HEADER NUCLEASE 21-SEP-05 2C1W TITLE THE STRUCTURE OF XENDOU: A SPLICING INDEPENDENT SNORNA TITLE 2 PROCESSING ENDORIBONUCLEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOU PROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: XENDOU; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS NUCLEASE, SNORNA, ENDORIBONUCLEASE, SPLICING INDEPENDENT KEYWDS 2 PROCESSING EXPDTA X-RAY DIFFRACTION AUTHOR F.RENZI,E.CAFFARELLI,P.LANEVE,I.BOZZONI,M.BRUNORI,B.VALLONE REVDAT 3 24-FEB-09 2C1W 1 VERSN REVDAT 2 23-AUG-06 2C1W 1 JRNL REVDAT 1 20-JUL-06 2C1W 0 JRNL AUTH F.RENZI,E.CAFFARELLI,P.LANEVE,I.BOZZONI,M.BRUNORI, JRNL AUTH 2 B.VALLONE JRNL TITL THE STRUCTURE OF THE ENDORIBONUCLEASE XENDOU: FROM JRNL TITL 2 SMALL NUCLEOLAR RNA PROCESSING TO SEVERE ACUTE JRNL TITL 3 RESPIRATORY SYNDROME CORONAVIRUS REPLICATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 12365 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16895992 JRNL DOI 10.1073/PNAS.0602426103 REMARK 2 REMARK 2 RESOLUTION. 2.2 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 46190 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 + TEST SET) : 0.274 REMARK 3 R VALUE (WORKING SET) : 0.274 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2463 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3232 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3160 REMARK 3 BIN FREE R VALUE SET COUNT : 183 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6915 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 438 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : 0.67000 REMARK 3 B33 (A**2) : 0.41000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.96000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.250 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.893 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.884 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7106 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9608 ; 1.897 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 864 ;14.708 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 390 ;38.496 ;24.282 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1305 ;21.004 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 52 ;20.711 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 996 ; 0.147 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5499 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3841 ; 0.270 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4725 ; 0.317 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 421 ; 0.208 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 72 ; 0.242 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.166 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4158 ; 2.516 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6734 ; 4.176 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2948 ; 2.372 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2849 ; 3.331 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. RESIDUES 1-5, 45-53, 290-292 FROM ALL THREE REMARK 3 NCS MONOMERS AND RESIDUES 150, 151 FROM MONOMER A, 54, 55, 288 REMARK 3 AND 289 FROM MONOMER C WERE DISORDERED AND WERE OMITTED FROM REMARK 3 THE MODEL. REMARK 4 REMARK 4 2C1W COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-SEP-05. REMARK 100 THE PDBE ID CODE IS EBI-25709. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64530 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.17000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SOLVE/RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.4 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M AMMONIUM SULPHATE, 0.2M REMARK 280 PHOSPHATE BUFFER PH5.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 82.22550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.60200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 82.22550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.60200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 GENERATING THE BIOMOLECULE 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: PQS 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 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 HOH B2026 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 ALA A 2 REMARK 465 SER A 3 REMARK 465 ASN A 4 REMARK 465 ARG A 5 REMARK 465 PRO A 45 REMARK 465 ALA A 46 REMARK 465 GLY A 47 REMARK 465 SER A 48 REMARK 465 ASN A 49 REMARK 465 GLN A 50 REMARK 465 ALA A 51 REMARK 465 ARG A 52 REMARK 465 ASP A 53 REMARK 465 ALA A 150 REMARK 465 PRO A 151 REMARK 465 ASP A 290 REMARK 465 LEU A 291 REMARK 465 TYR A 292 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 ASN B 4 REMARK 465 ARG B 5 REMARK 465 ALA B 46 REMARK 465 GLY B 47 REMARK 465 SER B 48 REMARK 465 ASN B 49 REMARK 465 GLN B 50 REMARK 465 ALA B 51 REMARK 465 ARG B 52 REMARK 465 ASP B 53 REMARK 465 ASP B 290 REMARK 465 LEU B 291 REMARK 465 TYR B 292 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 SER C 3 REMARK 465 ASN C 4 REMARK 465 ARG C 5 REMARK 465 PRO C 45 REMARK 465 ALA C 46 REMARK 465 GLY C 47 REMARK 465 SER C 48 REMARK 465 ASN C 49 REMARK 465 GLN C 50 REMARK 465 ALA C 51 REMARK 465 ARG C 52 REMARK 465 ASP C 53 REMARK 465 SER C 54 REMARK 465 ALA C 55 REMARK 465 ASN C 288 REMARK 465 PRO C 289 REMARK 465 ASP C 290 REMARK 465 LEU C 291 REMARK 465 TYR C 292 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 GLY A 89 N GLY A 89 CA 0.096 REMARK 500 TYR A 242 CD1 TYR A 242 CE1 0.120 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 56 CB - CA - C ANGL. DEV. = 13.1 DEGREES REMARK 500 THR A 88 N - CA - C ANGL. DEV. = -20.4 DEGREES REMARK 500 GLY A 89 N - CA - C ANGL. DEV. = 17.4 DEGREES REMARK 500 LYS A 169 CB - CA - C ANGL. DEV. = -29.3 DEGREES REMARK 500 LYS A 169 N - CA - C ANGL. DEV. = 21.4 DEGREES REMARK 500 GLN A 172 CB - CA - C ANGL. DEV. = -20.1 DEGREES REMARK 500 GLU A 173 N - CA - CB ANGL. DEV. = -14.2 DEGREES REMARK 500 GLY A 176 N - CA - C ANGL. DEV. = 19.2 DEGREES REMARK 500 LYS B 69 CB - CA - C ANGL. DEV. = -23.8 DEGREES REMARK 500 SER B 70 CB - CA - C ANGL. DEV. = -19.4 DEGREES REMARK 500 ARG B 71 N - CA - C ANGL. DEV. = -22.1 DEGREES REMARK 500 LYS C 69 CB - CA - C ANGL. DEV. = 14.9 DEGREES REMARK 500 SER C 70 N - CA - C ANGL. DEV. = 29.0 DEGREES REMARK 500 SER C 70 N - CA - CB ANGL. DEV. = -21.3 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 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 ARG A 26 -77.68 94.71 REMARK 500 MET A 27 133.12 -31.56 REMARK 500 SER A 56 -64.24 -146.69 REMARK 500 PHE A 57 153.83 -49.71 REMARK 500 ASP A 64 93.54 -54.87 REMARK 500 SER A 70 179.42 69.95 REMARK 500 ARG A 71 -39.44 85.04 REMARK 500 ASP A 87 -3.50 96.34 REMARK 500 SER A 153 -156.32 -97.34 REMARK 500 ARG A 154 65.56 91.73 REMARK 500 PRO A 155 103.01 -52.88 REMARK 500 ALA A 199 -161.75 -102.61 REMARK 500 VAL A 233 153.20 -48.09 REMARK 500 GLU A 261 -118.74 56.62 REMARK 500 GLN B 7 -157.72 -128.98 REMARK 500 ASP B 64 98.67 -69.73 REMARK 500 SER B 70 -9.10 81.62 REMARK 500 ARG B 71 -71.38 -102.87 REMARK 500 THR B 73 6.27 -55.54 REMARK 500 GLU B 173 -2.10 60.20 REMARK 500 ARG B 200 83.51 -62.15 REMARK 500 ASN B 202 15.85 -69.00 REMARK 500 LYS B 203 -162.48 -78.89 REMARK 500 GLU B 221 16.16 53.13 REMARK 500 LEU B 260 77.80 -110.74 REMARK 500 GLU B 261 -110.03 61.28 REMARK 500 ASN B 287 74.76 64.83 REMARK 500 TYR C 43 13.52 -150.80 REMARK 500 PHE C 57 114.06 -169.85 REMARK 500 LYS C 72 -152.29 -111.11 REMARK 500 VAL C 90 -96.47 51.54 REMARK 500 ALA C 91 68.51 -118.18 REMARK 500 PRO C 155 95.81 -56.54 REMARK 500 MET C 174 -105.80 65.80 REMARK 500 GLN C 201 -21.09 77.88 REMARK 500 ASN C 202 33.59 -90.58 REMARK 500 GLU C 221 -13.07 71.91 REMARK 500 GLU C 261 -104.02 50.09 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 ASN A 25 ARG A 26 124.62 REMARK 500 ARG A 26 MET A 27 -117.57 REMARK 500 ASP A 87 THR A 88 -140.53 REMARK 500 GLY A 152 SER A 153 146.41 REMARK 500 SER A 168 LYS A 169 -143.85 REMARK 500 GLY A 171 GLN A 172 -98.07 REMARK 500 MET A 175 GLY A 176 40.12 REMARK 500 GLY A 176 LEU A 177 -148.23 REMARK 500 MET B 174 MET B 175 -145.92 REMARK 500 ARG B 200 GLN B 201 -127.35 REMARK 500 SER C 56 PHE C 57 129.05 REMARK 500 LEU C 68 LYS C 69 -139.90 REMARK 500 LYS C 69 SER C 70 131.73 REMARK 500 ALA C 91 GLU C 92 -99.70 REMARK 500 THR C 286 ASN C 287 125.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 THR A 88 45.3 L L OUTSIDE RANGE REMARK 500 GLU A 173 50.5 L L OUTSIDE RANGE REMARK 500 GLU B 261 22.3 L L OUTSIDE RANGE REMARK 500 LYS C 69 9.2 L D EXPECTING SP3 REMARK 500 SER C 70 24.7 L L OUTSIDE RANGE REMARK 500 VAL C 90 23.7 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A1290 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B1290 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 C1288 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2C09 RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF XENDOU, A SPLICING REMARK 900 INDEPENDENT SNORNA PROCESSING ENDORIBONUCLEASE DBREF 2C1W A 1 292 UNP Q8JFY9 Q8JFY9_XENLA 1 292 DBREF 2C1W B 1 292 UNP Q8JFY9 Q8JFY9_XENLA 1 292 DBREF 2C1W C 1 292 UNP Q8JFY9 Q8JFY9_XENLA 1 292 SEQRES 1 A 292 MET ALA SER ASN ARG GLY GLN LEU ASN HIS GLU LEU SER SEQRES 2 A 292 LYS LEU PHE ASN GLU LEU TRP ASP ALA ASP GLN ASN ARG SEQRES 3 A 292 MET LYS SER GLY LYS ASP TYR ARG ILE SER LEU GLN GLY SEQRES 4 A 292 LYS ALA GLY TYR VAL PRO ALA GLY SER ASN GLN ALA ARG SEQRES 5 A 292 ASP SER ALA SER PHE PRO LEU PHE GLN PHE VAL ASP GLU SEQRES 6 A 292 GLU LYS LEU LYS SER ARG LYS THR PHE ALA THR PHE ILE SEQRES 7 A 292 SER LEU LEU ASP ASN TYR GLU MET ASP THR GLY VAL ALA SEQRES 8 A 292 GLU VAL VAL THR PRO GLU GLU ILE ALA GLU ASN ASN ASN SEQRES 9 A 292 PHE LEU ASP ALA ILE LEU GLU THR LYS VAL MET LYS MET SEQRES 10 A 292 ALA HIS ASP TYR LEU VAL ARG LYS ASN GLN ALA LYS PRO SEQRES 11 A 292 THR ARG ASN ASP PHE LYS VAL GLN LEU TYR ASN ILE TRP SEQRES 12 A 292 PHE GLN LEU TYR SER ARG ALA PRO GLY SER ARG PRO ASP SEQRES 13 A 292 SER CYS GLY PHE GLU HIS VAL PHE VAL GLY GLU SER LYS SEQRES 14 A 292 ARG GLY GLN GLU MET MET GLY LEU HIS ASN TRP VAL GLN SEQRES 15 A 292 PHE TYR LEU GLN GLU LYS ARG LYS ASN ILE ASP TYR LYS SEQRES 16 A 292 GLY TYR VAL ALA ARG GLN ASN LYS SER ARG PRO ASP GLU SEQRES 17 A 292 ASP ASP GLN VAL LEU ASN LEU GLN PHE ASN TRP LYS GLU SEQRES 18 A 292 MET VAL LYS PRO VAL GLY SER SER PHE ILE GLY VAL SER SEQRES 19 A 292 PRO GLU PHE GLU PHE ALA LEU TYR THR ILE VAL PHE LEU SEQRES 20 A 292 ALA SER GLN GLU LYS MET SER ARG GLU VAL VAL ARG LEU SEQRES 21 A 292 GLU GLU TYR GLU LEU GLN ILE VAL VAL ASN ARG HIS GLY SEQRES 22 A 292 ARG TYR ILE GLY THR ALA TYR PRO VAL LEU LEU SER THR SEQRES 23 A 292 ASN ASN PRO ASP LEU TYR SEQRES 1 B 292 MET ALA SER ASN ARG GLY GLN LEU ASN HIS GLU LEU SER SEQRES 2 B 292 LYS LEU PHE ASN GLU LEU TRP ASP ALA ASP GLN ASN ARG SEQRES 3 B 292 MET LYS SER GLY LYS ASP TYR ARG ILE SER LEU GLN GLY SEQRES 4 B 292 LYS ALA GLY TYR VAL PRO ALA GLY SER ASN GLN ALA ARG SEQRES 5 B 292 ASP SER ALA SER PHE PRO LEU PHE GLN PHE VAL ASP GLU SEQRES 6 B 292 GLU LYS LEU LYS SER ARG LYS THR PHE ALA THR PHE ILE SEQRES 7 B 292 SER LEU LEU ASP ASN TYR GLU MET ASP THR GLY VAL ALA SEQRES 8 B 292 GLU VAL VAL THR PRO GLU GLU ILE ALA GLU ASN ASN ASN SEQRES 9 B 292 PHE LEU ASP ALA ILE LEU GLU THR LYS VAL MET LYS MET SEQRES 10 B 292 ALA HIS ASP TYR LEU VAL ARG LYS ASN GLN ALA LYS PRO SEQRES 11 B 292 THR ARG ASN ASP PHE LYS VAL GLN LEU TYR ASN ILE TRP SEQRES 12 B 292 PHE GLN LEU TYR SER ARG ALA PRO GLY SER ARG PRO ASP SEQRES 13 B 292 SER CYS GLY PHE GLU HIS VAL PHE VAL GLY GLU SER LYS SEQRES 14 B 292 ARG GLY GLN GLU MET MET GLY LEU HIS ASN TRP VAL GLN SEQRES 15 B 292 PHE TYR LEU GLN GLU LYS ARG LYS ASN ILE ASP TYR LYS SEQRES 16 B 292 GLY TYR VAL ALA ARG GLN ASN LYS SER ARG PRO ASP GLU SEQRES 17 B 292 ASP ASP GLN VAL LEU ASN LEU GLN PHE ASN TRP LYS GLU SEQRES 18 B 292 MET VAL LYS PRO VAL GLY SER SER PHE ILE GLY VAL SER SEQRES 19 B 292 PRO GLU PHE GLU PHE ALA LEU TYR THR ILE VAL PHE LEU SEQRES 20 B 292 ALA SER GLN GLU LYS MET SER ARG GLU VAL VAL ARG LEU SEQRES 21 B 292 GLU GLU TYR GLU LEU GLN ILE VAL VAL ASN ARG HIS GLY SEQRES 22 B 292 ARG TYR ILE GLY THR ALA TYR PRO VAL LEU LEU SER THR SEQRES 23 B 292 ASN ASN PRO ASP LEU TYR SEQRES 1 C 292 MET ALA SER ASN ARG GLY GLN LEU ASN HIS GLU LEU SER SEQRES 2 C 292 LYS LEU PHE ASN GLU LEU TRP ASP ALA ASP GLN ASN ARG SEQRES 3 C 292 MET LYS SER GLY LYS ASP TYR ARG ILE SER LEU GLN GLY SEQRES 4 C 292 LYS ALA GLY TYR VAL PRO ALA GLY SER ASN GLN ALA ARG SEQRES 5 C 292 ASP SER ALA SER PHE PRO LEU PHE GLN PHE VAL ASP GLU SEQRES 6 C 292 GLU LYS LEU LYS SER ARG LYS THR PHE ALA THR PHE ILE SEQRES 7 C 292 SER LEU LEU ASP ASN TYR GLU MET ASP THR GLY VAL ALA SEQRES 8 C 292 GLU VAL VAL THR PRO GLU GLU ILE ALA GLU ASN ASN ASN SEQRES 9 C 292 PHE LEU ASP ALA ILE LEU GLU THR LYS VAL MET LYS MET SEQRES 10 C 292 ALA HIS ASP TYR LEU VAL ARG LYS ASN GLN ALA LYS PRO SEQRES 11 C 292 THR ARG ASN ASP PHE LYS VAL GLN LEU TYR ASN ILE TRP SEQRES 12 C 292 PHE GLN LEU TYR SER ARG ALA PRO GLY SER ARG PRO ASP SEQRES 13 C 292 SER CYS GLY PHE GLU HIS VAL PHE VAL GLY GLU SER LYS SEQRES 14 C 292 ARG GLY GLN GLU MET MET GLY LEU HIS ASN TRP VAL GLN SEQRES 15 C 292 PHE TYR LEU GLN GLU LYS ARG LYS ASN ILE ASP TYR LYS SEQRES 16 C 292 GLY TYR VAL ALA ARG GLN ASN LYS SER ARG PRO ASP GLU SEQRES 17 C 292 ASP ASP GLN VAL LEU ASN LEU GLN PHE ASN TRP LYS GLU SEQRES 18 C 292 MET VAL LYS PRO VAL GLY SER SER PHE ILE GLY VAL SER SEQRES 19 C 292 PRO GLU PHE GLU PHE ALA LEU TYR THR ILE VAL PHE LEU SEQRES 20 C 292 ALA SER GLN GLU LYS MET SER ARG GLU VAL VAL ARG LEU SEQRES 21 C 292 GLU GLU TYR GLU LEU GLN ILE VAL VAL ASN ARG HIS GLY SEQRES 22 C 292 ARG TYR ILE GLY THR ALA TYR PRO VAL LEU LEU SER THR SEQRES 23 C 292 ASN ASN PRO ASP LEU TYR HET PO4 A1290 5 HET PO4 B1290 5 HET PO4 C1288 5 HETNAM PO4 PHOSPHATE ION FORMUL 4 PO4 3(O4 P 3-) FORMUL 7 HOH *438(H2 O1) HELIX 1 1 ASN A 9 ALA A 22 1 14 HELIX 2 2 ASP A 64 LYS A 69 1 6 HELIX 3 3 THR A 73 ASP A 87 1 15 HELIX 4 4 THR A 95 LEU A 110 1 16 HELIX 5 5 THR A 112 LYS A 125 1 14 HELIX 6 6 THR A 131 GLN A 145 1 15 HELIX 7 7 CYS A 158 PHE A 164 1 7 HELIX 8 8 ASN A 179 ARG A 189 1 11 HELIX 9 9 SER A 234 ALA A 248 1 15 HELIX 10 10 ASN B 9 ALA B 22 1 14 HELIX 11 11 ASP B 64 LYS B 69 1 6 HELIX 12 12 THR B 73 TYR B 84 1 12 HELIX 13 13 THR B 95 LEU B 110 1 16 HELIX 14 14 THR B 112 LYS B 125 1 14 HELIX 15 15 THR B 131 PHE B 144 1 14 HELIX 16 16 CYS B 158 PHE B 164 1 7 HELIX 17 17 ASN B 179 ARG B 189 1 11 HELIX 18 18 SER B 234 ALA B 248 1 15 HELIX 19 19 ASN C 9 ALA C 22 1 14 HELIX 20 20 ASP C 64 SER C 70 1 7 HELIX 21 21 THR C 73 TYR C 84 1 12 HELIX 22 22 THR C 95 LEU C 110 1 16 HELIX 23 23 THR C 112 LYS C 125 1 14 HELIX 24 24 THR C 131 PHE C 144 1 14 HELIX 25 25 CYS C 158 PHE C 164 1 7 HELIX 26 26 ASN C 179 ARG C 189 1 11 HELIX 27 27 SER C 234 ALA C 248 1 15 SHEET 1 AA 2 TYR A 33 ILE A 35 0 SHEET 2 AA 2 PHE A 60 VAL A 63 -1 N GLN A 61 O ARG A 34 SHEET 1 AB 3 ILE A 192 TYR A 197 0 SHEET 2 AB 3 VAL A 212 TRP A 219 -1 O GLN A 216 N LYS A 195 SHEET 3 AB 3 GLY A 227 PHE A 230 -1 O GLY A 227 N LEU A 215 SHEET 1 AC 3 MET A 253 LEU A 260 0 SHEET 2 AC 3 TYR A 263 HIS A 272 -1 O TYR A 263 N LEU A 260 SHEET 3 AC 3 TYR A 275 SER A 285 -1 O TYR A 275 N HIS A 272 SHEET 1 BA 2 TYR B 33 ILE B 35 0 SHEET 2 BA 2 PHE B 60 VAL B 63 -1 N GLN B 61 O ARG B 34 SHEET 1 BB 3 ILE B 192 TYR B 197 0 SHEET 2 BB 3 VAL B 212 TRP B 219 -1 O GLN B 216 N LYS B 195 SHEET 3 BB 3 GLY B 227 PHE B 230 -1 O GLY B 227 N LEU B 215 SHEET 1 BC 3 ILE B 192 TYR B 197 0 SHEET 2 BC 3 VAL B 212 TRP B 219 -1 O GLN B 216 N LYS B 195 SHEET 3 BC 3 MET B 222 VAL B 223 -1 O MET B 222 N TRP B 219 SHEET 1 BD 3 MET B 253 LEU B 260 0 SHEET 2 BD 3 TYR B 263 HIS B 272 -1 O TYR B 263 N LEU B 260 SHEET 3 BD 3 TYR B 275 SER B 285 -1 O TYR B 275 N HIS B 272 SHEET 1 CA 2 TYR C 33 ILE C 35 0 SHEET 2 CA 2 PHE C 60 VAL C 63 -1 N GLN C 61 O ARG C 34 SHEET 1 CB 3 ILE C 192 TYR C 197 0 SHEET 2 CB 3 VAL C 212 TRP C 219 -1 O GLN C 216 N LYS C 195 SHEET 3 CB 3 GLY C 227 PHE C 230 -1 O GLY C 227 N LEU C 215 SHEET 1 CC 3 MET C 253 LEU C 260 0 SHEET 2 CC 3 TYR C 263 HIS C 272 -1 O TYR C 263 N LEU C 260 SHEET 3 CC 3 TYR C 275 SER C 285 -1 O TYR C 275 N HIS C 272 SITE 1 AC1 6 ARG A 149 HIS A 162 ASN A 270 HIS A 272 SITE 2 AC1 6 THR A 278 HOH A2161 SITE 1 AC2 4 ARG B 149 HIS B 272 GLY B 277 THR B 278 SITE 1 AC3 6 ARG C 149 HIS C 162 ASN C 270 HIS C 272 SITE 2 AC3 6 GLY C 277 THR C 278 CRYST1 164.451 53.204 133.466 90.00 121.86 90.00 C 1 2 1 12 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 0.006081 0.000000 0.003779 0.00000 SCALE2 0.000000 0.018796 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008822 0.00000 MTRIX1 1 0.903000 0.380000 0.203000 23.80529 1 MTRIX2 1 0.329000 -0.305000 -0.894000 25.74303 1 MTRIX3 1 -0.278000 0.874000 -0.400000 49.82897 1 MTRIX1 2 0.900000 0.365000 -0.239000 64.39597 1 MTRIX2 2 0.356000 -0.298000 0.886000 -17.31528 1 MTRIX3 2 0.252000 -0.882000 -0.398000 36.38666 1