PDB Short entry for 3DYQ HEADER HYDROLASE 28-JUL-08 3DYQ TITLE HUMAN PHOSPHODIESTRASE 9 (INHIBITED BY OMITTING DIVALENT CATION) IN TITLE 2 COMPLEX WITH CGMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH AFFINITY CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE COMPND 3 9A; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: CATALYTIC DOMAIN, UNP RESIDUES 242-566; COMPND 6 EC: 3.1.4.35; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PDE9A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHODIESTERASE, ENZYME MECHANISM, CGMP, HYDROLASE, MANGANESE, KEYWDS 2 METAL-BINDING, PHOSPHOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.LIU,M.N.MANSOUR,K.DILLMAN,J.PEREZ,D.DANLEY,F.MENNITI REVDAT 5 30-AUG-23 3DYQ 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 3DYQ 1 VERSN REVDAT 3 24-FEB-09 3DYQ 1 VERSN REVDAT 2 23-SEP-08 3DYQ 1 JRNL REVDAT 1 16-SEP-08 3DYQ 0 JRNL AUTH S.LIU,M.N.MANSOUR,K.S.DILLMAN,J.R.PEREZ,D.E.DANLEY,P.A.AEED, JRNL AUTH 2 S.P.SIMONS,P.K.LEMOTTE,F.S.MENNITI JRNL TITL STRUCTURAL BASIS FOR THE CATALYTIC MECHANISM OF HUMAN JRNL TITL 2 PHOSPHODIESTERASE 9. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 13309 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18757755 JRNL DOI 10.1073/PNAS.0708850105 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0008 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 46414 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 5261 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3396 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.3200 REMARK 3 BIN FREE R VALUE SET COUNT : 356 REMARK 3 BIN FREE R VALUE : 0.3680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5412 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 238 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.86000 REMARK 3 B22 (A**2) : 1.86000 REMARK 3 B33 (A**2) : -3.72000 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): 0.249 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.206 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.149 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.204 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5595 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3816 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7584 ; 1.350 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9298 ; 0.832 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 654 ; 6.529 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 278 ;33.991 ;24.317 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1000 ;17.570 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;21.603 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 817 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6101 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1129 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1557 ; 0.262 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4053 ; 0.213 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2827 ; 0.201 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2788 ; 0.092 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 250 ; 0.207 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 10 ; 0.203 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 21 ; 0.270 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 41 ; 0.300 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.268 ; 0.200 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): 3300 ; 0.717 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1288 ; 0.187 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5380 ; 1.499 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2389 ; 2.760 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2204 ; 4.327 ; 4.500 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 178 A 427 2 REMARK 3 1 B 178 B 427 2 REMARK 3 2 A 448 A 488 2 REMARK 3 2 B 448 B 488 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1723 ; 0.06 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 A (A): 2334 ; 0.22 ; 0.50 REMARK 3 TIGHT THERMAL 1 A (A**2): 1723 ; 0.16 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 2334 ; 0.75 ; 2.00 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 181 A 505 REMARK 3 ORIGIN FOR THE GROUP (A): 84.0341 45.6419 45.7999 REMARK 3 T TENSOR REMARK 3 T11: 0.0097 T22: -0.1955 REMARK 3 T33: -0.0564 T12: -0.0035 REMARK 3 T13: -0.0158 T23: 0.0097 REMARK 3 L TENSOR REMARK 3 L11: 1.0896 L22: 0.8195 REMARK 3 L33: 1.0227 L12: -0.6036 REMARK 3 L13: 0.0295 L23: 0.0048 REMARK 3 S TENSOR REMARK 3 S11: 0.0725 S12: -0.0468 S13: -0.0064 REMARK 3 S21: -0.0179 S22: -0.0218 S23: 0.1042 REMARK 3 S31: -0.0772 S32: -0.0207 S33: -0.0507 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 181 B 505 REMARK 3 ORIGIN FOR THE GROUP (A): 92.6988 31.9017 7.1034 REMARK 3 T TENSOR REMARK 3 T11: -0.0493 T22: -0.0991 REMARK 3 T33: -0.0561 T12: 0.0369 REMARK 3 T13: 0.0001 T23: -0.0196 REMARK 3 L TENSOR REMARK 3 L11: 0.5446 L22: 1.5557 REMARK 3 L33: 1.4445 L12: -0.1195 REMARK 3 L13: 0.2090 L23: -0.5023 REMARK 3 S TENSOR REMARK 3 S11: 0.0340 S12: 0.1404 S13: -0.0751 REMARK 3 S21: -0.0676 S22: -0.0343 S23: -0.0175 REMARK 3 S31: 0.1801 S32: 0.0269 S33: 0.0003 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3DYQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048656. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65299 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1TBM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 135.02050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.82500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.82500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.51025 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.82500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.82500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 202.53075 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.82500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.82500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.51025 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.82500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.82500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 202.53075 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 135.02050 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -170.0 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 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 155.47500 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 -51.82500 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 67.51025 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 LYS A 506 REMARK 465 LYS B 506 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 NE2 GLN B 279 O HOH B 43 1.70 REMARK 500 O HOH B 16 O HOH B 1073 2.06 REMARK 500 OH TYR A 490 O HOH A 1084 2.17 REMARK 500 O HOH A 46 O HOH A 1136 2.19 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 23 O HOH B 19 3645 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 CYS A 326 CB CYS A 326 SG -0.110 REMARK 500 GLU B 370 CG GLU B 370 CD 0.100 REMARK 500 CYS B 419 CB CYS B 419 SG -0.101 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 PHE A 251 -58.17 -120.25 REMARK 500 SER A 319 58.32 33.57 REMARK 500 ASN A 381 63.30 -162.87 REMARK 500 ARG A 444 -36.71 -27.43 REMARK 500 GLN A 504 -179.64 69.22 REMARK 500 SER B 319 62.80 28.48 REMARK 500 ASN B 381 62.66 -160.91 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 GLY A 178 SER A 179 -141.23 REMARK 500 GLU A 502 LEU A 503 143.23 REMARK 500 GLY B 178 SER B 179 -140.89 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 NA A 902 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 93 O REMARK 620 2 HOH A 95 O 79.2 REMARK 620 3 ASP A 293 OD1 78.9 147.4 REMARK 620 4 PCG A 900 O1A 163.9 102.4 105.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 901 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 256 NE2 REMARK 620 2 HIS A 292 NE2 75.1 REMARK 620 3 ASP A 293 OD2 79.3 68.1 REMARK 620 4 ASP A 402 OD1 81.2 72.5 139.3 REMARK 620 5 PCG A 900 O1A 122.9 160.9 106.7 114.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 901 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 256 NE2 REMARK 620 2 HIS B 292 NE2 85.0 REMARK 620 3 ASP B 293 OD2 83.5 73.0 REMARK 620 4 ASP B 402 OD1 77.4 79.0 147.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PCG A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IBM B 900 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DY8 RELATED DB: PDB REMARK 900 RELATED ID: 3DYL RELATED DB: PDB REMARK 900 RELATED ID: 3DYN RELATED DB: PDB REMARK 900 RELATED ID: 3DYS RELATED DB: PDB DBREF 3DYQ A 182 506 UNP O76083 PDE9A_HUMAN 242 566 DBREF 3DYQ B 182 506 UNP O76083 PDE9A_HUMAN 242 566 SEQADV 3DYQ GLY A 178 UNP O76083 EXPRESSION TAG SEQADV 3DYQ SER A 179 UNP O76083 EXPRESSION TAG SEQADV 3DYQ HIS A 180 UNP O76083 EXPRESSION TAG SEQADV 3DYQ MET A 181 UNP O76083 EXPRESSION TAG SEQADV 3DYQ GLY B 178 UNP O76083 EXPRESSION TAG SEQADV 3DYQ SER B 179 UNP O76083 EXPRESSION TAG SEQADV 3DYQ HIS B 180 UNP O76083 EXPRESSION TAG SEQADV 3DYQ MET B 181 UNP O76083 EXPRESSION TAG SEQRES 1 A 329 GLY SER HIS MET THR TYR PRO LYS TYR LEU LEU SER PRO SEQRES 2 A 329 GLU THR ILE GLU ALA LEU ARG LYS PRO THR PHE ASP VAL SEQRES 3 A 329 TRP LEU TRP GLU PRO ASN GLU MET LEU SER CYS LEU GLU SEQRES 4 A 329 HIS MET TYR HIS ASP LEU GLY LEU VAL ARG ASP PHE SER SEQRES 5 A 329 ILE ASN PRO VAL THR LEU ARG ARG TRP LEU PHE CYS VAL SEQRES 6 A 329 HIS ASP ASN TYR ARG ASN ASN PRO PHE HIS ASN PHE ARG SEQRES 7 A 329 HIS CYS PHE CYS VAL ALA GLN MET MET TYR SER MET VAL SEQRES 8 A 329 TRP LEU CYS SER LEU GLN GLU LYS PHE SER GLN THR ASP SEQRES 9 A 329 ILE LEU ILE LEU MET THR ALA ALA ILE CYS HIS ASP LEU SEQRES 10 A 329 ASP HIS PRO GLY TYR ASN ASN THR TYR GLN ILE ASN ALA SEQRES 11 A 329 ARG THR GLU LEU ALA VAL ARG TYR ASN ASP ILE SER PRO SEQRES 12 A 329 LEU GLU ASN HIS HIS CYS ALA VAL ALA PHE GLN ILE LEU SEQRES 13 A 329 ALA GLU PRO GLU CYS ASN ILE PHE SER ASN ILE PRO PRO SEQRES 14 A 329 ASP GLY PHE LYS GLN ILE ARG GLN GLY MET ILE THR LEU SEQRES 15 A 329 ILE LEU ALA THR ASP MET ALA ARG HIS ALA GLU ILE MET SEQRES 16 A 329 ASP SER PHE LYS GLU LYS MET GLU ASN PHE ASP TYR SER SEQRES 17 A 329 ASN GLU GLU HIS MET THR LEU LEU LYS MET ILE LEU ILE SEQRES 18 A 329 LYS CYS CYS ASP ILE SER ASN GLU VAL ARG PRO MET GLU SEQRES 19 A 329 VAL ALA GLU PRO TRP VAL ASP CYS LEU LEU GLU GLU TYR SEQRES 20 A 329 PHE MET GLN SER ASP ARG GLU LYS SER GLU GLY LEU PRO SEQRES 21 A 329 VAL ALA PRO PHE MET ASP ARG ASP LYS VAL THR LYS ALA SEQRES 22 A 329 THR ALA GLN ILE GLY PHE ILE LYS PHE VAL LEU ILE PRO SEQRES 23 A 329 MET PHE GLU THR VAL THR LYS LEU PHE PRO MET VAL GLU SEQRES 24 A 329 GLU ILE MET LEU GLN PRO LEU TRP GLU SER ARG ASP ARG SEQRES 25 A 329 TYR GLU GLU LEU LYS ARG ILE ASP ASP ALA MET LYS GLU SEQRES 26 A 329 LEU GLN LYS LYS SEQRES 1 B 329 GLY SER HIS MET THR TYR PRO LYS TYR LEU LEU SER PRO SEQRES 2 B 329 GLU THR ILE GLU ALA LEU ARG LYS PRO THR PHE ASP VAL SEQRES 3 B 329 TRP LEU TRP GLU PRO ASN GLU MET LEU SER CYS LEU GLU SEQRES 4 B 329 HIS MET TYR HIS ASP LEU GLY LEU VAL ARG ASP PHE SER SEQRES 5 B 329 ILE ASN PRO VAL THR LEU ARG ARG TRP LEU PHE CYS VAL SEQRES 6 B 329 HIS ASP ASN TYR ARG ASN ASN PRO PHE HIS ASN PHE ARG SEQRES 7 B 329 HIS CYS PHE CYS VAL ALA GLN MET MET TYR SER MET VAL SEQRES 8 B 329 TRP LEU CYS SER LEU GLN GLU LYS PHE SER GLN THR ASP SEQRES 9 B 329 ILE LEU ILE LEU MET THR ALA ALA ILE CYS HIS ASP LEU SEQRES 10 B 329 ASP HIS PRO GLY TYR ASN ASN THR TYR GLN ILE ASN ALA SEQRES 11 B 329 ARG THR GLU LEU ALA VAL ARG TYR ASN ASP ILE SER PRO SEQRES 12 B 329 LEU GLU ASN HIS HIS CYS ALA VAL ALA PHE GLN ILE LEU SEQRES 13 B 329 ALA GLU PRO GLU CYS ASN ILE PHE SER ASN ILE PRO PRO SEQRES 14 B 329 ASP GLY PHE LYS GLN ILE ARG GLN GLY MET ILE THR LEU SEQRES 15 B 329 ILE LEU ALA THR ASP MET ALA ARG HIS ALA GLU ILE MET SEQRES 16 B 329 ASP SER PHE LYS GLU LYS MET GLU ASN PHE ASP TYR SER SEQRES 17 B 329 ASN GLU GLU HIS MET THR LEU LEU LYS MET ILE LEU ILE SEQRES 18 B 329 LYS CYS CYS ASP ILE SER ASN GLU VAL ARG PRO MET GLU SEQRES 19 B 329 VAL ALA GLU PRO TRP VAL ASP CYS LEU LEU GLU GLU TYR SEQRES 20 B 329 PHE MET GLN SER ASP ARG GLU LYS SER GLU GLY LEU PRO SEQRES 21 B 329 VAL ALA PRO PHE MET ASP ARG ASP LYS VAL THR LYS ALA SEQRES 22 B 329 THR ALA GLN ILE GLY PHE ILE LYS PHE VAL LEU ILE PRO SEQRES 23 B 329 MET PHE GLU THR VAL THR LYS LEU PHE PRO MET VAL GLU SEQRES 24 B 329 GLU ILE MET LEU GLN PRO LEU TRP GLU SER ARG ASP ARG SEQRES 25 B 329 TYR GLU GLU LEU LYS ARG ILE ASP ASP ALA MET LYS GLU SEQRES 26 B 329 LEU GLN LYS LYS HET NA A 901 1 HET NA A 902 1 HET PCG A 900 23 HET NA B 901 1 HET NA B 902 1 HET IBM B 900 16 HETNAM NA SODIUM ION HETNAM PCG CYCLIC GUANOSINE MONOPHOSPHATE HETNAM IBM 3-ISOBUTYL-1-METHYLXANTHINE FORMUL 3 NA 4(NA 1+) FORMUL 5 PCG C10 H12 N5 O7 P FORMUL 8 IBM C10 H14 N4 O2 FORMUL 9 HOH *238(H2 O) HELIX 1 1 SER A 189 LEU A 196 1 8 HELIX 2 2 GLU A 207 LEU A 222 1 16 HELIX 3 3 GLY A 223 PHE A 228 1 6 HELIX 4 4 ASN A 231 TYR A 246 1 16 HELIX 5 5 ASN A 253 CYS A 271 1 19 HELIX 6 6 SER A 272 LYS A 276 5 5 HELIX 7 7 SER A 278 HIS A 292 1 15 HELIX 8 8 ASN A 300 ARG A 308 1 9 HELIX 9 9 THR A 309 TYR A 315 1 7 HELIX 10 10 SER A 319 GLU A 335 1 17 HELIX 11 11 PRO A 336 ASN A 339 5 4 HELIX 12 12 PRO A 345 THR A 363 1 19 HELIX 13 13 ASP A 364 ALA A 366 5 3 HELIX 14 14 ARG A 367 GLU A 380 1 14 HELIX 15 15 ASN A 386 ILE A 403 1 18 HELIX 16 16 SER A 404 ARG A 408 5 5 HELIX 17 17 PRO A 409 GLY A 435 1 27 HELIX 18 18 ALA A 439 ASP A 443 5 5 HELIX 19 19 THR A 448 VAL A 460 1 13 HELIX 20 20 VAL A 460 PHE A 472 1 13 HELIX 21 21 PRO A 473 LYS A 501 1 29 HELIX 22 22 SER B 189 LEU B 196 1 8 HELIX 23 23 GLU B 207 LEU B 222 1 16 HELIX 24 24 GLY B 223 SER B 229 1 7 HELIX 25 25 ASN B 231 TYR B 246 1 16 HELIX 26 26 ASN B 253 CYS B 271 1 19 HELIX 27 27 SER B 272 PHE B 277 1 6 HELIX 28 28 SER B 278 HIS B 292 1 15 HELIX 29 29 ASN B 300 ALA B 307 1 8 HELIX 30 30 THR B 309 TYR B 315 1 7 HELIX 31 31 SER B 319 GLU B 335 1 17 HELIX 32 32 PRO B 336 ASN B 339 5 4 HELIX 33 33 PRO B 345 THR B 363 1 19 HELIX 34 34 ASP B 364 ALA B 366 5 3 HELIX 35 35 ARG B 367 GLU B 380 1 14 HELIX 36 36 ASN B 386 ILE B 403 1 18 HELIX 37 37 SER B 404 ARG B 408 5 5 HELIX 38 38 PRO B 409 GLY B 435 1 27 HELIX 39 39 ALA B 439 ASP B 443 5 5 HELIX 40 40 THR B 448 VAL B 460 1 13 HELIX 41 41 VAL B 460 PHE B 472 1 13 HELIX 42 42 PRO B 473 LYS B 505 1 33 LINK O HOH A 93 NA NA A 902 1555 1555 2.24 LINK O HOH A 95 NA NA A 902 1555 1555 2.28 LINK NE2 HIS A 256 NA NA A 901 1555 1555 2.51 LINK NE2 HIS A 292 NA NA A 901 1555 1555 2.44 LINK OD2 ASP A 293 NA NA A 901 1555 1555 2.11 LINK OD1 ASP A 293 NA NA A 902 1555 1555 2.34 LINK OD1 ASP A 402 NA NA A 901 1555 1555 2.10 LINK O1A PCG A 900 NA NA A 901 1555 1555 2.61 LINK O1A PCG A 900 NA NA A 902 1555 1555 2.92 LINK NE2 HIS B 256 NA NA B 901 1555 1555 2.68 LINK NE2 HIS B 292 NA NA B 901 1555 1555 2.38 LINK OD2 ASP B 293 NA NA B 901 1555 1555 2.14 LINK OD1 ASP B 293 NA NA B 902 1555 1555 2.28 LINK OD1 ASP B 402 NA NA B 901 1555 1555 2.13 SITE 1 AC1 6 HIS A 256 HIS A 292 ASP A 293 ASP A 402 SITE 2 AC1 6 PCG A 900 NA A 902 SITE 1 AC2 5 HOH A 93 HOH A 95 ASP A 293 PCG A 900 SITE 2 AC2 5 NA A 901 SITE 1 AC3 5 HIS B 256 HIS B 292 ASP B 293 ASP B 402 SITE 2 AC3 5 NA B 902 SITE 1 AC4 2 ASP B 293 NA B 901 SITE 1 AC5 13 HOH A 92 HIS A 252 MET A 365 ASP A 402 SITE 2 AC5 13 ILE A 403 LEU A 420 TYR A 424 ALA A 452 SITE 3 AC5 13 GLN A 453 PHE A 456 NA A 901 NA A 902 SITE 4 AC5 13 HOH A1020 SITE 1 AC6 10 ALA A 499 MET A 500 ILE B 403 LEU B 420 SITE 2 AC6 10 TYR B 424 ALA B 452 GLN B 453 PHE B 456 SITE 3 AC6 10 HOH B1037 HOH B1049 CRYST1 103.650 103.650 270.041 90.00 90.00 90.00 P 41 21 2 16 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 0.009648 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009648 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003703 0.00000