HEADER HYDROLASE 28-JUL-08 3DYS TITLE HUMAN PHOSPHODIESTRASE-5'GMP COMPLEX (EP), PRODUCED BY SOAKING WITH TITLE 2 20MM CGMP+20 MM MNCL2+20 MM MGCL2 FOR 2 HOURS, AND FLASH-COOLED TO TITLE 3 LIQUID NITROGEN TEMPERATURE WHEN SUBSTRATE WAS STILL ABUDANT. 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 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 3DYS 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 3DYS 1 VERSN REVDAT 3 24-FEB-09 3DYS 1 VERSN REVDAT 2 23-SEP-08 3DYS 1 JRNL REVDAT 1 16-SEP-08 3DYS 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. 2.30 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) : 2.30 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 : 59549 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 6712 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4283 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 467 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5384 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 463 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 42.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.75000 REMARK 3 B22 (A**2) : 1.75000 REMARK 3 B33 (A**2) : -3.50000 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): 0.180 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.160 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.109 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.562 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5568 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3797 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7546 ; 1.237 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9252 ; 0.920 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 650 ; 5.378 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 277 ;34.345 ;24.332 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 995 ;15.001 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;19.481 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 814 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6068 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1121 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1291 ; 0.218 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3875 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2743 ; 0.180 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2615 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 366 ; 0.169 ; 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): 14 ; 0.254 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 43 ; 0.288 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.119 ; 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): 4299 ; 0.843 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1279 ; 0.132 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5352 ; 0.917 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2697 ; 1.711 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2194 ; 2.473 ; 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 : 0 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1461 ; 0.08 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 B (A): 1979 ; 0.13 ; 0.50 REMARK 3 TIGHT THERMAL 1 A (A**2): 1461 ; 0.34 ; 0.50 REMARK 3 MEDIUM THERMAL 1 B (A**2): 1979 ; 0.39 ; 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 182 A 505 REMARK 3 ORIGIN FOR THE GROUP (A): 84.5122 45.6233 45.7448 REMARK 3 T TENSOR REMARK 3 T11: -0.0465 T22: -0.2378 REMARK 3 T33: -0.1300 T12: -0.0278 REMARK 3 T13: -0.0216 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 1.5472 L22: 1.7537 REMARK 3 L33: 1.7492 L12: -0.8291 REMARK 3 L13: -0.2694 L23: 0.0217 REMARK 3 S TENSOR REMARK 3 S11: 0.0869 S12: -0.1319 S13: 0.0190 REMARK 3 S21: 0.1201 S22: -0.0175 S23: 0.1276 REMARK 3 S31: -0.1103 S32: -0.0266 S33: -0.0694 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): 92.7615 31.7958 7.0245 REMARK 3 T TENSOR REMARK 3 T11: -0.1145 T22: -0.1300 REMARK 3 T33: -0.1342 T12: 0.0357 REMARK 3 T13: 0.0284 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 1.2182 L22: 2.2452 REMARK 3 L33: 2.0181 L12: -0.3832 REMARK 3 L13: 0.3480 L23: -0.2679 REMARK 3 S TENSOR REMARK 3 S11: 0.0188 S12: 0.2501 S13: -0.1003 REMARK 3 S21: -0.1728 S22: -0.0276 S23: -0.0299 REMARK 3 S31: 0.1445 S32: 0.0850 S33: 0.0089 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 3DYS 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_1000048658. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66436 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.69 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 134.88100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.99600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.99600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.44050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.99600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.99600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 202.32150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.99600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.99600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.44050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.99600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.99600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 202.32150 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 134.88100 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: 4010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 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 155.98800 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 -51.99600 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 67.44050 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 178 REMARK 465 SER A 179 REMARK 465 HIS A 180 REMARK 465 MET A 181 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 1173 O HOH B 1174 1.72 REMARK 500 O HOH B 1105 O HOH B 1142 2.11 REMARK 500 OH TYR A 299 O HOH A 1079 2.17 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 -0.148 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 184 125.89 -36.40 REMARK 500 SER A 319 61.37 31.72 REMARK 500 ASN A 381 73.92 -167.19 REMARK 500 SER B 319 63.76 25.61 REMARK 500 ASN B 381 65.05 -167.67 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 5GP A 900 O2P 89.0 85.5 REMARK 620 4 5GP A 900 O3P 95.6 89.0 64.1 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 88.8 REMARK 620 3 5GP A 900 O1P 102.3 68.5 REMARK 620 4 HOH A1131 O 168.0 87.7 87.1 REMARK 620 5 HOH A1132 O 79.3 95.0 163.3 89.6 REMARK 620 6 HOH A1133 O 90.8 167.3 99.2 95.1 97.4 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 92.9 REMARK 620 3 ASP B 402 OD1 93.0 171.4 REMARK 620 4 HOH B1185 O 72.6 85.3 90.5 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 B1185 O 94.7 REMARK 620 3 HOH B1186 O 105.5 74.5 REMARK 620 4 HOH B1187 O 169.5 83.6 84.0 REMARK 620 5 HOH B1188 O 93.8 166.7 93.4 89.9 REMARK 620 6 HOH B1189 O 86.4 95.2 164.6 83.5 95.6 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 A 65 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 89 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5GP A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IBM B 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 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: 3DY8 RELATED DB: PDB REMARK 900 RELATED ID: 3DYL RELATED DB: PDB REMARK 900 RELATED ID: 3DYN RELATED DB: PDB REMARK 900 RELATED ID: 3DYQ RELATED DB: PDB DBREF 3DYS A 182 506 UNP O76083 PDE9A_HUMAN 242 566 DBREF 3DYS B 182 506 UNP O76083 PDE9A_HUMAN 242 566 SEQADV 3DYS GLY A 178 UNP O76083 EXPRESSION TAG SEQADV 3DYS SER A 179 UNP O76083 EXPRESSION TAG SEQADV 3DYS HIS A 180 UNP O76083 EXPRESSION TAG SEQADV 3DYS MET A 181 UNP O76083 EXPRESSION TAG SEQADV 3DYS GLY B 178 UNP O76083 EXPRESSION TAG SEQADV 3DYS SER B 179 UNP O76083 EXPRESSION TAG SEQADV 3DYS HIS B 180 UNP O76083 EXPRESSION TAG SEQADV 3DYS 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 MN A 65 1 HET 5GP A 900 24 HET MN B 901 1 HET MG B 902 1 HET MN B 89 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 4(MN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 6 5GP C10 H14 N5 O8 P FORMUL 10 IBM C10 H14 N4 O2 FORMUL 11 FMT C H2 O2 FORMUL 12 HOH *463(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 SER A 229 1 7 HELIX 4 4 ASN A 231 ASN A 245 1 15 HELIX 5 5 ASN A 253 SER A 272 1 20 HELIX 6 6 SER A 272 PHE A 277 1 6 HELIX 7 7 SER A 278 HIS A 292 1 15 HELIX 8 8 ASN A 300 ALA A 307 1 8 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 ALA A 362 1 18 HELIX 13 13 THR A 363 ALA A 366 5 4 HELIX 14 14 ARG A 367 MET A 379 1 13 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 MET A 474 GLU A 502 1 29 HELIX 22 22 SER B 189 LEU B 196 1 8 HELIX 23 23 ASP B 202 TRP B 206 5 5 HELIX 24 24 GLU B 207 LEU B 222 1 16 HELIX 25 25 GLY B 223 SER B 229 1 7 HELIX 26 26 ASN B 231 ASN B 245 1 15 HELIX 27 27 ASN B 253 CYS B 271 1 19 HELIX 28 28 SER B 272 PHE B 277 1 6 HELIX 29 29 SER B 278 HIS B 292 1 15 HELIX 30 30 ASN B 300 ALA B 307 1 8 HELIX 31 31 THR B 309 TYR B 315 1 7 HELIX 32 32 SER B 319 ALA B 334 1 16 HELIX 33 33 GLU B 335 ASN B 339 5 5 HELIX 34 34 PRO B 345 ALA B 362 1 18 HELIX 35 35 THR B 363 ALA B 366 5 4 HELIX 36 36 ARG B 367 GLU B 380 1 14 HELIX 37 37 ASN B 386 ILE B 403 1 18 HELIX 38 38 SER B 404 ARG B 408 5 5 HELIX 39 39 PRO B 409 GLY B 435 1 27 HELIX 40 40 ALA B 439 ASP B 443 5 5 HELIX 41 41 THR B 448 VAL B 460 1 13 HELIX 42 42 VAL B 460 PHE B 472 1 13 HELIX 43 43 MET B 474 MET B 479 1 6 HELIX 44 44 MET B 479 LYS B 505 1 27 LINK MN MN A 65 O HOH A 990 1555 1555 2.45 LINK OD2 ASP A 293 MN MN A 901 1555 1555 2.04 LINK OD1 ASP A 293 MG MG A 902 1555 1555 2.09 LINK OD1 ASP A 402 MN MN A 901 1555 1555 2.23 LINK O2P 5GP A 900 MN MN A 901 1555 1555 2.34 LINK O3P 5GP A 900 MN MN A 901 1555 1555 2.41 LINK O2P 5GP A 900 MG MG A 902 1555 1555 2.27 LINK O1P 5GP A 900 MG MG A 902 1555 1555 2.32 LINK MG MG A 902 O HOH A1131 1555 1555 2.18 LINK MG MG A 902 O HOH A1132 1555 1555 2.05 LINK MG MG A 902 O HOH A1133 1555 1555 2.17 LINK O1 FMT B 1 MN MN B 901 1555 1555 2.13 LINK MN MN B 89 O HOH B1184 1555 1555 2.47 LINK OD2 ASP B 293 MN MN B 901 1555 1555 2.10 LINK OD1 ASP B 293 MG MG B 902 1555 1555 2.05 LINK OD1 ASP B 402 MN MN B 901 1555 1555 2.11 LINK MN MN B 901 O HOH B1185 1555 1555 2.39 LINK MG MG B 902 O HOH B1185 1555 1555 2.14 LINK MG MG B 902 O HOH B1186 1555 1555 2.17 LINK MG MG B 902 O HOH B1187 1555 1555 2.07 LINK MG MG B 902 O HOH B1188 1555 1555 2.07 LINK MG MG B 902 O HOH B1189 1555 1555 2.09 SITE 1 AC1 5 HIS A 256 HIS A 292 ASP A 293 ASP A 402 SITE 2 AC1 5 5GP A 900 SITE 1 AC2 5 ASP A 293 5GP A 900 HOH A1131 HOH A1132 SITE 2 AC2 5 HOH A1133 SITE 1 AC3 5 ASP A 244 TYR A 246 HOH A 990 HOH A1046 SITE 2 AC3 5 HOH A1110 SITE 1 AC4 6 FMT B 1 HIS B 256 HIS B 292 ASP B 293 SITE 2 AC4 6 ASP B 402 HOH B1185 SITE 1 AC5 6 ASP B 293 HOH B1185 HOH B1186 HOH B1187 SITE 2 AC5 6 HOH B1188 HOH B1189 SITE 1 AC6 6 ASP B 244 TYR B 246 HOH B1037 HOH B1129 SITE 2 AC6 6 HOH B1147 HOH B1184 SITE 1 AC7 20 HIS A 252 HIS A 256 HIS A 292 ASP A 293 SITE 2 AC7 20 ASP A 402 ILE A 403 LEU A 420 TYR A 424 SITE 3 AC7 20 ALA A 452 GLN A 453 PHE A 456 MN A 901 SITE 4 AC7 20 MG A 902 HOH A 914 HOH A 915 HOH A 917 SITE 5 AC7 20 HOH A 950 HOH A 961 HOH A1038 HOH A1131 SITE 1 AC8 10 ALA A 499 MET A 500 LEU B 420 TYR B 424 SITE 2 AC8 10 ALA B 452 GLN B 453 PHE B 456 HOH B 993 SITE 3 AC8 10 HOH B1029 HOH B1045 SITE 1 AC9 9 PHE B 251 HIS B 252 HIS B 256 ASP B 293 SITE 2 AC9 9 ASP B 402 MN B 901 HOH B1058 HOH B1185 SITE 3 AC9 9 HOH B1186 CRYST1 103.992 103.992 269.762 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 0.009616 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009616 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003707 0.00000