HEADER HYDROLASE 30-MAY-08 3DBA TITLE CRYSTAL STRUCTURE OF THE CGMP-BOUND GAF A DOMAIN FROM THE TITLE 2 PHOTORECEPTOR PHOSPHODIESTERASE 6C COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONE CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE SUBUNIT COMPND 3 ALPHA'; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: GAF A DOMAIN (UNP RESIDUES 55-225); COMPND 6 SYNONYM: CGMP PHOSPHODIESTERASE 6C; COMPND 7 EC: 3.1.4.35; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: BANTAM,CHICKENS; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 STRAIN: RHODE ISLAND RED; SOURCE 6 GENE: PDE6C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C41 CELLS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRUNH KEYWDS 3', 5' CGMP, GAF DOMAIN, CYCLIC NUCLEOTIDE PHOSPHODIESTERASE, CGMP, KEYWDS 2 HYDROLASE, LIPOPROTEIN, MEMBRANE, PRENYLATION, SENSORY TRANSDUCTION, KEYWDS 3 VISION EXPDTA X-RAY DIFFRACTION AUTHOR S.E.MARTINEZ,C.C.HEIKAUS,R.E.KLEVIT,J.A.BEAVO REVDAT 6 21-FEB-24 3DBA 1 REMARK SEQADV REVDAT 5 13-JUL-11 3DBA 1 VERSN REVDAT 4 24-FEB-09 3DBA 1 VERSN REVDAT 3 23-SEP-08 3DBA 1 JRNL REVDAT 2 15-JUL-08 3DBA 1 HELIX REVDAT 1 01-JUL-08 3DBA 0 JRNL AUTH S.E.MARTINEZ,C.C.HEIKAUS,R.E.KLEVIT,J.A.BEAVO JRNL TITL THE STRUCTURE OF THE GAF A DOMAIN FROM PHOSPHODIESTERASE 6C JRNL TITL 2 REVEALS DETERMINANTS OF CGMP BINDING, A CONSERVED BINDING JRNL TITL 3 SURFACE, AND A LARGE CGMP-DEPENDENT CONFORMATIONAL CHANGE. JRNL REF J.BIOL.CHEM. V. 283 25913 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18614542 JRNL DOI 10.1074/JBC.M802891200 REMARK 2 REMARK 2 RESOLUTION. 2.57 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) : 2.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 17159 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) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 860 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) : 2.57 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1170 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.3540 REMARK 3 BIN FREE R VALUE SET COUNT : 61 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2736 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 57.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.33000 REMARK 3 B22 (A**2) : 7.33000 REMARK 3 B33 (A**2) : -11.00000 REMARK 3 B12 (A**2) : 3.67000 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): 0.454 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.285 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.282 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 28.428 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2861 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1958 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3865 ; 1.259 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4806 ; 0.813 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 340 ; 6.946 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 126 ;32.161 ;25.079 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 532 ;17.936 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;15.664 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 446 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3054 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 542 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 673 ; 0.216 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1948 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1368 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1568 ; 0.083 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 104 ; 0.154 ; 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): 25 ; 0.260 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 54 ; 0.244 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.226 ; 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): 2218 ; 3.075 ; 7.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 682 ; 0.768 ; 7.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2784 ; 3.907 ;10.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1345 ; 2.752 ; 7.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1081 ; 3.623 ;10.000 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 : 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 55 A 225 REMARK 3 ORIGIN FOR THE GROUP (A): 14.5166 38.6205 15.6737 REMARK 3 T TENSOR REMARK 3 T11: -.1307 T22: -.4125 REMARK 3 T33: -.1399 T12: -.2421 REMARK 3 T13: -.0137 T23: .0515 REMARK 3 L TENSOR REMARK 3 L11: 2.4754 L22: 2.6078 REMARK 3 L33: 8.7551 L12: -1.1617 REMARK 3 L13: -1.5658 L23: 1.0191 REMARK 3 S TENSOR REMARK 3 S11: -.0115 S12: .0375 S13: -.0347 REMARK 3 S21: .1716 S22: .0040 S23: .3088 REMARK 3 S31: -.1444 S32: -.7290 S33: .0075 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 55 B 225 REMARK 3 ORIGIN FOR THE GROUP (A): 38.8247 17.1889 14.8022 REMARK 3 T TENSOR REMARK 3 T11: .3573 T22: -.1842 REMARK 3 T33: -.1241 T12: .0284 REMARK 3 T13: -.0558 T23: .0209 REMARK 3 L TENSOR REMARK 3 L11: 4.3089 L22: 5.7070 REMARK 3 L33: 7.8351 L12: -1.4756 REMARK 3 L13: 2.4084 L23: .2128 REMARK 3 S TENSOR REMARK 3 S11: .5301 S12: .8492 S13: -.0519 REMARK 3 S21: -.9781 S22: -.2802 S23: -.2950 REMARK 3 S31: 1.2436 S32: .9836 S33: -.2500 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 : 1.40 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 3DBA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000047823. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97912 REMARK 200 MONOCHROMATOR : KOHZU DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17389 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.570 REMARK 200 RESOLUTION RANGE LOW (A) : 43.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 51.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 56.5000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE, PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 132.35533 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 66.17767 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 66.17767 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 132.35533 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL 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 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 54 REMARK 465 LEU A 226 REMARK 465 GLU A 227 REMARK 465 HIS A 228 REMARK 465 HIS A 229 REMARK 465 HIS A 230 REMARK 465 HIS A 231 REMARK 465 HIS A 232 REMARK 465 HIS A 233 REMARK 465 MET B 54 REMARK 465 LEU B 226 REMARK 465 GLU B 227 REMARK 465 HIS B 228 REMARK 465 HIS B 229 REMARK 465 HIS B 230 REMARK 465 HIS B 231 REMARK 465 HIS B 232 REMARK 465 HIS B 233 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 LEU A 56 -76.83 -28.73 REMARK 500 ASP A 71 84.11 -55.79 REMARK 500 GLU A 72 -81.65 -150.04 REMARK 500 ALA A 73 -129.95 -78.45 REMARK 500 ARG A 113 -59.58 -146.50 REMARK 500 HIS A 163 -44.89 92.17 REMARK 500 ASN A 198 84.48 51.48 REMARK 500 ALA A 202 161.53 178.55 REMARK 500 LEU A 224 42.36 -73.74 REMARK 500 SER B 75 91.95 54.35 REMARK 500 ARG B 113 -55.54 -140.94 REMARK 500 PRO B 130 -9.61 -55.08 REMARK 500 LYS B 132 64.62 -161.33 REMARK 500 ASP B 157 94.29 -166.97 REMARK 500 LYS B 159 -26.96 80.82 REMARK 500 VAL B 177 -53.91 -120.87 REMARK 500 MET B 179 128.40 -171.15 REMARK 500 ASN B 198 85.33 55.10 REMARK 500 LEU B 224 49.40 -82.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 35G A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 35G B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 7 REMARK 999 REMARK 999 SEQUENCE REMARK 999 ACCORDING TO THE AUTHORS SEQUENCING OF THE EXPRESSION PLASMID REMARK 999 REVEALED AN APPARENT MUTATION R93A, WITH REFERENCE TO THE MRNA REMARK 999 SEQUENCE IN ENTREZ ENTRY NM_204986. HOWEVER, A CHICKEN GENOMIC REMARK 999 CONTIG ENTREZ NW_001471719 SHOWS AN ALA CODON GCC INSTEAD OF THE REMARK 999 ARG CODON CGC. NEARLY ALL PDE6 SEQUENCES HAVE AN ALA AT THIS REMARK 999 POSITION. IN THE MODEL, THIS ALA IS COMPLETELY BURIED IN A PACKED REMARK 999 HYDROPHOBIC ENVIRONMENT. THEREFORE, THE ENTREZ MRNA ENTRY LIKELY REMARK 999 HAS A TRANSPOSITION ERROR OF THE FIRST TWO BASES IN THIS CODON. DBREF 3DBA A 55 225 UNP P52731 PDE6C_CHICK 55 225 DBREF 3DBA B 55 225 UNP P52731 PDE6C_CHICK 55 225 SEQADV 3DBA MET A 54 UNP P52731 EXPRESSION TAG SEQADV 3DBA ALA A 93 UNP P52731 ARG 93 SEE REMARK 999 SEQADV 3DBA LEU A 226 UNP P52731 EXPRESSION TAG SEQADV 3DBA GLU A 227 UNP P52731 EXPRESSION TAG SEQADV 3DBA HIS A 228 UNP P52731 EXPRESSION TAG SEQADV 3DBA HIS A 229 UNP P52731 EXPRESSION TAG SEQADV 3DBA HIS A 230 UNP P52731 EXPRESSION TAG SEQADV 3DBA HIS A 231 UNP P52731 EXPRESSION TAG SEQADV 3DBA HIS A 232 UNP P52731 EXPRESSION TAG SEQADV 3DBA HIS A 233 UNP P52731 EXPRESSION TAG SEQADV 3DBA MET B 54 UNP P52731 EXPRESSION TAG SEQADV 3DBA ALA B 93 UNP P52731 ARG 93 SEE REMARK 999 SEQADV 3DBA LEU B 226 UNP P52731 EXPRESSION TAG SEQADV 3DBA GLU B 227 UNP P52731 EXPRESSION TAG SEQADV 3DBA HIS B 228 UNP P52731 EXPRESSION TAG SEQADV 3DBA HIS B 229 UNP P52731 EXPRESSION TAG SEQADV 3DBA HIS B 230 UNP P52731 EXPRESSION TAG SEQADV 3DBA HIS B 231 UNP P52731 EXPRESSION TAG SEQADV 3DBA HIS B 232 UNP P52731 EXPRESSION TAG SEQADV 3DBA HIS B 233 UNP P52731 EXPRESSION TAG SEQRES 1 A 180 MET ARG LEU GLU GLU CYS ASN ILE LEU PHE GLU LEU LEU SEQRES 2 A 180 THR GLU ILE GLN ASP GLU ALA GLY SER MET GLU LYS ILE SEQRES 3 A 180 VAL HIS LYS THR LEU GLN ARG LEU SER GLN LEU LEU ALA SEQRES 4 A 180 ALA ASP ARG CYS SER MET PHE ILE CYS ARG SER ARG ASN SEQRES 5 A 180 GLY ILE PRO GLU VAL ALA THR ARG LEU LEU ASN VAL THR SEQRES 6 A 180 PRO THR SER LYS PHE GLU ASP ASN LEU VAL ASN PRO ASP SEQRES 7 A 180 LYS GLU THR VAL PHE PRO LEU ASP ILE GLY ILE ALA GLY SEQRES 8 A 180 TRP VAL ALA HIS THR LYS LYS PHE PHE ASN ILE PRO ASP SEQRES 9 A 180 VAL LYS LYS ASN ASN HIS PHE SER ASP TYR LEU ASP LYS SEQRES 10 A 180 LYS THR GLY TYR THR THR VAL ASN MET MET ALA ILE PRO SEQRES 11 A 180 ILE THR GLN GLY LYS GLU VAL LEU ALA VAL VAL MET ALA SEQRES 12 A 180 LEU ASN LYS LEU ASN ALA SER GLU PHE SER LYS GLU ASP SEQRES 13 A 180 GLU GLU VAL PHE LYS LYS TYR LEU ASN PHE ILE SER LEU SEQRES 14 A 180 VAL LEU ARG LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 180 MET ARG LEU GLU GLU CYS ASN ILE LEU PHE GLU LEU LEU SEQRES 2 B 180 THR GLU ILE GLN ASP GLU ALA GLY SER MET GLU LYS ILE SEQRES 3 B 180 VAL HIS LYS THR LEU GLN ARG LEU SER GLN LEU LEU ALA SEQRES 4 B 180 ALA ASP ARG CYS SER MET PHE ILE CYS ARG SER ARG ASN SEQRES 5 B 180 GLY ILE PRO GLU VAL ALA THR ARG LEU LEU ASN VAL THR SEQRES 6 B 180 PRO THR SER LYS PHE GLU ASP ASN LEU VAL ASN PRO ASP SEQRES 7 B 180 LYS GLU THR VAL PHE PRO LEU ASP ILE GLY ILE ALA GLY SEQRES 8 B 180 TRP VAL ALA HIS THR LYS LYS PHE PHE ASN ILE PRO ASP SEQRES 9 B 180 VAL LYS LYS ASN ASN HIS PHE SER ASP TYR LEU ASP LYS SEQRES 10 B 180 LYS THR GLY TYR THR THR VAL ASN MET MET ALA ILE PRO SEQRES 11 B 180 ILE THR GLN GLY LYS GLU VAL LEU ALA VAL VAL MET ALA SEQRES 12 B 180 LEU ASN LYS LEU ASN ALA SER GLU PHE SER LYS GLU ASP SEQRES 13 B 180 GLU GLU VAL PHE LYS LYS TYR LEU ASN PHE ILE SER LEU SEQRES 14 B 180 VAL LEU ARG LEU GLU HIS HIS HIS HIS HIS HIS HET 35G A 1 23 HET GOL A 3 6 HET GOL A 4 6 HET GOL A 5 6 HET 35G B 2 23 HET GOL B 6 6 HET GOL B 7 6 HETNAM 35G GUANOSINE-3',5'-MONOPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 35G 2(C10 H12 N5 O7 P) FORMUL 4 GOL 5(C3 H8 O3) FORMUL 10 HOH *79(H2 O) HELIX 1 1 ARG A 55 THR A 67 1 13 HELIX 2 2 GLY A 74 ALA A 92 1 19 HELIX 3 3 LYS A 122 LEU A 127 1 6 HELIX 4 5 GLY A 141 LYS A 150 1 10 HELIX 5 7 ASP A 166 GLY A 173 1 8 HELIX 6 8 SER A 206 LEU A 224 1 19 HELIX 7 9 GLU B 57 GLU B 68 1 12 HELIX 8 10 MET B 76 ALA B 92 1 17 HELIX 9 11 LYS B 122 LEU B 127 1 6 HELIX 10 13 GLY B 141 LYS B 150 1 10 HELIX 11 14 ASP B 166 GLY B 173 1 8 HELIX 12 15 SER B 206 LEU B 224 1 19 SHEET 1 A 6 THR A 134 PHE A 136 0 SHEET 2 A 6 ILE A 107 VAL A 117 -1 N VAL A 110 O PHE A 136 SHEET 3 A 6 ALA A 92 ARG A 104 -1 N CYS A 96 O VAL A 117 SHEET 4 A 6 GLU A 189 LYS A 199 -1 N LEU A 197 O ARG A 95 SHEET 5 A 6 ASN A 178 GLN A 186 -1 N GLN A 186 O GLU A 189 SHEET 6 A 6 PHE A 153 ILE A 155 -1 N ILE A 155 O MET A 179 SHEET 1 B 6 THR B 134 PHE B 136 0 SHEET 2 B 6 PRO B 108 VAL B 117 -1 N VAL B 110 O PHE B 136 SHEET 3 B 6 ALA B 92 ARG B 104 -1 N CYS B 96 O VAL B 117 SHEET 4 B 6 GLU B 189 LYS B 199 -1 O VAL B 193 N PHE B 99 SHEET 5 B 6 ASN B 178 GLN B 186 -1 N ILE B 184 O ALA B 192 SHEET 6 B 6 PHE B 153 ILE B 155 -1 N ILE B 155 O MET B 179 CISPEP 1 ALA A 73 GLY A 74 0 6.51 CISPEP 2 ARG B 104 ASN B 105 0 -8.48 SITE 1 AC1 16 SER A 97 PHE A 99 LEU A 115 ASN A 116 SITE 2 AC1 16 GLY A 141 ILE A 142 ALA A 143 PHE A 164 SITE 3 AC1 16 SER A 165 LEU A 168 ASP A 169 THR A 172 SITE 4 AC1 16 TYR A 174 THR A 176 LEU A 197 HOH A 254 SITE 1 AC2 18 SER B 97 PHE B 99 LEU B 115 ASN B 116 SITE 2 AC2 18 PHE B 136 GLY B 141 ILE B 142 ALA B 143 SITE 3 AC2 18 PHE B 164 SER B 165 LEU B 168 TYR B 174 SITE 4 AC2 18 THR B 176 MET B 179 LEU B 197 HOH B 246 SITE 5 AC2 18 HOH B 248 HOH B 276 SITE 1 AC3 2 TYR A 167 HOH A 275 SITE 1 AC4 4 TRP A 145 LYS A 151 PHE A 153 HIS A 163 SITE 1 AC5 4 HIS A 81 LYS A 82 GLN A 85 PHE A 123 SITE 1 AC6 3 HIS B 81 GLN B 85 PHE B 123 CRYST1 67.598 67.598 198.533 90.00 90.00 120.00 P 32 2 1 12 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 0.014793 0.008541 0.000000 0.00000 SCALE2 0.000000 0.017082 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005037 0.00000