HEADER HYDROLASE 31-JAN-22 7QZK TITLE CRYSTAL STRUCTURE OF MOUSE CNPASE CATALYTIC DOMAIN, V318I MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2',3'-CYCLIC-NUCLEOTIDE 3'-PHOSPHODIESTERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CNP,CNPASE; COMPND 5 EC: 3.1.4.37; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: CNP, CNP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CNPASE, 2H PHOSPHODIESTERASE, MUTATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.MARKUSSON,P.KURSULA REVDAT 2 07-FEB-24 7QZK 1 REMARK REVDAT 1 15-FEB-23 7QZK 0 JRNL AUTH S.MARKUSSON,P.KURSULA JRNL TITL CRYSTAL STRUCTURE OF MOUSE CNPASE CATALYTIC DOMAIN, V318I JRNL TITL 2 MUTANT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 22300 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.970 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 39.2200 - 4.0000 1.00 1514 149 0.1671 0.1892 REMARK 3 2 4.0000 - 3.1800 1.00 1476 146 0.1372 0.1734 REMARK 3 3 3.1800 - 2.7700 1.00 1483 145 0.1621 0.2462 REMARK 3 4 2.7700 - 2.5200 1.00 1461 144 0.1608 0.2333 REMARK 3 5 2.5200 - 2.3400 0.93 1362 135 0.1606 0.2203 REMARK 3 6 2.3400 - 2.2000 0.96 1401 138 0.1506 0.2111 REMARK 3 7 2.2000 - 2.0900 0.99 1445 142 0.1645 0.2319 REMARK 3 8 2.0900 - 2.0000 0.99 1464 144 0.1985 0.2510 REMARK 3 9 2.0000 - 1.9200 0.99 1456 143 0.1913 0.2026 REMARK 3 10 1.9200 - 1.8600 0.99 1435 142 0.1999 0.2635 REMARK 3 11 1.8600 - 1.8000 0.99 1439 142 0.2307 0.2929 REMARK 3 12 1.8000 - 1.7500 1.00 1463 144 0.2832 0.3201 REMARK 3 13 1.7500 - 1.7000 1.00 1451 143 0.3284 0.3717 REMARK 3 14 1.7000 - 1.6600 0.99 1450 143 0.3666 0.3840 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.261 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.009 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.04 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 : 0.010 1729 REMARK 3 ANGLE : 1.096 2334 REMARK 3 CHIRALITY : 0.063 250 REMARK 3 PLANARITY : 0.011 299 REMARK 3 DIHEDRAL : 15.609 644 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7QZK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292120697. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.968 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22318 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.700 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 (%): 37.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% PEG3350 AND 50 MM TRI-SODIUM REMARK 280 CITRATE (PH 3.5), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 23.91500 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 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: MONOMERIC 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 634 O HOH A 644 1.96 REMARK 500 O HOH A 646 O HOH A 649 1.98 REMARK 500 O HOH A 502 O HOH A 632 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 508 O HOH A 592 2555 1.90 REMARK 500 O HOH A 519 O HOH A 530 2556 2.18 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 HIS A 204 4.10 -66.69 REMARK 500 PHE A 205 -52.57 -123.32 REMARK 500 PHE A 221 54.03 -90.71 REMARK 500 THR A 233 -61.26 -99.69 REMARK 500 REMARK 500 REMARK: NULL DBREF 7QZK A 159 378 UNP P16330 CN37_MOUSE 179 398 SEQADV 7QZK GLY A 158 UNP P16330 EXPRESSION TAG SEQADV 7QZK ILE A 318 UNP P16330 VAL 338 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 ILE GLN PRO VAL 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 CIT A 401 18 HETNAM CIT CITRIC ACID FORMUL 2 CIT C6 H8 O7 FORMUL 3 HOH *152(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 VAL 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 TYR A 376 N TYR A 168 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 GLN A 278 N ALA A 267 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 TYR A 376 N TYR A 168 SHEET 4 AA2 5 GLY A 349 GLY A 355 -1 N TYR A 352 O MET A 360 SHEET 5 AA2 5 GLY A 344 LEU A 346 -1 N GLY A 344 O LEU A 351 CRYST1 39.530 47.830 51.180 90.00 97.21 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 0.025297 0.000000 0.003200 0.00000 SCALE2 0.000000 0.020907 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019695 0.00000