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 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 MASTER 270 0 1 9 11 0 3 6 0 0 0 17 END