HEADER HYDROLASE 08-SEP-14 4WDF 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 4WDF 1 REMARK REVDAT 3 07-MAR-18 4WDF 1 REMARK REVDAT 2 25-NOV-15 4WDF 1 JRNL REVDAT 1 23-SEP-15 4WDF 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 13858 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1385 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 35.2870 - 4.3068 0.99 1282 142 0.1770 0.2337 REMARK 3 2 4.3068 - 3.4193 0.99 1246 139 0.1772 0.2291 REMARK 3 3 3.4193 - 2.9874 1.00 1257 140 0.1974 0.2420 REMARK 3 4 2.9874 - 2.7143 1.00 1234 135 0.2175 0.2894 REMARK 3 5 2.7143 - 2.5199 1.00 1274 142 0.2170 0.2641 REMARK 3 6 2.5199 - 2.3713 1.00 1225 136 0.2242 0.2879 REMARK 3 7 2.3713 - 2.2526 1.00 1233 137 0.2370 0.2639 REMARK 3 8 2.2526 - 2.1545 0.99 1223 136 0.2624 0.3306 REMARK 3 9 2.1545 - 2.0716 1.00 1243 139 0.2912 0.3638 REMARK 3 10 2.0716 - 2.0001 1.00 1256 139 0.3089 0.3726 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.48 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 : 0.005 1728 REMARK 3 ANGLE : 0.898 2335 REMARK 3 CHIRALITY : 0.033 250 REMARK 3 PLANARITY : 0.003 294 REMARK 3 DIHEDRAL : 14.590 631 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 163 THROUGH 259 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.5073 6.4269 72.6850 REMARK 3 T TENSOR REMARK 3 T11: 0.2660 T22: 0.2474 REMARK 3 T33: 0.2739 T12: 0.0434 REMARK 3 T13: 0.0647 T23: -0.0148 REMARK 3 L TENSOR REMARK 3 L11: 3.7678 L22: 2.9057 REMARK 3 L33: 2.5868 L12: 1.4765 REMARK 3 L13: 1.3724 L23: 0.1883 REMARK 3 S TENSOR REMARK 3 S11: -0.1077 S12: 0.0316 S13: -0.2117 REMARK 3 S21: -0.2051 S22: 0.1509 S23: -0.1137 REMARK 3 S31: 0.0529 S32: -0.1802 S33: -0.0385 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 260 THROUGH 378 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.5834 6.2609 64.5015 REMARK 3 T TENSOR REMARK 3 T11: 0.4176 T22: 0.3121 REMARK 3 T33: 0.3555 T12: -0.0316 REMARK 3 T13: 0.1125 T23: -0.0204 REMARK 3 L TENSOR REMARK 3 L11: 2.2381 L22: 3.9278 REMARK 3 L33: 3.1930 L12: 1.6659 REMARK 3 L13: 0.3096 L23: 0.7705 REMARK 3 S TENSOR REMARK 3 S11: -0.3294 S12: 0.3699 S13: -0.3218 REMARK 3 S21: -0.9107 S22: 0.3132 S23: -0.4758 REMARK 3 S31: 0.1253 S32: 0.0994 S33: 0.0068 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 4WDF 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_1000203617. 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, XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13871 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.94200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.450 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 (%): 42.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 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 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 23.50500 REMARK 290 SMTRY3 2 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: 670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 LYS A 162 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 -67.55 -97.25 REMARK 500 ALA A 321 -1.00 71.49 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 SER A 338 GLN A 339 -148.74 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 4WDF A 159 378 UNP P16330 CN37_MOUSE 179 398 SEQADV 4WDF GLY A 158 UNP P16330 EXPRESSION TAG SEQADV 4WDF 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 *69(H2 O) HELIX 1 AA1 THR A 174 HIS A 195 1 22 HELIX 2 AA2 HIS A 195 GLU A 201 1 7 HELIX 3 AA3 LEU A 202 PHE A 205 5 4 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 249 1 7 HELIX 7 AA7 GLN A 250 TYR A 257 1 8 HELIX 8 AA8 THR A 282 GLN A 287 1 6 HELIX 9 AA9 PRO A 296 GLU A 300 5 5 HELIX 10 AB1 ALA A 321 LYS A 335 1 15 SHEET 1 AA1 9 GLY A 344 LEU A 346 0 SHEET 2 AA1 9 GLY A 349 SER A 353 -1 O LEU A 351 N GLY A 344 SHEET 3 AA1 9 TRP A 359 TYR A 376 -1 O MET A 360 N TYR A 352 SHEET 4 AA1 9 ALA A 260 VAL A 270 -1 N ILE A 265 O MET A 367 SHEET 5 AA1 9 THR A 274 VAL A 280 -1 O GLN A 278 N ALA A 267 SHEET 6 AA1 9 HIS A 309 CYS A 314 -1 O VAL A 310 N ALA A 277 SHEET 7 AA1 9 HIS A 230 PHE A 235 -1 N HIS A 230 O THR A 311 SHEET 8 AA1 9 TYR A 168 LEU A 173 -1 N TRP A 171 O CYS A 231 SHEET 9 AA1 9 TRP A 359 TYR A 376 -1 O ILE A 372 N PHE A 172 SITE 1 AC1 10 LEU A 167 TYR A 168 HIS A 230 THR A 232 SITE 2 AC1 10 PHE A 235 HIS A 309 THR A 311 PRO A 320 SITE 3 AC1 10 ALA A 321 HOH A 566 CRYST1 41.090 47.010 53.650 90.00 95.67 90.00 P 1 21 1 2 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 0.024337 0.000000 0.002417 0.00000 SCALE2 0.000000 0.021272 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018731 0.00000