HEADER HYDROLASE 12-DEC-17 5YZ4 TITLE STRUCTURE OF THE PIN DOMAIN ENDONUCLEASE UTP24 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RRNA-PROCESSING PROTEIN FCF1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 60-192; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE 972H-; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 284812; SOURCE 5 STRAIN: 972H-; SOURCE 6 GENE: FCF1; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PIN DOMAIN, RIBONUCLEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.DU,W.AN,K.YE REVDAT 5 06-NOV-24 5YZ4 1 REMARK REVDAT 4 22-NOV-23 5YZ4 1 LINK REVDAT 3 03-JUL-19 5YZ4 1 JRNL REVDAT 2 27-FEB-19 5YZ4 1 HEADER COMPND SOURCE KEYWDS REVDAT 2 2 1 REMARK DBREF SEQRES HELIX REVDAT 2 3 1 SHEET SSBOND LINK SITE REVDAT 2 4 1 ATOM REVDAT 1 19-DEC-18 5YZ4 0 JRNL AUTH W.AN,Y.DU,K.YE JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF UTP24, AN ENDONUCLEASE JRNL TITL 2 FOR PROCESSING 18S RIBOSOMAL RNA. JRNL REF PLOS ONE V. 13 95723 2018 JRNL REFN ESSN 1932-6203 JRNL PMID 29641590 JRNL DOI 10.1371/JOURNAL.PONE.0195723 REMARK 2 REMARK 2 RESOLUTION. 2.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.4 REMARK 3 NUMBER OF REFLECTIONS : 6721 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 668 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 40.5985 - 3.6497 1.00 1445 163 0.1916 0.2548 REMARK 3 2 3.6497 - 2.8971 0.98 1359 151 0.2166 0.2726 REMARK 3 3 2.8971 - 2.5310 0.92 1270 137 0.2596 0.3070 REMARK 3 4 2.5310 - 2.2996 0.80 1088 115 0.2772 0.3580 REMARK 3 5 2.2996 - 2.1348 0.66 891 102 0.2830 0.3968 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.720 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 : 0.008 1090 REMARK 3 ANGLE : 0.903 1471 REMARK 3 CHIRALITY : 0.055 172 REMARK 3 PLANARITY : 0.012 186 REMARK 3 DIHEDRAL : 18.519 679 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5YZ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006144. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979135 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7270 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.130 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 (%) : 94.5 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.18400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 1.00000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 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: 4MJ7 REMARK 200 REMARK 200 REMARK: CLUSTER REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M CALCIUM ACETATE AND 20% REMARK 280 POLYETHYLENE GLYCOL 3350, PH 8.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.13100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.13100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 24.37000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.66400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.37000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.66400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 37.13100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.37000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 36.66400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 37.13100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.37000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 36.66400 REMARK 290 SMTRY3 8 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: MONOMERIC 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 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 CA CA A 201 LIES ON A SPECIAL POSITION. 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 PRO A 63 C - N - CD ANGL. DEV. = -13.1 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 LYS A 135 158.24 -44.88 REMARK 500 THR A 137 -127.54 -126.84 REMARK 500 LYS A 151 30.41 -88.16 REMARK 500 VAL A 188 -32.17 -146.09 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 62 PRO A 63 133.36 REMARK 500 PRO A 63 PRO A 64 140.65 REMARK 500 GLY A 112 ILE A 113 -149.79 REMARK 500 THR A 137 TYR A 138 -140.89 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 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 103 SG REMARK 620 2 CYS A 132 SG 105.0 REMARK 620 3 HIS A 134 NE2 127.9 119.4 REMARK 620 4 CYS A 142 SG 88.9 110.5 99.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 128 OE1 REMARK 620 2 GLU A 128 OE1 0.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 202 DBREF 5YZ4 A 60 192 UNP O13610 FCF1_SCHPO 60 192 SEQRES 1 A 133 SER LEU GLY PRO PRO TYR HIS VAL ILE ILE ASP THR ASN SEQRES 2 A 133 PHE ILE ASN PHE CYS LEU GLN GLN LYS ILE ASP LEU PHE SEQRES 3 A 133 GLU GLY LEU MET THR CYS LEU TYR ALA LYS THR ILE PRO SEQRES 4 A 133 CYS ILE SER ASP CYS VAL MET ALA GLU LEU GLU LYS LEU SEQRES 5 A 133 GLY ILE ARG TYR ARG ILE ALA LEU ARG ILE ALA LYS ASP SEQRES 6 A 133 GLU ARG PHE GLU ARG LEU PRO CYS THR HIS LYS GLY THR SEQRES 7 A 133 TYR ALA ASP ASP CYS ILE VAL GLN ARG VAL MET GLN HIS SEQRES 8 A 133 LYS CYS TYR LEU VAL ALA THR ASN ASP LYS ASN LEU LYS SEQRES 9 A 133 GLN ARG ILE ARG LYS ILE PRO GLY ILE PRO ILE LEU SER SEQRES 10 A 133 VAL ALA ASN HIS LYS ILE ARG VAL GLU ARG LEU VAL ASP SEQRES 11 A 133 VAL VAL ASP HET CA A 201 1 HET ZN A 202 1 HETNAM CA CALCIUM ION HETNAM ZN ZINC ION FORMUL 2 CA CA 2+ FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *14(H2 O) HELIX 1 AA1 ASN A 72 GLN A 80 1 9 HELIX 2 AA2 ASP A 83 TYR A 93 1 11 HELIX 3 AA3 ASP A 102 LEU A 111 1 10 HELIX 4 AA4 GLY A 112 ARG A 114 5 3 HELIX 5 AA5 TYR A 115 LYS A 123 1 9 HELIX 6 AA6 TYR A 138 HIS A 150 1 13 HELIX 7 AA7 ASP A 159 ARG A 167 1 9 SHEET 1 AA1 6 GLU A 128 LEU A 130 0 SHEET 2 AA1 6 THR A 96 SER A 101 1 N PRO A 98 O GLU A 128 SHEET 3 AA1 6 TYR A 65 ILE A 69 1 N TYR A 65 O ILE A 97 SHEET 4 AA1 6 LEU A 154 ALA A 156 1 O LEU A 154 N ILE A 68 SHEET 5 AA1 6 ILE A 174 ALA A 178 1 O LEU A 175 N VAL A 155 SHEET 6 AA1 6 LYS A 181 ARG A 186 -1 O LYS A 181 N ALA A 178 SSBOND 1 CYS A 152 CYS A 152 1555 3555 2.04 LINK SG CYS A 103 ZN ZN A 202 1555 1555 2.54 LINK OE1 GLU A 128 CA CA A 201 1555 1555 2.12 LINK OE1 GLU A 128 CA CA A 201 1555 3555 2.12 LINK SG CYS A 132 ZN ZN A 202 1555 1555 2.31 LINK NE2 HIS A 134 ZN ZN A 202 1555 1555 1.84 LINK SG CYS A 142 ZN ZN A 202 1555 1555 2.23 SITE 1 AC1 2 HIS A 66 GLU A 128 SITE 1 AC2 4 CYS A 103 CYS A 132 HIS A 134 CYS A 142 CRYST1 48.740 73.328 74.262 90.00 90.00 90.00 C 2 2 21 8 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 0.020517 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013637 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013466 0.00000