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
(ATOM LINES ARE NOT SHOWN.)
END