HEADER HYDROLASE 08-SEP-14 4WDG TITLE CATALYTIC DOMAIN OF MOUSE 2',3'-CYCLIC NUCLEOTIDE 3'- TITLE 2 PHOSPHODIESTERASE, WITH MUTATION V321A, COMPLEXED WITH 2',5'-ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2',3'-CYCLIC-NUCLEOTIDE 3'-PHOSPHODIESTERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 179-378; COMPND 5 SYNONYM: CNPASE; COMPND 6 EC: 3.1.4.37; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: CNP, CNP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTH27 KEYWDS HYDROLASE, MYELIN, NERVOUS SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.MYLLYKOSKI,A.RAASAKKA,P.KURSULA REVDAT 4 10-JAN-24 4WDG 1 REMARK REVDAT 3 07-MAR-18 4WDG 1 REMARK REVDAT 2 25-NOV-15 4WDG 1 JRNL REVDAT 1 23-SEP-15 4WDG 0 JRNL AUTH A.RAASAKKA,M.MYLLYKOSKI,S.LAULUMAA,M.LEHTIMAKI,M.HARTLEIN, JRNL AUTH 2 M.MOULIN,I.KURSULA,P.KURSULA JRNL TITL DETERMINANTS OF LIGAND BINDING AND CATALYTIC ACTIVITY IN THE JRNL TITL 2 MYELIN ENZYME 2',3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE. JRNL REF SCI REP V. 5 16520 2015 JRNL REFN ESSN 2045-2322 JRNL PMID 26563764 JRNL DOI 10.1038/SREP16520 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 13596 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1359 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 53.4631 - 4.4157 0.99 1324 147 0.1710 0.2399 REMARK 3 2 4.4157 - 3.5051 1.00 1253 139 0.1789 0.2342 REMARK 3 3 3.5051 - 3.0621 1.00 1245 139 0.2186 0.2781 REMARK 3 4 3.0621 - 2.7821 1.00 1203 133 0.3031 0.3615 REMARK 3 5 2.7821 - 2.5827 1.00 1209 134 0.3368 0.3651 REMARK 3 6 2.5827 - 2.4305 1.00 1203 134 0.3371 0.4294 REMARK 3 7 2.4305 - 2.3087 1.00 1213 134 0.3524 0.4078 REMARK 3 8 2.3087 - 2.2082 0.99 1197 135 0.3725 0.3735 REMARK 3 9 2.2082 - 2.1232 1.00 1191 132 0.3734 0.4169 REMARK 3 10 2.1232 - 2.0499 0.99 1199 132 0.4100 0.4178 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 77.09 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 : 0.003 1727 REMARK 3 ANGLE : 0.701 2331 REMARK 3 CHIRALITY : 0.024 250 REMARK 3 PLANARITY : 0.003 292 REMARK 3 DIHEDRAL : 13.721 631 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 162 THROUGH 290 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.9589 8.1956 -18.0117 REMARK 3 T TENSOR REMARK 3 T11: 0.4302 T22: 0.2842 REMARK 3 T33: 0.3261 T12: -0.0368 REMARK 3 T13: 0.0815 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 4.0062 L22: 5.0668 REMARK 3 L33: 3.7551 L12: -1.5457 REMARK 3 L13: 1.8373 L23: -0.9562 REMARK 3 S TENSOR REMARK 3 S11: 0.0394 S12: -0.0320 S13: -0.1002 REMARK 3 S21: 0.5179 S22: 0.0359 S23: 0.0356 REMARK 3 S31: 0.0735 S32: 0.2131 S33: -0.0982 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 291 THROUGH 378 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.0814 4.7198 -10.5199 REMARK 3 T TENSOR REMARK 3 T11: 0.6847 T22: 0.4154 REMARK 3 T33: 0.5072 T12: 0.0211 REMARK 3 T13: 0.1200 T23: 0.0215 REMARK 3 L TENSOR REMARK 3 L11: 2.1285 L22: 4.9668 REMARK 3 L33: 3.5381 L12: -2.0490 REMARK 3 L13: 0.3903 L23: -2.6027 REMARK 3 S TENSOR REMARK 3 S11: -0.1999 S12: -0.3667 S13: -0.2717 REMARK 3 S21: 1.1355 S22: 0.3890 S23: 0.6262 REMARK 3 S31: -0.0093 S32: -0.2343 S33: -0.0569 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 4WDG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000203618. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03149 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13665 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 1.65100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.080 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2XMI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA-ACETATE, PEG 4000 / 6000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 20.66500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.44500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.47000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.44500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.66500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.47000 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL 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 GLY A 158 REMARK 465 GLY A 159 REMARK 465 LEU A 160 REMARK 465 GLU A 161 REMARK 465 GLU A 210 REMARK 465 PRO A 211 REMARK 465 LYS A 212 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 THR A 233 -61.28 -98.64 REMARK 500 ASP A 294 70.82 -66.01 REMARK 500 THR A 374 -167.51 -164.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue A2P A 401 DBREF 4WDG A 159 378 UNP P16330 CN37_MOUSE 179 398 SEQADV 4WDG GLY A 158 UNP P16330 EXPRESSION TAG SEQADV 4WDG ALA A 321 UNP P16330 VAL 341 ENGINEERED MUTATION SEQRES 1 A 221 GLY GLY LEU GLU LYS ASP PHE LEU PRO LEU TYR PHE GLY SEQRES 2 A 221 TRP PHE LEU THR LYS LYS SER SER GLU THR LEU ARG LYS SEQRES 3 A 221 ALA GLY GLN VAL PHE LEU GLU GLU LEU GLY ASN HIS LYS SEQRES 4 A 221 ALA PHE LYS LYS GLU LEU ARG HIS PHE ILE SER GLY ASP SEQRES 5 A 221 GLU PRO LYS GLU LYS LEU GLU LEU VAL SER TYR PHE GLY SEQRES 6 A 221 LYS ARG PRO PRO GLY VAL LEU HIS CYS THR THR LYS PHE SEQRES 7 A 221 CYS ASP TYR GLY LYS ALA ALA GLY ALA GLU GLU TYR ALA SEQRES 8 A 221 GLN GLN GLU VAL VAL LYS ARG SER TYR GLY LYS ALA PHE SEQRES 9 A 221 LYS LEU SER ILE SER ALA LEU PHE VAL THR PRO LYS THR SEQRES 10 A 221 ALA GLY ALA GLN VAL VAL LEU THR ASP GLN GLU LEU GLN SEQRES 11 A 221 LEU TRP PRO SER ASP LEU ASP LYS PRO SER ALA SER GLU SEQRES 12 A 221 GLY LEU PRO PRO GLY SER ARG ALA HIS VAL THR LEU GLY SEQRES 13 A 221 CYS ALA ALA ASP VAL GLN PRO ALA GLN THR GLY LEU ASP SEQRES 14 A 221 LEU LEU ASP ILE LEU GLN GLN VAL LYS GLY GLY SER GLN SEQRES 15 A 221 GLY GLU ALA VAL GLY GLU LEU PRO ARG GLY LYS LEU TYR SEQRES 16 A 221 SER LEU GLY LYS GLY ARG TRP MET LEU SER LEU THR LYS SEQRES 17 A 221 LYS MET GLU VAL LYS ALA ILE PHE THR GLY TYR TYR GLY HET A2P A 401 38 HETNAM A2P ADENOSINE-2'-5'-DIPHOSPHATE FORMUL 2 A2P C10 H15 N5 O10 P2 FORMUL 3 HOH *39(H2 O) HELIX 1 AA1 THR A 174 HIS A 195 1 22 HELIX 2 AA2 HIS A 195 LYS A 200 1 6 HELIX 3 AA3 GLU A 201 PHE A 205 5 5 HELIX 4 AA4 GLU A 216 PHE A 221 1 6 HELIX 5 AA5 ASP A 237 LYS A 240 5 4 HELIX 6 AA6 GLY A 243 GLN A 250 1 8 HELIX 7 AA7 GLN A 250 TYR A 257 1 8 HELIX 8 AA8 GLN A 284 LEU A 288 5 5 HELIX 9 AA9 ALA A 321 GLY A 336 1 16 SHEET 1 AA1 6 HIS A 230 PHE A 235 0 SHEET 2 AA1 6 TYR A 168 LEU A 173 -1 N TRP A 171 O CYS A 231 SHEET 3 AA1 6 ARG A 358 TYR A 376 -1 O ILE A 372 N PHE A 172 SHEET 4 AA1 6 ALA A 260 VAL A 270 -1 N LEU A 268 O LEU A 361 SHEET 5 AA1 6 THR A 274 VAL A 280 -1 O VAL A 280 N SER A 264 SHEET 6 AA1 6 HIS A 309 CYS A 314 -1 O LEU A 312 N ALA A 275 SHEET 1 AA2 5 HIS A 230 PHE A 235 0 SHEET 2 AA2 5 TYR A 168 LEU A 173 -1 N TRP A 171 O CYS A 231 SHEET 3 AA2 5 ARG A 358 TYR A 376 -1 O ILE A 372 N PHE A 172 SHEET 4 AA2 5 GLY A 349 GLY A 355 -1 N GLY A 355 O ARG A 358 SHEET 5 AA2 5 GLY A 344 LEU A 346 -1 N LEU A 346 O GLY A 349 SITE 1 AC1 9 HIS A 230 THR A 232 PHE A 235 HIS A 309 SITE 2 AC1 9 THR A 311 ALA A 321 THR A 323 HOH A 527 SITE 3 AC1 9 HOH A 535 CRYST1 41.330 46.940 106.890 90.00 90.00 90.00 P 21 21 21 4 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 0.024195 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021304 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009355 0.00000