HEADER TRANSLATION,HYDROLASE 08-JUL-05 2A8Q TITLE 2.6 ANGSTROM CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE NUCLEAR TITLE 2 SNORNA DECAPPING NUDIX HYDROLASE X29 AND MANGANESE IN THE PRESENCE OF TITLE 3 7-METHYL-GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: U8 SNORNA-BINDING PROTEIN X29; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.6.1.-; 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: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DES)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET19B KEYWDS MODIFIED NUDIX HYDROLASE FOLD, TRANSLATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.N.SCARSDALE,B.A.PECULIS,H.T.WRIGHT REVDAT 5 23-AUG-23 2A8Q 1 REMARK SEQADV LINK REVDAT 4 24-JUL-19 2A8Q 1 REMARK LINK REVDAT 3 13-JUL-11 2A8Q 1 VERSN REVDAT 2 24-FEB-09 2A8Q 1 VERSN REVDAT 1 28-MAR-06 2A8Q 0 JRNL AUTH J.N.SCARSDALE,B.A.PECULIS,H.T.WRIGHT JRNL TITL CRYSTAL STRUCTURES OF U8 SNORNA DECAPPING NUDIX HYDROLASE, JRNL TITL 2 X29, AND ITS METAL AND CAP COMPLEXES JRNL REF STRUCTURE V. 14 331 2006 JRNL REFN ISSN 0969-2126 JRNL PMID 16472752 JRNL DOI 10.1016/J.STR.2005.11.010 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.A.PECULIS,J.N.SCARSDALE,H.T.WRIGHT REMARK 1 TITL CRYSTALS OF X29, A XENOPUS LAEVIS U8 SNORNA BINDING PROTEIN REMARK 1 TITL 2 WITH NUCLEAR DECAPPING ACTIVITY REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 60 1668 2004 REMARK 1 REFN ISSN 0907-4449 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.GHOSH,B.PETERSON,N.TOMASEVIC,B.A.PECULIS REMARK 1 TITL XENOPUS U8 SNORNA BINDING PROTEIN IS A CONSERVED NUCLEAR REMARK 1 TITL 2 DECAPPING ENZYME REMARK 1 REF MOL.CELL V. 13 817 2004 REMARK 1 REFN ISSN 1097-2765 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 14223 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1443 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 886 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.3450 REMARK 3 BIN FREE R VALUE SET COUNT : 109 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2900 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 73.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.85000 REMARK 3 B22 (A**2) : -0.74000 REMARK 3 B33 (A**2) : -3.11000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.985 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.339 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.228 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 22.428 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2963 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4002 ; 1.161 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 378 ; 5.080 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;34.961 ;23.534 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 492 ;14.413 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;17.905 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 457 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2238 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1246 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2017 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 114 ; 0.120 ; 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): 13 ; 0.150 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1943 ; 1.715 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2998 ; 2.773 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1109 ; 4.449 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1004 ; 6.405 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 18 A 209 REMARK 3 ORIGIN FOR THE GROUP (A): 24.1000 40.9176 6.6923 REMARK 3 T TENSOR REMARK 3 T11: -0.0816 T22: -0.0316 REMARK 3 T33: -0.1414 T12: -0.1365 REMARK 3 T13: 0.0286 T23: -0.0738 REMARK 3 L TENSOR REMARK 3 L11: 3.9516 L22: 5.3113 REMARK 3 L33: 5.8747 L12: -0.7347 REMARK 3 L13: 0.5236 L23: -1.2116 REMARK 3 S TENSOR REMARK 3 S11: 0.1461 S12: -0.9100 S13: 0.6298 REMARK 3 S21: 0.8331 S22: -0.1573 S23: -0.0951 REMARK 3 S31: -0.5483 S32: -0.1080 S33: 0.0112 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 18 B 208 REMARK 3 ORIGIN FOR THE GROUP (A): 24.1723 33.8519 -18.0826 REMARK 3 T TENSOR REMARK 3 T11: -0.1693 T22: -0.1907 REMARK 3 T33: -0.1936 T12: 0.0472 REMARK 3 T13: 0.0376 T23: 0.0431 REMARK 3 L TENSOR REMARK 3 L11: 2.3509 L22: 4.7316 REMARK 3 L33: 4.2429 L12: 0.2881 REMARK 3 L13: -0.3662 L23: 0.5624 REMARK 3 S TENSOR REMARK 3 S11: 0.0510 S12: 0.2730 S13: -0.0550 REMARK 3 S21: -0.4767 S22: -0.0545 S23: -0.1689 REMARK 3 S31: 0.1448 S32: -0.0499 S33: 0.0035 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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: INITIAL REFINEMENT WITH SUMULATED REMARK 3 ANNEALING USING TORSION ANGLE DYNAMICS IN CNS V1.0 FOLLOWED BY REMARK 3 REFINEMENT IN REFMAC5 REMARK 4 REMARK 4 2A8Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000033628. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-AUG-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.68 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 : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC CONFOCAL OPTICS REMARK 200 OPTICS : OSMIC CONFOCAL OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14707 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 29.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : 0.05000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.9000 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) : 2.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.43300 REMARK 200 R SYM FOR SHELL (I) : 0.43300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1U20 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4-5 MG/ML X29, 0.025M HEPES PH 7.68, REMARK 280 3/75% PEG 6000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 24.91400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.93000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.14200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.93000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.91400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.14200 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL 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 1 REMARK 465 ALA A 2 REMARK 465 GLU A 3 REMARK 465 SER A 4 REMARK 465 ARG A 5 REMARK 465 SER A 6 REMARK 465 PRO A 7 REMARK 465 ASP A 8 REMARK 465 ARG A 9 REMARK 465 GLY A 10 REMARK 465 ALA A 11 REMARK 465 LYS A 12 REMARK 465 GLU A 13 REMARK 465 ASP A 14 REMARK 465 LYS A 15 REMARK 465 PRO A 16 REMARK 465 ARG A 17 REMARK 465 ASP A 76 REMARK 465 THR A 77 REMARK 465 LEU A 210 REMARK 465 GLN A 211 REMARK 465 TYR A 212 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLU B 3 REMARK 465 SER B 4 REMARK 465 ARG B 5 REMARK 465 SER B 6 REMARK 465 PRO B 7 REMARK 465 ASP B 8 REMARK 465 ARG B 9 REMARK 465 GLY B 10 REMARK 465 ALA B 11 REMARK 465 LYS B 12 REMARK 465 GLU B 13 REMARK 465 ASP B 14 REMARK 465 LYS B 15 REMARK 465 PRO B 16 REMARK 465 ARG B 17 REMARK 465 ARG B 209 REMARK 465 LEU B 210 REMARK 465 GLN B 211 REMARK 465 TYR B 212 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 PRO A 18 CG CD REMARK 470 ARG A 19 CG CD NE CZ NH1 NH2 REMARK 470 SER A 22 OG REMARK 470 ARG A 23 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 25 CG CD OE1 OE2 REMARK 470 SER A 26 OG REMARK 470 LEU A 27 CG CD1 CD2 REMARK 470 GLN A 28 CG CD OE1 NE2 REMARK 470 LEU A 29 CG CD1 CD2 REMARK 470 GLU A 30 CG CD OE1 OE2 REMARK 470 TYR A 32 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 33 CG CD CE NZ REMARK 470 HIS A 34 CG ND1 CD2 CE1 NE2 REMARK 470 VAL A 75 CG1 CG2 REMARK 470 ARG A 78 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 80 CG1 CG2 CD1 REMARK 470 LYS A 87 CG CD CE NZ REMARK 470 ARG A 88 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 101 CG1 CG2 REMARK 470 GLU A 102 CG CD OE1 OE2 REMARK 470 VAL A 103 CG1 CG2 REMARK 470 THR A 104 OG1 CG2 REMARK 470 GLN A 112 CG CD OE1 NE2 REMARK 470 ARG A 114 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 116 CG ND1 CD2 CE1 NE2 REMARK 470 PRO A 117 CG CD REMARK 470 GLN A 118 CG CD OE1 NE2 REMARK 470 LYS A 119 CG CD CE NZ REMARK 470 LYS A 130 CG CD CE NZ REMARK 470 ARG A 136 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 190 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 193 CG CD CE NZ REMARK 470 GLU A 202 CG CD OE1 OE2 REMARK 470 LYS A 205 CG CD CE NZ REMARK 470 HIS A 208 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 209 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 25 CG CD OE1 OE2 REMARK 470 GLU B 30 CG CD OE1 OE2 REMARK 470 LYS B 87 CD CE NZ REMARK 470 GLU B 102 CG CD OE1 OE2 REMARK 470 GLN B 118 CG CD OE1 NE2 REMARK 470 LYS B 130 CG CD CE NZ REMARK 470 ARG B 163 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 205 CG CD CE NZ 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 GLU A 115 CD GLU A 115 OE1 0.272 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 PRO A 18 N - CA - CB ANGL. DEV. = 7.3 DEGREES REMARK 500 GLU A 115 CG - CD - OE1 ANGL. DEV. = -12.8 DEGREES REMARK 500 PRO A 117 N - CA - CB ANGL. DEV. = 7.5 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 TYR A 32 143.20 49.61 REMARK 500 ARG A 51 -47.09 -133.22 REMARK 500 ARG A 55 -62.24 70.35 REMARK 500 ASP A 79 -131.67 -76.67 REMARK 500 ILE A 80 -77.73 -86.74 REMARK 500 ARG A 109 -51.25 -135.12 REMARK 500 GLU A 115 9.37 -151.20 REMARK 500 PRO A 117 56.39 -159.22 REMARK 500 GLN A 118 140.59 68.46 REMARK 500 LEU A 149 -97.88 -122.01 REMARK 500 VAL A 166 -48.22 -132.13 REMARK 500 ASN A 180 -9.97 82.63 REMARK 500 ARG B 19 117.13 67.03 REMARK 500 PHE B 49 28.29 49.55 REMARK 500 ASP B 50 12.87 56.12 REMARK 500 ARG B 55 -62.02 72.88 REMARK 500 ASP B 79 -60.08 -96.80 REMARK 500 ARG B 109 -51.60 -128.91 REMARK 500 LYS B 119 97.09 -53.49 REMARK 500 LEU B 149 -103.90 -125.84 REMARK 500 VAL B 166 -56.64 -126.83 REMARK 500 ASN B 180 -22.40 99.47 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 A 300 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 72 O REMARK 620 2 GLU A 93 OE2 61.6 REMARK 620 3 POP A1307 O3 94.1 85.8 REMARK 620 4 POP A1307 O6 91.4 152.6 92.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 301 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 89 OE2 REMARK 620 2 GLU A 93 OE2 103.0 REMARK 620 3 POP A1307 O3 114.4 93.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 89 OE1 REMARK 620 2 GLU A 89 OE2 53.5 REMARK 620 3 POP A1307 O1 143.6 103.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP A 1307 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U20 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE XENOPUS LAEVIS NUDIX HYDROLASE SNORNA REMARK 900 DECAPPING PROTEIN X29 REMARK 900 RELATED ID: 2A8P RELATED DB: PDB REMARK 900 RELATED ID: 2A8R RELATED DB: PDB REMARK 900 RELATED ID: 2A8S RELATED DB: PDB REMARK 900 RELATED ID: 2A8T RELATED DB: PDB DBREF 2A8Q A 1 212 UNP Q569R2 Q569R2_XENLA 1 207 DBREF 2A8Q B 1 212 UNP Q569R2 Q569R2_XENLA 1 207 SEQADV 2A8Q YCM A 174 UNP Q569R2 CYS 174 MODIFIED RESIDUE SEQADV 2A8Q YCM B 174 UNP Q569R2 CYS 174 MODIFIED RESIDUE SEQRES 1 A 212 MET ALA GLU SER ARG SER PRO ASP ARG GLY ALA LYS GLU SEQRES 2 A 212 ASP LYS PRO ARG PRO ARG ASN ILE SER ARG GLU GLU SER SEQRES 3 A 212 LEU GLN LEU GLU GLY TYR LYS HIS ALA CYS HIS ALA LEU SEQRES 4 A 212 LEU HIS ALA PRO SER GLN ALA LYS LEU PHE ASP ARG VAL SEQRES 5 A 212 PRO ILE ARG ARG VAL LEU LEU MET MET MET ARG PHE ASP SEQRES 6 A 212 GLY ARG LEU GLY PHE PRO GLY GLY PHE VAL ASP THR ARG SEQRES 7 A 212 ASP ILE SER LEU GLU GLU GLY LEU LYS ARG GLU LEU GLU SEQRES 8 A 212 GLU GLU LEU GLY PRO ALA LEU ALA THR VAL GLU VAL THR SEQRES 9 A 212 GLU ASP ASP TYR ARG SER SER GLN VAL ARG GLU HIS PRO SEQRES 10 A 212 GLN LYS CYS VAL THR HIS PHE TYR ILE LYS GLU LEU LYS SEQRES 11 A 212 LEU GLU GLU ILE GLU ARG ILE GLU ALA GLU ALA VAL ASN SEQRES 12 A 212 ALA LYS ASP HIS GLY LEU GLU VAL MET GLY LEU ILE ARG SEQRES 13 A 212 VAL PRO LEU TYR THR LEU ARG ASP ARG VAL GLY GLY LEU SEQRES 14 A 212 PRO ALA PHE LEU YCM ASN ASN PHE ILE GLY ASN SER LYS SEQRES 15 A 212 SER GLN LEU LEU TYR ALA LEU ARG SER LEU LYS LEU LEU SEQRES 16 A 212 ARG GLU ASP GLN ILE GLN GLU VAL LEU LYS ALA SER HIS SEQRES 17 A 212 ARG LEU GLN TYR SEQRES 1 B 212 MET ALA GLU SER ARG SER PRO ASP ARG GLY ALA LYS GLU SEQRES 2 B 212 ASP LYS PRO ARG PRO ARG ASN ILE SER ARG GLU GLU SER SEQRES 3 B 212 LEU GLN LEU GLU GLY TYR LYS HIS ALA CYS HIS ALA LEU SEQRES 4 B 212 LEU HIS ALA PRO SER GLN ALA LYS LEU PHE ASP ARG VAL SEQRES 5 B 212 PRO ILE ARG ARG VAL LEU LEU MET MET MET ARG PHE ASP SEQRES 6 B 212 GLY ARG LEU GLY PHE PRO GLY GLY PHE VAL ASP THR ARG SEQRES 7 B 212 ASP ILE SER LEU GLU GLU GLY LEU LYS ARG GLU LEU GLU SEQRES 8 B 212 GLU GLU LEU GLY PRO ALA LEU ALA THR VAL GLU VAL THR SEQRES 9 B 212 GLU ASP ASP TYR ARG SER SER GLN VAL ARG GLU HIS PRO SEQRES 10 B 212 GLN LYS CYS VAL THR HIS PHE TYR ILE LYS GLU LEU LYS SEQRES 11 B 212 LEU GLU GLU ILE GLU ARG ILE GLU ALA GLU ALA VAL ASN SEQRES 12 B 212 ALA LYS ASP HIS GLY LEU GLU VAL MET GLY LEU ILE ARG SEQRES 13 B 212 VAL PRO LEU TYR THR LEU ARG ASP ARG VAL GLY GLY LEU SEQRES 14 B 212 PRO ALA PHE LEU YCM ASN ASN PHE ILE GLY ASN SER LYS SEQRES 15 B 212 SER GLN LEU LEU TYR ALA LEU ARG SER LEU LYS LEU LEU SEQRES 16 B 212 ARG GLU ASP GLN ILE GLN GLU VAL LEU LYS ALA SER HIS SEQRES 17 B 212 ARG LEU GLN TYR MODRES 2A8Q YCM A 174 CYS S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE MODRES 2A8Q YCM B 174 CYS S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE HET YCM A 174 10 HET YCM B 174 10 HET MN A 300 1 HET MN A 301 1 HET MN A 302 1 HET POP A1307 9 HET MN B 304 1 HET MN B 305 1 HETNAM YCM S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE HETNAM MN MANGANESE (II) ION HETNAM POP PYROPHOSPHATE 2- HETSYN YCM CYSTEINE-S-ACETAMIDE FORMUL 1 YCM 2(C5 H10 N2 O3 S) FORMUL 3 MN 5(MN 2+) FORMUL 6 POP H2 O7 P2 2- FORMUL 9 HOH *44(H2 O) HELIX 1 1 SER A 22 GLN A 28 1 7 HELIX 2 2 PHE A 49 ARG A 51 5 3 HELIX 3 3 SER A 81 GLY A 95 1 15 HELIX 4 4 PRO A 96 VAL A 101 5 6 HELIX 5 5 THR A 104 ASP A 106 5 3 HELIX 6 6 LYS A 130 VAL A 142 1 13 HELIX 7 7 GLY A 168 LEU A 173 1 6 HELIX 8 8 ASN A 180 LEU A 192 1 13 HELIX 9 9 ARG A 196 HIS A 208 1 13 HELIX 10 10 SER B 22 LEU B 29 1 8 HELIX 11 11 PHE B 49 ARG B 51 5 3 HELIX 12 12 SER B 81 GLY B 95 1 15 HELIX 13 13 PRO B 96 THR B 100 5 5 HELIX 14 14 THR B 104 ASP B 106 5 3 HELIX 15 15 LYS B 130 VAL B 142 1 13 HELIX 16 16 GLY B 168 LEU B 173 1 6 HELIX 17 17 ASN B 180 LEU B 192 1 13 HELIX 18 18 ARG B 196 HIS B 208 1 13 SHEET 1 A 6 ASN A 20 ILE A 21 0 SHEET 2 A 6 TYR A 108 ARG A 114 -1 O SER A 111 N ILE A 21 SHEET 3 A 6 CYS A 120 GLU A 128 -1 O CYS A 120 N ARG A 114 SHEET 4 A 6 LYS A 33 LEU A 48 1 N ALA A 35 O HIS A 123 SHEET 5 A 6 VAL A 52 ARG A 63 -1 O VAL A 57 N ALA A 42 SHEET 6 A 6 GLY A 72 PHE A 74 0 SHEET 1 B 4 LEU A 68 GLY A 69 0 SHEET 2 B 4 VAL A 52 ARG A 63 -1 N MET A 61 O GLY A 69 SHEET 3 B 4 LYS A 33 LEU A 48 -1 N ALA A 42 O VAL A 57 SHEET 4 B 4 VAL A 151 ARG A 156 0 SHEET 1 C 5 LEU B 68 GLY B 69 0 SHEET 2 C 5 VAL B 52 ARG B 63 -1 N MET B 61 O GLY B 69 SHEET 3 C 5 LYS B 33 LEU B 48 -1 N ALA B 42 O VAL B 57 SHEET 4 C 5 CYS B 120 GLU B 128 1 O HIS B 123 N ALA B 35 SHEET 5 C 5 TYR B 108 ARG B 114 -1 N SER B 110 O PHE B 124 SHEET 1 D 4 GLY B 72 VAL B 75 0 SHEET 2 D 4 LYS B 33 LEU B 48 -1 N CYS B 36 O GLY B 73 SHEET 3 D 4 VAL B 52 ARG B 63 -1 O VAL B 57 N ALA B 42 SHEET 4 D 4 VAL B 151 ARG B 156 -1 O MET B 152 N MET B 62 LINK C LEU A 173 N YCM A 174 1555 1555 1.34 LINK C YCM A 174 N ASN A 175 1555 1555 1.33 LINK C LEU B 173 N YCM B 174 1555 1555 1.33 LINK C YCM B 174 N ASN B 175 1555 1555 1.33 LINK O GLY A 72 MN MN A 300 1555 1555 2.37 LINK OE2 GLU A 89 MN MN A 301 1555 1555 2.23 LINK OE1 GLU A 89 MN MN A 302 1555 1555 2.26 LINK OE2 GLU A 89 MN MN A 302 1555 1555 2.57 LINK OE2 GLU A 93 MN MN A 300 1555 1555 2.48 LINK OE2 GLU A 93 MN MN A 301 1555 1555 2.27 LINK MN MN A 300 O3 POP A1307 1555 1555 2.29 LINK MN MN A 300 O6 POP A1307 1555 1555 2.52 LINK MN MN A 301 O3 POP A1307 1555 1555 2.18 LINK MN MN A 302 O1 POP A1307 1555 1555 2.21 LINK O GLY B 72 MN MN B 304 1555 1555 2.04 LINK OE2 GLU B 93 MN MN B 305 1555 1555 2.54 CISPEP 1 HIS B 116 PRO B 117 0 9.17 SITE 1 AC1 4 GLY A 72 GLU A 93 MN A 301 POP A1307 SITE 1 AC2 6 GLY A 72 GLU A 89 GLU A 93 MN A 300 SITE 2 AC2 6 MN A 302 POP A1307 SITE 1 AC3 3 GLU A 89 MN A 301 POP A1307 SITE 1 AC4 4 GLY B 72 GLU B 93 MN B 305 HOH B 309 SITE 1 AC5 4 GLY B 72 GLU B 89 GLU B 93 MN B 304 SITE 1 AC6 9 HIS A 37 ARG A 63 GLY A 72 GLY A 73 SITE 2 AC6 9 PHE A 74 GLU A 93 MN A 300 MN A 301 SITE 3 AC6 9 MN A 302 CRYST1 49.828 82.284 111.860 90.00 90.00 90.00 P 21 21 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 0.020069 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012153 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008940 0.00000