HEADER HYDROLASE 25-JUL-08 3DY8 TITLE HUMAN PHOSPHODIESTERASE 9 IN COMPLEX WITH PRODUCT 5'-GMP (E+P COMPLEX) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN PHOSPHODIESTERASE 9; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, UNP RESIDUES 242-566; COMPND 5 EC: 3.1.4.35; COMPND 6 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 PHOSPHODIESTRASE, 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 21-FEB-24 3DY8 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 3DY8 1 VERSN REVDAT 3 24-FEB-09 3DY8 1 VERSN REVDAT 2 23-SEP-08 3DY8 1 JRNL REVDAT 1 16-SEP-08 3DY8 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. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 69234 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 7800 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4904 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 556 REMARK 3 BIN FREE R VALUE : 0.2540 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 : 47 REMARK 3 SOLVENT ATOMS : 478 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 40.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.75000 REMARK 3 B22 (A**2) : 0.75000 REMARK 3 B33 (A**2) : -1.50000 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): 0.142 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.131 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.530 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5597 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3815 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7584 ; 1.444 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9296 ; 1.031 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 654 ; 5.389 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 278 ;33.084 ;24.317 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1000 ;15.425 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;24.037 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 817 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6102 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1126 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1260 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3835 ; 0.188 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2730 ; 0.180 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2626 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 373 ; 0.180 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 12 ; 0.200 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 40 ; 0.253 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.133 ; 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): 4315 ; 0.992 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1288 ; 0.188 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5381 ; 1.114 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2702 ; 3.888 ; 6.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2203 ; 4.913 ; 6.500 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 ; 0.05 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 A (A): 2334 ; 0.20 ; 0.50 REMARK 3 TIGHT THERMAL 1 A (A**2): 1723 ; 0.14 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 2334 ; 0.63 ; 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): 83.9603 45.0728 45.8753 REMARK 3 T TENSOR REMARK 3 T11: -0.0036 T22: -0.1977 REMARK 3 T33: -0.0820 T12: -0.0184 REMARK 3 T13: -0.0265 T23: -0.0054 REMARK 3 L TENSOR REMARK 3 L11: 1.3494 L22: 1.3226 REMARK 3 L33: 1.3943 L12: -0.7421 REMARK 3 L13: -0.0983 L23: -0.0286 REMARK 3 S TENSOR REMARK 3 S11: 0.1313 S12: -0.0590 S13: -0.0123 REMARK 3 S21: -0.0132 S22: -0.0570 S23: 0.1960 REMARK 3 S31: -0.0971 S32: -0.0633 S33: -0.0743 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): 92.1232 31.4484 7.0896 REMARK 3 T TENSOR REMARK 3 T11: -0.0689 T22: -0.1077 REMARK 3 T33: -0.0983 T12: 0.0489 REMARK 3 T13: 0.0017 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.7342 L22: 1.6084 REMARK 3 L33: 1.6463 L12: -0.2415 REMARK 3 L13: 0.1616 L23: -0.5101 REMARK 3 S TENSOR REMARK 3 S11: 0.0142 S12: 0.1421 S13: -0.0884 REMARK 3 S21: -0.0702 S22: -0.0139 S23: -0.0427 REMARK 3 S31: 0.1587 S32: 0.0046 S33: -0.0003 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 3DY8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048638. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-06 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77975 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 46.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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 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: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.63 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 134.71450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.69700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.69700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.35725 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.69700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.69700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 202.07175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.69700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.69700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.35725 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.69700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.69700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 202.07175 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 134.71450 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 O HOH B 1252 O HOH B 1253 1.95 REMARK 500 OH TYR A 424 O2' 5GP A 900 2.11 REMARK 500 O HOH A 907 O HOH A 1057 2.13 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 -0.132 REMARK 500 GLU B 370 CG GLU B 370 CD 0.100 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ARG B 236 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 CYS B 257 CA - CB - SG ANGL. DEV. = 6.7 DEGREES 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 PRO A 184 152.20 -49.33 REMARK 500 ASP A 317 15.89 59.85 REMARK 500 SER A 319 60.96 28.50 REMARK 500 ASN A 381 69.25 -165.86 REMARK 500 GLN A 504 65.24 -104.18 REMARK 500 SER B 319 60.73 30.21 REMARK 500 ASN B 381 72.99 -166.48 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 MN A 901 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 293 OD2 REMARK 620 2 ASP A 402 OD1 170.4 REMARK 620 3 HOH A1138 O 93.4 81.0 REMARK 620 4 HOH A1139 O 96.6 89.6 76.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 902 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 293 OD1 REMARK 620 2 5GP A 900 O2P 93.7 REMARK 620 3 HOH A1136 O 85.8 105.7 REMARK 620 4 HOH A1137 O 95.8 153.0 100.2 REMARK 620 5 HOH A1138 O 91.2 17.5 88.3 169.3 REMARK 620 6 HOH A1140 O 98.6 66.5 171.2 87.1 84.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 901 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 FMT B 1 O1 REMARK 620 2 ASP B 293 OD2 99.6 REMARK 620 3 ASP B 402 OD1 90.4 167.0 REMARK 620 4 HOH B1265 O 82.1 87.1 86.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 902 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 293 OD1 REMARK 620 2 HOH B1265 O 95.9 REMARK 620 3 HOH B1266 O 106.4 81.3 REMARK 620 4 HOH B1267 O 168.5 86.2 85.1 REMARK 620 5 HOH B1268 O 92.9 171.0 94.6 85.5 REMARK 620 6 HOH B1269 O 81.9 87.0 166.2 86.9 96.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5GP 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 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DYL RELATED DB: PDB REMARK 900 RELATED ID: 3DYN RELATED DB: PDB REMARK 900 RELATED ID: 3DYQ RELATED DB: PDB REMARK 900 RELATED ID: 3DYS RELATED DB: PDB DBREF 3DY8 A 182 506 UNP O76083 PDE9A_HUMAN 242 566 DBREF 3DY8 B 182 506 UNP O76083 PDE9A_HUMAN 242 566 SEQADV 3DY8 GLY A 178 UNP O76083 EXPRESSION TAG SEQADV 3DY8 SER A 179 UNP O76083 EXPRESSION TAG SEQADV 3DY8 HIS A 180 UNP O76083 EXPRESSION TAG SEQADV 3DY8 MET A 181 UNP O76083 EXPRESSION TAG SEQADV 3DY8 GLY B 178 UNP O76083 EXPRESSION TAG SEQADV 3DY8 SER B 179 UNP O76083 EXPRESSION TAG SEQADV 3DY8 HIS B 180 UNP O76083 EXPRESSION TAG SEQADV 3DY8 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 MN A 901 1 HET MG A 902 1 HET 5GP A 900 24 HET MN B 901 1 HET MG B 902 1 HET IBM B 900 16 HET FMT B 1 3 HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE HETNAM IBM 3-ISOBUTYL-1-METHYLXANTHINE HETNAM FMT FORMIC ACID FORMUL 3 MN 2(MN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 5 5GP C10 H14 N5 O8 P FORMUL 8 IBM C10 H14 N4 O2 FORMUL 9 FMT C H2 O2 FORMUL 10 HOH *478(H2 O) HELIX 1 1 SER A 189 LEU A 196 1 8 HELIX 2 2 ASP A 202 TRP A 206 5 5 HELIX 3 3 GLU A 207 LEU A 222 1 16 HELIX 4 4 GLY A 223 SER A 229 1 7 HELIX 5 5 ASN A 231 ASN A 245 1 15 HELIX 6 6 ASN A 253 CYS A 271 1 19 HELIX 7 7 SER A 272 LYS A 276 5 5 HELIX 8 8 SER A 278 HIS A 292 1 15 HELIX 9 9 ASN A 300 ARG A 308 1 9 HELIX 10 10 THR A 309 TYR A 315 1 7 HELIX 11 11 SER A 319 ALA A 334 1 16 HELIX 12 12 GLU A 335 ASN A 339 5 5 HELIX 13 13 PRO A 345 THR A 363 1 19 HELIX 14 14 ASP A 364 ALA A 366 5 3 HELIX 15 15 ARG A 367 GLU A 380 1 14 HELIX 16 16 ASN A 386 ILE A 403 1 18 HELIX 17 17 SER A 404 ARG A 408 5 5 HELIX 18 18 PRO A 409 GLU A 434 1 26 HELIX 19 19 ALA A 439 ASP A 443 5 5 HELIX 20 20 THR A 448 VAL A 460 1 13 HELIX 21 21 VAL A 460 PHE A 472 1 13 HELIX 22 22 MET A 474 MET A 479 1 6 HELIX 23 23 MET A 479 GLU A 502 1 24 HELIX 24 24 SER B 189 LEU B 196 1 8 HELIX 25 25 ASP B 202 TRP B 206 5 5 HELIX 26 26 GLU B 207 LEU B 222 1 16 HELIX 27 27 GLY B 223 SER B 229 1 7 HELIX 28 28 ASN B 231 TYR B 246 1 16 HELIX 29 29 ASN B 253 CYS B 271 1 19 HELIX 30 30 SER B 272 PHE B 277 1 6 HELIX 31 31 SER B 278 HIS B 292 1 15 HELIX 32 32 ASN B 300 ARG B 308 1 9 HELIX 33 33 THR B 309 ASN B 316 1 8 HELIX 34 34 SER B 319 ALA B 334 1 16 HELIX 35 35 GLU B 335 ASN B 339 5 5 HELIX 36 36 PRO B 345 ALA B 362 1 18 HELIX 37 37 THR B 363 ALA B 366 5 4 HELIX 38 38 ARG B 367 GLU B 380 1 14 HELIX 39 39 ASN B 386 ILE B 403 1 18 HELIX 40 40 SER B 404 ARG B 408 5 5 HELIX 41 41 PRO B 409 GLY B 435 1 27 HELIX 42 42 ALA B 439 ASP B 443 5 5 HELIX 43 43 THR B 448 VAL B 460 1 13 HELIX 44 44 VAL B 460 PHE B 472 1 13 HELIX 45 45 MET B 474 MET B 479 1 6 HELIX 46 46 MET B 479 LYS B 505 1 27 LINK OD2 ASP A 293 MN MN A 901 1555 1555 2.05 LINK OD1 ASP A 293 MG MG A 902 1555 1555 2.18 LINK OD1 ASP A 402 MN MN A 901 1555 1555 2.19 LINK O2P 5GP A 900 MG MG A 902 1555 1555 2.19 LINK MN MN A 901 O HOH A1138 1555 1555 2.36 LINK MN MN A 901 O HOH A1139 1555 1555 1.97 LINK MG MG A 902 O HOH A1136 1555 1555 2.17 LINK MG MG A 902 O HOH A1137 1555 1555 2.34 LINK MG MG A 902 O HOH A1138 1555 1555 2.41 LINK MG MG A 902 O HOH A1140 1555 1555 2.10 LINK O1 FMT B 1 MN MN B 901 1555 1555 2.19 LINK OD2 ASP B 293 MN MN B 901 1555 1555 2.13 LINK OD1 ASP B 293 MG MG B 902 1555 1555 2.19 LINK OD1 ASP B 402 MN MN B 901 1555 1555 2.15 LINK MN MN B 901 O HOH B1265 1555 1555 2.39 LINK MG MG B 902 O HOH B1265 1555 1555 2.25 LINK MG MG B 902 O HOH B1266 1555 1555 2.25 LINK MG MG B 902 O HOH B1267 1555 1555 2.32 LINK MG MG B 902 O HOH B1268 1555 1555 2.22 LINK MG MG B 902 O HOH B1269 1555 1555 2.18 SITE 1 AC1 7 HIS A 256 HIS A 292 ASP A 293 ASP A 402 SITE 2 AC1 7 5GP A 900 HOH A1138 HOH A1139 SITE 1 AC2 7 ASP A 293 5GP A 900 HOH A1135 HOH A1136 SITE 2 AC2 7 HOH A1137 HOH A1138 HOH A1140 SITE 1 AC3 6 FMT B 1 HIS B 256 HIS B 292 ASP B 293 SITE 2 AC3 6 ASP B 402 HOH B1265 SITE 1 AC4 6 ASP B 293 HOH B1265 HOH B1266 HOH B1267 SITE 2 AC4 6 HOH B1268 HOH B1269 SITE 1 AC5 21 HIS A 252 HIS A 256 ASP A 293 MET A 365 SITE 2 AC5 21 ASP A 402 ILE A 403 LEU A 420 TYR A 424 SITE 3 AC5 21 ALA A 452 GLN A 453 PHE A 456 MN A 901 SITE 4 AC5 21 MG A 902 HOH A 914 HOH A 915 HOH A 917 SITE 5 AC5 21 HOH A 951 HOH A1138 HOH A1139 HOH A1140 SITE 6 AC5 21 HOH A1141 SITE 1 AC6 10 ALA A 499 FMT B 1 LEU B 420 TYR B 424 SITE 2 AC6 10 ALA B 452 GLN B 453 PHE B 456 HOH B1066 SITE 3 AC6 10 HOH B1104 HOH B1121 SITE 1 AC7 10 PHE B 251 HIS B 252 HIS B 256 ASP B 293 SITE 2 AC7 10 ASP B 402 IBM B 900 MN B 901 HOH B1066 SITE 3 AC7 10 HOH B1258 HOH B1265 CRYST1 103.394 103.394 269.429 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 0.009672 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009672 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003712 0.00000