HOH A3004 O 95.2 166.9 85.5 81.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 240 OE2 REMARK 620 2 ASP A 365 OD2 109.3 REMARK 620 3 HOH A3003 O 85.9 98.2 REMARK 620 4 U A3001 OP2 125.8 124.8 86.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U A 3001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HBJ RELATED DB: PDB REMARK 900 NATIVE RRP6P REMARK 900 RELATED ID: 2HBK RELATED DB: PDB REMARK 900 RRP6P IN COMPLEX WITH MN REMARK 900 RELATED ID: 2HBL RELATED DB: PDB REMARK 900 RRP6P IN COMPLEX WITH MN, ZN, AND AMP DBREF 2HBM A 129 536 UNP Q12149 RRP6_YEAST 129 536 SEQADV 2HBM GLY A 127 UNP Q12149 CLONING ARTIFACT SEQADV 2HBM MET A 128 UNP Q12149 CLONING ARTIFACT SEQADV 2HBM ALA A 361 UNP Q12149 TYR 361 ENGINEERED SEQRES 1 A 410 GLY MET VAL GLU LYS PRO GLN LEU LYS PHE LYS SER PRO SEQRES 2 A 410 ILE ASP ASN SER GLU SER HIS PRO PHE ILE PRO LEU LEU SEQRES 3 A 410 LYS GLU LYS PRO ASN ALA LEU LYS PRO LEU SER GLU SER SEQRES 4 A 410 LEU ARG LEU VAL ASP ASP ASP GLU ASN ASN PRO SER HIS SEQRES 5 A 410 TYR PRO HIS PRO TYR GLU TYR GLU ILE ASP HIS GLN GLU SEQRES 6 A 410 TYR SER PRO GLU ILE LEU GLN ILE ARG GLU GLU ILE PRO SEQRES 7 A 410 SER LYS SER TRP ASP ASP SER VAL PRO ILE TRP VAL ASP SEQRES 8 A 410 THR SER THR GLU LEU GLU SER MET LEU GLU ASP LEU LYS SEQRES 9 A 410 ASN THR LYS GLU ILE ALA VAL ASP LEU GLU HIS HIS ASP SEQRES 10 A 410 TYR ARG SER TYR TYR GLY ILE VAL CYS LEU MET GLN ILE SEQRES 11 A 410 SER THR ARG GLU ARG ASP TYR LEU VAL ASP THR LEU LYS SEQRES 12 A 410 LEU ARG GLU ASN LEU HIS ILE LEU ASN GLU VAL PHE THR SEQRES 13 A 410 ASN PRO SER ILE VAL LYS VAL PHE HIS GLY ALA PHE MET SEQRES 14 A 410 ASP ILE ILE TRP LEU GLN ARG ASP LEU GLY LEU TYR VAL SEQRES 15 A 410 VAL GLY LEU PHE ASP THR TYR HIS ALA SER LYS ALA ILE SEQRES 16 A 410 GLY LEU PRO ARG HIS SER LEU ALA TYR LEU LEU GLU ASN SEQRES 17 A 410 PHE ALA ASN PHE LYS THR SER LYS LYS TYR GLN LEU ALA SEQRES 18 A 410 ASP TRP ARG ILE ARG PRO LEU SER LYS PRO MET THR ALA SEQRES 19 A 410 ALA ALA ARG ALA ASP THR HIS PHE LEU LEU ASN ILE TYR SEQRES 20 A 410 ASP GLN LEU ARG ASN LYS LEU ILE GLU SER ASN LYS LEU SEQRES 21 A 410 ALA GLY VAL LEU TYR GLU SER ARG ASN VAL ALA LYS ARG SEQRES 22 A 410 ARG PHE GLU TYR SER LYS TYR ARG PRO LEU THR PRO SER SEQRES 23 A 410 SER GLU VAL TYR SER PRO ILE GLU LYS GLU SER PRO TRP SEQRES 24 A 410 LYS ILE LEU MET TYR GLN TYR ASN ILE PRO PRO GLU ARG SEQRES 25 A 410 GLU VAL LEU VAL ARG GLU LEU TYR GLN TRP ARG ASP LEU SEQRES 26 A 410 ILE ALA ARG ARG ASP ASP GLU SER PRO ARG PHE VAL MET SEQRES 27 A 410 PRO ASN GLN LEU LEU ALA ALA LEU VAL ALA TYR THR PRO SEQRES 28 A 410 THR ASP VAL ILE GLY VAL VAL SER LEU THR ASN GLY VAL SEQRES 29 A 410 THR GLU HIS VAL ARG GLN ASN ALA LYS LEU LEU ALA ASN SEQRES 30 A 410 LEU ILE ARG ASP ALA LEU ARG ASN ILE LYS ASN THR ASN SEQRES 31 A 410 GLU GLU ALA THR PRO ILE PRO SER SER GLU THR LYS ALA SEQRES 32 A 410 ASP GLY ILE LEU LEU GLU THR HET ZN A1001 1 HET MN A1002 1 HET U A3001 21 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM U URIDINE-5'-MONOPHOSPHATE FORMUL 2 ZN ZN 2+ FORMUL 3 MN MN 2+ FORMUL 4 U C9 H13 N2 O9 P FORMUL 5 HOH *135(H2 O) HELIX 1 1 LYS A 131 PHE A 136 5 6 HELIX 2 2 PRO A 161 LEU A 166 1 6 HELIX 3 3 TYR A 183 GLN A 190 1 8 HELIX 4 4 SER A 193 LEU A 197 5 5 HELIX 5 5 SER A 207 SER A 211 5 5 HELIX 6 6 THR A 218 LYS A 230 1 13 HELIX 7 7 ASN A 273 ILE A 276 5 4 HELIX 8 8 LEU A 277 THR A 282 1 6 HELIX 9 9 MET A 295 GLY A 305 1 11 HELIX 10 10 THR A 314 GLY A 322 1 9 HELIX 11 11 SER A 327 ALA A 336 1 10 HELIX 12 12 SER A 341 GLN A 345 5 5 HELIX 13 13 SER A 355 ALA A 364 1 10 HELIX 14 14 PHE A 368 SER A 383 1 16 HELIX 15 15 LYS A 385 ARG A 399 1 15 HELIX 16 16 TYR A 403 ARG A 407 5 5 HELIX 17 17 ARG A 438 ASP A 457 1 20 HELIX 18 18 SER A 459 MET A 464 1 6 HELIX 19 19 PRO A 465 THR A 476 1 12 HELIX 20 20 ASP A 479 SER A 485 1 7 HELIX 21 21 THR A 491 GLN A 496 1 6 HELIX 22 22 ASN A 497 ASN A 514 1 18 SHEET 1 A 6 ILE A 214 VAL A 216 0 SHEET 2 A 6 ASP A 262 VAL A 265 1 O LEU A 264 N VAL A 216 SHEET 3 A 6 ILE A 250 SER A 257 -1 N ILE A 256 O TYR A 263 SHEET 4 A 6 GLU A 234 HIS A 242 -1 N ASP A 238 O GLN A 255 SHEET 5 A 6 VAL A 287 PHE A 290 1 O VAL A 289 N VAL A 237 SHEET 6 A 6 LEU A 311 ASP A 313 1 O PHE A 312 N PHE A 290 SHEET 1 B 2 ARG A 400 PHE A 401 0 SHEET 2 B 2 VAL A 415 TYR A 416 1 O TYR A 416 N ARG A 400 LINK OD1 ASP A 238 MN MN A1002 1555 1555 2.18 LINK OE2 GLU A 240 ZN ZN A1001 1555 1555 2.14 LINK OD2 ASP A 365 ZN ZN A1001 1555 1555 1.95 LINK ZN ZN A1001 O HOH A3003 1555 1555 2.23 LINK ZN ZN A1001 OP2 U A3001 1555 1555 2.16 LINK MN MN A1002 O HOH A3006 1555 1555 1.71 LINK MN MN A1002 OP1 U A3001 1555 1555 2.14 LINK MN MN A1002 O HOH A3005 1555 1555 2.22 LINK MN MN A1002 O HOH A3004 1555 1555 2.13 CISPEP 1 ARG A 352 PRO A 353 0 -0.03 SITE 1 AC1 5 ASP A 238 GLU A 240 ASP A 365 U A3001 SITE 2 AC1 5 HOH A3003 SITE 1 AC2 5 ASP A 238 U A3001 HOH A3004 HOH A3005 SITE 2 AC2 5 HOH A3006 SITE 1 AC3 16 ASP A 238 LEU A 239 GLU A 240 HIS A 241 SITE 2 AC3 16 TRP A 299 LYS A 342 GLN A 345 TRP A 349 SITE 3 AC3 16 ASP A 365 ZN A1001 MN A1002 HOH A3003 SITE 4 AC3 16 HOH A3004 HOH A3006 HOH A3007 HOH A3010 CRYST1 110.577 110.577 79.330 90.00 90.00 120.00 P 31 2 1 6 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 0.009043 0.005221 0.000000 0.00000 SCALE2 0.000000 0.010443 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012606 0.00000 MASTER 370 0 3 22 8 0 8 6 0 0 0 32 END