HEADER HYDROLASE 03-FEB-09 3G45 TITLE CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 4B WITH REGULATORY DOMAIN TITLE 2 AND D155988 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: S241 CLOOP, RESIDUES 241-289 AND 305-659; COMPND 5 SYNONYM: DPDE4, PDE32; COMPND 6 EC: 3.1.4.17; 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: PDE4B, DPDE4; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS PHOSPHODIESTERASE, ALTERNATIVE SPLICING, CAMP, HYDROLASE, KEYWDS 2 PHOSPHOPROTEIN, POLYMORPHISM EXPDTA X-RAY DIFFRACTION AUTHOR B.L.STAKER REVDAT 3 21-FEB-24 3G45 1 REMARK LINK REVDAT 2 26-JUL-17 3G45 1 SOURCE REMARK REVDAT 1 19-JAN-10 3G45 0 JRNL AUTH A.B.BURGIN,O.T.MAGNUSSON,J.SINGH,P.WITTE,B.L.STAKER, JRNL AUTH 2 J.M.BJORNSSON,M.THORSTEINSDOTTIR,S.HRAFNSDOTTIR,T.HAGEN, JRNL AUTH 3 A.S.KISELYOV,L.J.STEWART,M.E.GURNEY JRNL TITL DESIGN OF PHOSPHODIESTERASE 4D (PDE4D) ALLOSTERIC MODULATORS JRNL TITL 2 FOR ENHANCING COGNITION WITH IMPROVED SAFETY. JRNL REF NAT.BIOTECHNOL. V. 28 63 2010 JRNL REFN ISSN 1087-0156 JRNL PMID 20037581 JRNL DOI 10.1038/NBT.1598 REMARK 2 REMARK 2 RESOLUTION. 2.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 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) : 2.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 28027 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1413 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) : 2.63 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1960 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE SET COUNT : 115 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5977 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.37000 REMARK 3 B22 (A**2) : -0.37000 REMARK 3 B33 (A**2) : 0.55000 REMARK 3 B12 (A**2) : -0.18000 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): 0.821 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.299 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.210 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.943 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6153 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4015 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8336 ; 1.338 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9812 ; 1.030 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 737 ; 5.737 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 310 ;38.244 ;24.968 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1087 ;17.918 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;19.091 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 938 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6813 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1223 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 3697 ; 0.552 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1484 ; 0.088 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5989 ; 1.126 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2456 ; 1.852 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2347 ; 3.159 ; 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 REMARK 4 REMARK 4 3G45 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000051399. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38397 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.23900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.81200 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM NAACETATE, 20MM CALCIUM REMARK 280 CHLORIDE, 15% MPD, PH 4.6, VAPOR DIFFUSION, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K, PH 4.60 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.23800 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 62.47600 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 300 REMARK: AUTHORS STATE THAT THE BIOLOGICAL UNIT IS THE SAME AS REMARK 300 ASYMMETRIC UNIT. 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: 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: 3 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 MET A 240 REMARK 465 SER A 241 REMARK 465 VAL A 242 REMARK 465 SER A 243 REMARK 465 GLU A 244 REMARK 465 MET A 245 REMARK 465 ALA A 246 REMARK 465 LYS A 287 REMARK 465 GLN A 288 REMARK 465 ASN A 289 REMARK 465 ASP A 290 REMARK 465 VAL A 291 REMARK 465 GLU A 292 REMARK 465 ILE A 293 REMARK 465 PRO A 294 REMARK 465 LYS A 295 REMARK 465 VAL A 296 REMARK 465 THR A 297 REMARK 465 ALA A 298 REMARK 465 GLU A 299 REMARK 465 GLU A 300 REMARK 465 ALA A 301 REMARK 465 PRO A 302 REMARK 465 GLN A 303 REMARK 465 PRO A 304 REMARK 465 MET A 305 REMARK 465 THR A 306 REMARK 465 GLN A 307 REMARK 465 ILE A 308 REMARK 465 SER A 309 REMARK 465 GLY A 310 REMARK 465 VAL A 311 REMARK 465 LYS A 312 REMARK 465 LYS A 313 REMARK 465 LEU A 314 REMARK 465 MET A 315 REMARK 465 HIS A 316 REMARK 465 SER A 317 REMARK 465 SER A 318 REMARK 465 SER A 319 REMARK 465 LEU A 320 REMARK 465 ASN A 321 REMARK 465 ASN A 322 REMARK 465 SER A 659 REMARK 465 HIS A 660 REMARK 465 HIS A 661 REMARK 465 HIS A 662 REMARK 465 HIS A 663 REMARK 465 HIS A 664 REMARK 465 HIS A 665 REMARK 465 MET B 240 REMARK 465 SER B 241 REMARK 465 VAL B 242 REMARK 465 SER B 243 REMARK 465 GLU B 244 REMARK 465 MET B 245 REMARK 465 ALA B 246 REMARK 465 LYS B 287 REMARK 465 GLN B 288 REMARK 465 ASN B 289 REMARK 465 ASP B 290 REMARK 465 VAL B 291 REMARK 465 GLU B 292 REMARK 465 ILE B 293 REMARK 465 PRO B 294 REMARK 465 LYS B 295 REMARK 465 VAL B 296 REMARK 465 THR B 297 REMARK 465 ALA B 298 REMARK 465 GLU B 299 REMARK 465 GLU B 300 REMARK 465 ALA B 301 REMARK 465 PRO B 302 REMARK 465 GLN B 303 REMARK 465 PRO B 304 REMARK 465 MET B 305 REMARK 465 THR B 306 REMARK 465 GLN B 307 REMARK 465 ILE B 308 REMARK 465 SER B 309 REMARK 465 GLY B 310 REMARK 465 VAL B 311 REMARK 465 LYS B 312 REMARK 465 LYS B 313 REMARK 465 LEU B 314 REMARK 465 MET B 315 REMARK 465 HIS B 316 REMARK 465 SER B 317 REMARK 465 SER B 318 REMARK 465 SER B 319 REMARK 465 LEU B 320 REMARK 465 ASN B 321 REMARK 465 ASN B 322 REMARK 465 THR B 323 REMARK 465 SER B 659 REMARK 465 HIS B 660 REMARK 465 HIS B 661 REMARK 465 HIS B 662 REMARK 465 HIS B 663 REMARK 465 HIS B 664 REMARK 465 HIS B 665 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 251 CG CD CE NZ REMARK 470 ARG A 252 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 251 CG CD CE NZ REMARK 470 ARG B 266 CG CD NE CZ NH1 NH2 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 ILE B 325 CG1 - CB - CG2 ANGL. DEV. = 14.2 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 TYR A 405 -51.71 -122.34 REMARK 500 ASP A 471 -1.82 64.32 REMARK 500 THR A 539 -124.90 -93.95 REMARK 500 SER A 541 32.32 70.09 REMARK 500 ILE A 622 -51.63 -131.25 REMARK 500 SER B 265 167.76 173.43 REMARK 500 ASN B 334 47.07 -108.05 REMARK 500 SER B 541 23.87 -149.88 REMARK 500 ILE B 622 -54.24 -135.87 REMARK 500 ALA B 638 28.80 -79.98 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 SER B 540 SER B 541 138.25 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 ZN A 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 410 NE2 REMARK 620 2 HIS A 446 NE2 98.8 REMARK 620 3 ASP A 447 OD2 87.4 79.9 REMARK 620 4 ASP A 564 OD1 87.2 98.5 174.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 802 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 92 O REMARK 620 2 HOH B 98 O 78.1 REMARK 620 3 ASP B 447 OD1 78.8 149.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 410 NE2 REMARK 620 2 HIS B 446 NE2 91.8 REMARK 620 3 ASP B 447 OD2 85.4 78.9 REMARK 620 4 ASP B 564 OD1 88.9 90.0 167.3 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 ZN A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 988 A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 988 B 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3G4G RELATED DB: PDB REMARK 900 RELATED ID: 3G4I RELATED DB: PDB REMARK 900 RELATED ID: 3G4K RELATED DB: PDB REMARK 900 RELATED ID: 3G4L RELATED DB: PDB REMARK 900 RELATED ID: 3G58 RELATED DB: PDB REMARK 900 RELATED ID: 3GPZ RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT THE LINKER REGION IS FROM PDE4C THAT WAS SWAPPED REMARK 999 TO REPLACE THE NATURAL LINKER, AS THE NATURAL LINKER WAS HIGHLY REMARK 999 CHARGED. DBREF 3G45 A 241 294 UNP Q07343 PDE4B_HUMAN 241 289 DBREF 3G45 A 305 659 UNP Q07343 PDE4B_HUMAN 305 659 DBREF 3G45 B 241 294 UNP Q07343 PDE4B_HUMAN 241 289 DBREF 3G45 B 305 659 UNP Q07343 PDE4B_HUMAN 305 659 SEQADV 3G45 MET A 240 UNP Q07343 EXPRESSION TAG SEQADV 3G45 LYS A 295 UNP Q07343 LINKER SEQADV 3G45 VAL A 296 UNP Q07343 LINKER SEQADV 3G45 THR A 297 UNP Q07343 LINKER SEQADV 3G45 ALA A 298 UNP Q07343 LINKER SEQADV 3G45 GLU A 299 UNP Q07343 LINKER SEQADV 3G45 GLU A 300 UNP Q07343 LINKER SEQADV 3G45 ALA A 301 UNP Q07343 LINKER SEQADV 3G45 PRO A 302 UNP Q07343 LINKER SEQADV 3G45 GLN A 303 UNP Q07343 LINKER SEQADV 3G45 PRO A 304 UNP Q07343 LINKER SEQADV 3G45 HIS A 660 UNP Q07343 EXPRESSION TAG SEQADV 3G45 HIS A 661 UNP Q07343 EXPRESSION TAG SEQADV 3G45 HIS A 662 UNP Q07343 EXPRESSION TAG SEQADV 3G45 HIS A 663 UNP Q07343 EXPRESSION TAG SEQADV 3G45 HIS A 664 UNP Q07343 EXPRESSION TAG SEQADV 3G45 HIS A 665 UNP Q07343 EXPRESSION TAG SEQADV 3G45 MET B 240 UNP Q07343 EXPRESSION TAG SEQADV 3G45 LYS B 295 UNP Q07343 LINKER SEQADV 3G45 VAL B 296 UNP Q07343 LINKER SEQADV 3G45 THR B 297 UNP Q07343 LINKER SEQADV 3G45 ALA B 298 UNP Q07343 LINKER SEQADV 3G45 GLU B 299 UNP Q07343 LINKER SEQADV 3G45 GLU B 300 UNP Q07343 LINKER SEQADV 3G45 ALA B 301 UNP Q07343 LINKER SEQADV 3G45 PRO B 302 UNP Q07343 LINKER SEQADV 3G45 GLN B 303 UNP Q07343 LINKER SEQADV 3G45 PRO B 304 UNP Q07343 LINKER SEQADV 3G45 HIS B 660 UNP Q07343 EXPRESSION TAG SEQADV 3G45 HIS B 661 UNP Q07343 EXPRESSION TAG SEQADV 3G45 HIS B 662 UNP Q07343 EXPRESSION TAG SEQADV 3G45 HIS B 663 UNP Q07343 EXPRESSION TAG SEQADV 3G45 HIS B 664 UNP Q07343 EXPRESSION TAG SEQADV 3G45 HIS B 665 UNP Q07343 EXPRESSION TAG SEQRES 1 A 421 MET SER VAL SER GLU MET ALA SER ASN LYS PHE LYS ARG SEQRES 2 A 421 MET LEU ASN ARG GLU LEU THR HIS LEU SER GLU MET SER SEQRES 3 A 421 ARG SER GLY ASN GLN VAL SER GLU TYR ILE SER ASN THR SEQRES 4 A 421 PHE LEU ASP LYS GLN ASN ASP VAL GLU ILE PRO LYS VAL SEQRES 5 A 421 THR ALA GLU GLU ALA PRO GLN PRO MET THR GLN ILE SER SEQRES 6 A 421 GLY VAL LYS LYS LEU MET HIS SER SER SER LEU ASN ASN SEQRES 7 A 421 THR SER ILE SER ARG PHE GLY VAL ASN THR GLU ASN GLU SEQRES 8 A 421 ASP HIS LEU ALA LYS GLU LEU GLU ASP LEU ASN LYS TRP SEQRES 9 A 421 GLY LEU ASN ILE PHE ASN VAL ALA GLY TYR SER HIS ASN SEQRES 10 A 421 ARG PRO LEU THR CYS ILE MET TYR ALA ILE PHE GLN GLU SEQRES 11 A 421 ARG ASP LEU LEU LYS THR PHE ARG ILE SER SER ASP THR SEQRES 12 A 421 PHE ILE THR TYR MET MET THR LEU GLU ASP HIS TYR HIS SEQRES 13 A 421 SER ASP VAL ALA TYR HIS ASN SER LEU HIS ALA ALA ASP SEQRES 14 A 421 VAL ALA GLN SER THR HIS VAL LEU LEU SER THR PRO ALA SEQRES 15 A 421 LEU ASP ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA SEQRES 16 A 421 ILE PHE ALA ALA ALA ILE HIS ASP VAL ASP HIS PRO GLY SEQRES 17 A 421 VAL SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU SEQRES 18 A 421 ALA LEU MET TYR ASN ASP GLU SER VAL LEU GLU ASN HIS SEQRES 19 A 421 HIS LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU HIS SEQRES 20 A 421 CYS ASP ILE PHE MET ASN LEU THR LYS LYS GLN ARG GLN SEQRES 21 A 421 THR LEU ARG LYS MET VAL ILE ASP MET VAL LEU ALA THR SEQRES 22 A 421 ASP MET SER LYS HIS MET SER LEU LEU ALA ASP LEU LYS SEQRES 23 A 421 THR MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL SEQRES 24 A 421 LEU LEU LEU ASP ASN TYR THR ASP ARG ILE GLN VAL LEU SEQRES 25 A 421 ARG ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR SEQRES 26 A 421 LYS SER LEU GLU LEU TYR ARG GLN TRP THR ASP ARG ILE SEQRES 27 A 421 MET GLU GLU PHE PHE GLN GLN GLY ASP LYS GLU ARG GLU SEQRES 28 A 421 ARG GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS THR SEQRES 29 A 421 ALA SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR SEQRES 30 A 421 ILE VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL SEQRES 31 A 421 GLN PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP SEQRES 32 A 421 ASN ARG ASN TRP TYR GLN SER MET ILE PRO GLN SER HIS SEQRES 33 A 421 HIS HIS HIS HIS HIS SEQRES 1 B 421 MET SER VAL SER GLU MET ALA SER ASN LYS PHE LYS ARG SEQRES 2 B 421 MET LEU ASN ARG GLU LEU THR HIS LEU SER GLU MET SER SEQRES 3 B 421 ARG SER GLY ASN GLN VAL SER GLU TYR ILE SER ASN THR SEQRES 4 B 421 PHE LEU ASP LYS GLN ASN ASP VAL GLU ILE PRO LYS VAL SEQRES 5 B 421 THR ALA GLU GLU ALA PRO GLN PRO MET THR GLN ILE SER SEQRES 6 B 421 GLY VAL LYS LYS LEU MET HIS SER SER SER LEU ASN ASN SEQRES 7 B 421 THR SER ILE SER ARG PHE GLY VAL ASN THR GLU ASN GLU SEQRES 8 B 421 ASP HIS LEU ALA LYS GLU LEU GLU ASP LEU ASN LYS TRP SEQRES 9 B 421 GLY LEU ASN ILE PHE ASN VAL ALA GLY TYR SER HIS ASN SEQRES 10 B 421 ARG PRO LEU THR CYS ILE MET TYR ALA ILE PHE GLN GLU SEQRES 11 B 421 ARG ASP LEU LEU LYS THR PHE ARG ILE SER SER ASP THR SEQRES 12 B 421 PHE ILE THR TYR MET MET THR LEU GLU ASP HIS TYR HIS SEQRES 13 B 421 SER ASP VAL ALA TYR HIS ASN SER LEU HIS ALA ALA ASP SEQRES 14 B 421 VAL ALA GLN SER THR HIS VAL LEU LEU SER THR PRO ALA SEQRES 15 B 421 LEU ASP ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA SEQRES 16 B 421 ILE PHE ALA ALA ALA ILE HIS ASP VAL ASP HIS PRO GLY SEQRES 17 B 421 VAL SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU SEQRES 18 B 421 ALA LEU MET TYR ASN ASP GLU SER VAL LEU GLU ASN HIS SEQRES 19 B 421 HIS LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU HIS SEQRES 20 B 421 CYS ASP ILE PHE MET ASN LEU THR LYS LYS GLN ARG GLN SEQRES 21 B 421 THR LEU ARG LYS MET VAL ILE ASP MET VAL LEU ALA THR SEQRES 22 B 421 ASP MET SER LYS HIS MET SER LEU LEU ALA ASP LEU LYS SEQRES 23 B 421 THR MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL SEQRES 24 B 421 LEU LEU LEU ASP ASN TYR THR ASP ARG ILE GLN VAL LEU SEQRES 25 B 421 ARG ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR SEQRES 26 B 421 LYS SER LEU GLU LEU TYR ARG GLN TRP THR ASP ARG ILE SEQRES 27 B 421 MET GLU GLU PHE PHE GLN GLN GLY ASP LYS GLU ARG GLU SEQRES 28 B 421 ARG GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS THR SEQRES 29 B 421 ALA SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR SEQRES 30 B 421 ILE VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL SEQRES 31 B 421 GLN PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP SEQRES 32 B 421 ASN ARG ASN TRP TYR GLN SER MET ILE PRO GLN SER HIS SEQRES 33 B 421 HIS HIS HIS HIS HIS HET ZN A 801 1 HET MG A 802 1 HET 988 A 901 26 HET ZN B 801 1 HET MG B 802 1 HET 988 B 901 26 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM 988 8-(3-NITROPHENYL)-6-(PYRIDIN-4-YLMETHYL)QUINOLINE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 5 988 2(C21 H15 N3 O2) FORMUL 9 HOH *100(H2 O) HELIX 1 1 SER A 247 SER A 265 1 19 HELIX 2 2 SER A 265 PHE A 279 1 15 HELIX 3 3 THR A 323 PHE A 328 1 6 HELIX 4 4 ASN A 334 LEU A 342 1 9 HELIX 5 5 GLU A 343 LEU A 345 5 3 HELIX 6 6 ASN A 351 SER A 359 1 9 HELIX 7 7 ARG A 362 ARG A 375 1 14 HELIX 8 8 ASP A 376 PHE A 381 1 6 HELIX 9 9 SER A 384 TYR A 399 1 16 HELIX 10 10 ASN A 407 LEU A 422 1 16 HELIX 11 11 THR A 432 HIS A 446 1 15 HELIX 12 12 SER A 454 THR A 461 1 8 HELIX 13 13 SER A 463 TYR A 469 1 7 HELIX 14 14 SER A 473 LEU A 486 1 14 HELIX 15 15 LEU A 487 GLU A 489 5 3 HELIX 16 16 THR A 499 ALA A 516 1 18 HELIX 17 17 THR A 517 SER A 520 5 4 HELIX 18 18 LYS A 521 THR A 535 1 15 HELIX 19 19 ASN A 548 LEU A 565 1 18 HELIX 20 20 SER A 566 LYS A 570 5 5 HELIX 21 21 SER A 571 ARG A 596 1 26 HELIX 22 22 SER A 610 ILE A 622 1 13 HELIX 23 23 ILE A 622 VAL A 634 1 13 HELIX 24 24 ALA A 638 MET A 655 1 18 HELIX 25 25 SER B 247 MET B 264 1 18 HELIX 26 26 SER B 265 PHE B 279 1 15 HELIX 27 27 SER B 324 GLY B 329 1 6 HELIX 28 28 ASN B 334 LEU B 342 1 9 HELIX 29 29 GLU B 343 LEU B 345 5 3 HELIX 30 30 ASN B 351 SER B 359 1 9 HELIX 31 31 ARG B 362 ARG B 375 1 14 HELIX 32 32 ASP B 376 PHE B 381 1 6 HELIX 33 33 SER B 384 HIS B 398 1 15 HELIX 34 34 ASN B 407 LEU B 422 1 16 HELIX 35 35 THR B 432 HIS B 446 1 15 HELIX 36 36 SER B 454 THR B 461 1 8 HELIX 37 37 SER B 463 ASN B 470 1 8 HELIX 38 38 SER B 473 LEU B 486 1 14 HELIX 39 39 LEU B 487 GLU B 489 5 3 HELIX 40 40 THR B 499 ALA B 516 1 18 HELIX 41 41 THR B 517 SER B 520 5 4 HELIX 42 42 LYS B 521 THR B 535 1 15 HELIX 43 43 ASN B 548 LEU B 565 1 18 HELIX 44 44 SER B 566 LYS B 570 5 5 HELIX 45 45 SER B 571 ARG B 596 1 26 HELIX 46 46 SER B 610 ILE B 622 1 13 HELIX 47 47 ILE B 622 GLN B 635 1 14 HELIX 48 48 ALA B 638 MET B 655 1 18 LINK NE2 HIS A 410 ZN ZN A 801 1555 1555 2.15 LINK NE2 HIS A 446 ZN ZN A 801 1555 1555 1.96 LINK OD2 ASP A 447 ZN ZN A 801 1555 1555 2.31 LINK OD1 ASP A 447 MG MG A 802 1555 1555 2.26 LINK OD1 ASP A 564 ZN ZN A 801 1555 1555 2.39 LINK O HOH B 92 MG MG B 802 1555 1555 2.34 LINK O HOH B 98 MG MG B 802 1555 1555 2.54 LINK NE2 HIS B 410 ZN ZN B 801 1555 1555 2.13 LINK NE2 HIS B 446 ZN ZN B 801 1555 1555 2.06 LINK OD2 ASP B 447 ZN ZN B 801 1555 1555 2.14 LINK OD1 ASP B 447 MG MG B 802 1555 1555 2.19 LINK OD1 ASP B 564 ZN ZN B 801 1555 1555 2.22 CISPEP 1 GLN A 635 PRO A 636 0 4.66 CISPEP 2 GLN B 635 PRO B 636 0 9.68 SITE 1 AC1 6 HOH A 32 HIS A 410 HIS A 446 ASP A 447 SITE 2 AC1 6 ASP A 564 MG A 802 SITE 1 AC2 2 ASP A 447 ZN A 801 SITE 1 AC3 9 VAL A 271 TYR A 274 HIS A 406 ASN A 567 SITE 2 AC3 9 THR A 579 ILE A 582 MET A 603 GLN A 615 SITE 3 AC3 9 PHE A 618 SITE 1 AC4 4 HIS B 410 HIS B 446 ASP B 447 ASP B 564 SITE 1 AC5 3 HOH B 92 HOH B 98 ASP B 447 SITE 1 AC6 10 TYR B 274 HIS B 406 MET B 519 ASN B 567 SITE 2 AC6 10 THR B 579 ILE B 582 PHE B 586 SER B 614 SITE 3 AC6 10 GLN B 615 PHE B 618 CRYST1 95.004 95.004 93.714 90.00 90.00 120.00 P 31 6 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 0.010526 0.006077 0.000000 0.00000 SCALE2 0.000000 0.012154 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010671 0.00000