PDB Short entry for 5E8F HEADER HYDROLASE 14-OCT-15 5E8F TITLE STRUCTURE OF FULLY MODIFIED GERANYLGERANYLATED PDE6C PEPTIDE IN TITLE 2 COMPLEX WITH PDE6D COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC COMPND 3 PHOSPHODIESTERASE SUBUNIT DELTA; COMPND 4 CHAIN: A, C; COMPND 5 FRAGMENT: UNP RESIDUES 2-150; COMPND 6 SYNONYM: GMP-PDE DELTA,PROTEIN P17; COMPND 7 EC: 3.1.4.35; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: CONE CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE SUBUNIT COMPND 11 ALPHA'; COMPND 12 CHAIN: D, E; COMPND 13 FRAGMENT: UNP RESIDUES 851-855; COMPND 14 SYNONYM: CGMP PHOSPHODIESTERASE 6C; COMPND 15 EC: 3.1.4.35; COMPND 16 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: PDE6D, PDED; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: PDE6C, PDEA2; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PRENYL BINDING PROTEIN, IMMUNOGLOBULIN-LIKE BETA SANDWITCH FOLD, KEYWDS 2 GERANYLGERANYL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.K.FANSA,N.J.O'REILLY,S.A.ISMAIL,A.WITTINGHOFER REVDAT 3 10-JAN-24 5E8F 1 LINK REVDAT 2 16-DEC-15 5E8F 1 JRNL REVDAT 1 18-NOV-15 5E8F 0 JRNL AUTH E.K.FANSA,N.J.O'REILLY,S.ISMAIL,A.WITTINGHOFER JRNL TITL THE N- AND C-TERMINAL ENDS OF RPGR CAN BIND TO PDE6 DELTA. JRNL REF EMBO REP. V. 16 1583 2015 JRNL REFN ESSN 1469-3178 JRNL PMID 26553937 JRNL DOI 10.15252/EMBR.201541404 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 21194 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1116 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1554 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2503 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.90000 REMARK 3 B22 (A**2) : 0.11000 REMARK 3 B33 (A**2) : -1.01000 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): 0.212 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.194 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.129 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.700 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2591 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2533 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3477 ; 1.973 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5831 ; 0.992 ; 3.009 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 300 ; 7.093 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;40.020 ;24.098 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 481 ;16.095 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;15.022 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 374 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2854 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 600 ; 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): 1218 ; 2.820 ; 3.010 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1216 ; 2.820 ; 3.009 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1512 ; 3.726 ; 4.494 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5E8F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214528. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00001 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE 5.7.0032 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22232 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 29.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.290 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.35 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.16300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 10.24 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 3.15 REMARK 200 STARTING MODEL: 3T5G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES (PH 7.5), 0.2 M LI2SO4, 25 REMARK 280 % PEG4000 AND 0.1 M NAOAC, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 59.26500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.26500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 38.85500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.71500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.85500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.71500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.26500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.85500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.71500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.26500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.85500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.71500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, E 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 SER A 2 REMARK 465 ALA A 3 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 C 210 O HOH C 232 2.02 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 THR E 854 C CMT E 855 N 0.248 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASN A 21 CB - CA - C ANGL. DEV. = -12.8 DEGREES REMARK 500 THR E 854 O - C - N ANGL. DEV. = -23.2 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 LEU A 38 -8.26 -55.44 REMARK 500 LYS A 73 80.30 -154.77 REMARK 500 PRO A 113 151.97 -48.98 REMARK 500 ASP A 136 -105.00 59.14 REMARK 500 ASP C 136 -106.63 55.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 THR E 854 -20.13 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 GER D 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GER E 901 DBREF 5E8F A 2 150 UNP O43924 PDE6D_HUMAN 2 150 DBREF 5E8F C 2 150 UNP O43924 PDE6D_HUMAN 2 150 DBREF 5E8F D 851 855 UNP P51160 PDE6C_HUMAN 851 855 DBREF 5E8F E 851 855 UNP P51160 PDE6C_HUMAN 851 855 SEQRES 1 A 149 SER ALA LYS ASP GLU ARG ALA ARG GLU ILE LEU ARG GLY SEQRES 2 A 149 PHE LYS LEU ASN TRP MET ASN LEU ARG ASP ALA GLU THR SEQRES 3 A 149 GLY LYS ILE LEU TRP GLN GLY THR GLU ASP LEU SER VAL SEQRES 4 A 149 PRO GLY VAL GLU HIS GLU ALA ARG VAL PRO LYS LYS ILE SEQRES 5 A 149 LEU LYS CYS LYS ALA VAL SER ARG GLU LEU ASN PHE SER SEQRES 6 A 149 SER THR GLU GLN MET GLU LYS PHE ARG LEU GLU GLN LYS SEQRES 7 A 149 VAL TYR PHE LYS GLY GLN CYS LEU GLU GLU TRP PHE PHE SEQRES 8 A 149 GLU PHE GLY PHE VAL ILE PRO ASN SER THR ASN THR TRP SEQRES 9 A 149 GLN SER LEU ILE GLU ALA ALA PRO GLU SER GLN MET MET SEQRES 10 A 149 PRO ALA SER VAL LEU THR GLY ASN VAL ILE ILE GLU THR SEQRES 11 A 149 LYS PHE PHE ASP ASP ASP LEU LEU VAL SER THR SER ARG SEQRES 12 A 149 VAL ARG LEU PHE TYR VAL SEQRES 1 C 149 SER ALA LYS ASP GLU ARG ALA ARG GLU ILE LEU ARG GLY SEQRES 2 C 149 PHE LYS LEU ASN TRP MET ASN LEU ARG ASP ALA GLU THR SEQRES 3 C 149 GLY LYS ILE LEU TRP GLN GLY THR GLU ASP LEU SER VAL SEQRES 4 C 149 PRO GLY VAL GLU HIS GLU ALA ARG VAL PRO LYS LYS ILE SEQRES 5 C 149 LEU LYS CYS LYS ALA VAL SER ARG GLU LEU ASN PHE SER SEQRES 6 C 149 SER THR GLU GLN MET GLU LYS PHE ARG LEU GLU GLN LYS SEQRES 7 C 149 VAL TYR PHE LYS GLY GLN CYS LEU GLU GLU TRP PHE PHE SEQRES 8 C 149 GLU PHE GLY PHE VAL ILE PRO ASN SER THR ASN THR TRP SEQRES 9 C 149 GLN SER LEU ILE GLU ALA ALA PRO GLU SER GLN MET MET SEQRES 10 C 149 PRO ALA SER VAL LEU THR GLY ASN VAL ILE ILE GLU THR SEQRES 11 C 149 LYS PHE PHE ASP ASP ASP LEU LEU VAL SER THR SER ARG SEQRES 12 C 149 VAL ARG LEU PHE TYR VAL SEQRES 1 D 5 LYS SER LYS THR CMT SEQRES 1 E 5 LYS SER LYS THR CMT MODRES 5E8F CMT D 855 CYS MODIFIED RESIDUE MODRES 5E8F CMT E 855 CYS MODIFIED RESIDUE HET CMT D 855 8 HET CMT E 855 8 HET GER D 901 20 HET GER E 901 20 HETNAM CMT O-METHYLCYSTEINE HETNAM GER GERAN-8-YL GERAN FORMUL 3 CMT 2(C4 H9 N O2 S) FORMUL 5 GER 2(C20 H34) FORMUL 7 HOH *108(H2 O) HELIX 1 AA1 LYS A 4 GLY A 14 1 11 HELIX 2 AA2 LYS A 52 CYS A 56 5 5 HELIX 3 AA3 PRO A 113 MET A 117 5 5 HELIX 4 AA4 PRO A 119 THR A 124 1 6 HELIX 5 AA5 ALA C 3 GLY C 14 1 12 HELIX 6 AA6 LYS C 52 CYS C 56 5 5 HELIX 7 AA7 PRO C 113 MET C 117 5 5 HELIX 8 AA8 PRO C 119 THR C 124 1 6 SHEET 1 AA1 4 ILE A 30 GLY A 34 0 SHEET 2 AA1 4 PHE A 15 ASP A 24 -1 N LEU A 22 O TRP A 32 SHEET 3 AA1 4 ALA A 58 SER A 67 -1 O ASN A 64 N TRP A 19 SHEET 4 AA1 4 SER A 101 GLU A 110 -1 O ASN A 103 N PHE A 65 SHEET 1 AA2 5 GLU A 44 PRO A 50 0 SHEET 2 AA2 5 LEU A 138 VAL A 150 1 O PHE A 148 N ALA A 47 SHEET 3 AA2 5 VAL A 127 ASP A 135 -1 N PHE A 133 O VAL A 140 SHEET 4 AA2 5 MET A 71 PHE A 82 -1 N TYR A 81 O ILE A 128 SHEET 5 AA2 5 GLN A 85 VAL A 97 -1 O PHE A 92 N LEU A 76 SHEET 1 AA3 4 ILE C 30 GLY C 34 0 SHEET 2 AA3 4 PHE C 15 ASP C 24 -1 N LEU C 22 O LEU C 31 SHEET 3 AA3 4 ALA C 58 SER C 67 -1 O ASN C 64 N TRP C 19 SHEET 4 AA3 4 SER C 101 GLU C 110 -1 O SER C 107 N ARG C 61 SHEET 1 AA4 5 GLU C 44 PRO C 50 0 SHEET 2 AA4 5 LEU C 138 VAL C 150 1 O PHE C 148 N VAL C 49 SHEET 3 AA4 5 VAL C 127 ASP C 135 -1 N PHE C 133 O VAL C 140 SHEET 4 AA4 5 MET C 71 PHE C 82 -1 N GLU C 77 O LYS C 132 SHEET 5 AA4 5 GLN C 85 VAL C 97 -1 O GLN C 85 N PHE C 82 LINK SG CMT D 855 C1 GER D 901 1555 1555 1.81 LINK C THR E 854 N CMT E 855 1555 1555 1.58 LINK SG CMT E 855 C1 GER E 901 1555 1555 1.82 SITE 1 AC1 7 MET A 20 SER A 39 GLN A 78 ILE A 129 SITE 2 AC1 7 THR A 131 PHE A 133 CMT D 855 SITE 1 AC2 4 SER C 39 GLN C 78 ILE C 129 CMT E 855 CRYST1 77.710 81.430 118.530 90.00 90.00 90.00 C 2 2 21 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 0.012868 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012280 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008437 0.00000