HEADER LIPID BINDING PROTEIN 02-DEC-15 5F2U TITLE STRUCTURE OF FULLY MODIFIED FARNESYLATED INPP5E PEPTIDE IN COMPLEX TITLE 2 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, B; COMPND 5 SYNONYM: GMP-PDE DELTA,PROTEIN P17; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 5-PHOSPHATASE, S- COMPND 9 FARNESYL-L-CYSTEINE METHYL ESTER; COMPND 10 CHAIN: C, D; COMPND 11 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 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS LIPID BINDING PROTEIN, IMMUNOGLOBULIN-LIKE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.K.FANSA,S.ISAMIL,A.WITTINGHOFER REVDAT 5 10-JAN-24 5F2U 1 REMARK LINK REVDAT 4 07-JUL-21 5F2U 1 COMPND SOURCE REMARK DBREF REVDAT 4 2 1 SEQRES LINK SITE ATOM REVDAT 3 30-JUN-21 5F2U 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 SEQRES LINK SITE ATOM REVDAT 2 20-APR-16 5F2U 1 JRNL REVDAT 1 13-APR-16 5F2U 0 JRNL AUTH E.K.FANSA,S.K.KOESLING,E.ZENT,A.WITTINGHOFER,S.ISMAIL JRNL TITL PDE6DELTA-MEDIATED SORTING OF INPP5E INTO THE CILIUM IS JRNL TITL 2 DETERMINED BY CARGO-CARRIER AFFINITY. JRNL REF NAT COMMUN V. 7 11366 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27063844 JRNL DOI 10.1038/NCOMMS11366 REMARK 2 REMARK 2 RESOLUTION. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 30251 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1593 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2170 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 115 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2496 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.09000 REMARK 3 B22 (A**2) : 1.37000 REMARK 3 B33 (A**2) : -0.28000 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): 0.118 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.115 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.710 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2576 ; 0.020 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2500 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3462 ; 2.011 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5752 ; 0.854 ; 3.007 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 301 ; 6.510 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;39.564 ;24.098 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 471 ;13.632 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;11.662 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 377 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2843 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 599 ; 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): 1222 ; 2.980 ; 3.041 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1220 ; 2.969 ; 3.039 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1517 ; 3.728 ; 4.537 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 5F2U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000215878. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 1.007 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 : 30251 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 19.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.390 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.58 REMARK 200 R MERGE FOR SHELL (I) : 0.67200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.090 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 (%): 52.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M SODIUM MALONATE, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, 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 58.60500 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 58.60500 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 38.73500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.60000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.73500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.60000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.60500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.73500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.60000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.60500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.73500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.60000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 B 2 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 CMT C 644 OXT REMARK 470 CMT D 644 OXT 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 ILE C 643 C CMT C 644 N 0.207 REMARK 500 ILE D 643 C CMT D 644 N 0.223 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 ASP A 24 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 144 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 146 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ILE D 643 O - C - N ANGL. DEV. = -12.3 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 LYS A 73 77.21 -152.19 REMARK 500 ASP A 136 -104.76 57.61 REMARK 500 ASP B 37 94.11 -69.38 REMARK 500 ASP B 136 -106.46 56.86 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 ILE D 643 11.30 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 Di-peptide CMT C 701 and ILE C REMARK 800 643 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues CMT C 701 and FAR C REMARK 800 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues CMT D 701 and FAR D REMARK 800 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide CMT D 701 and ILE D REMARK 800 643 DBREF 5F2U A 2 150 UNP O43924 PDE6D_HUMAN 2 150 DBREF 5F2U B 2 150 UNP O43924 PDE6D_HUMAN 2 150 DBREF 5F2U C 640 644 PDB 5F2U 5F2U 640 644 DBREF 5F2U D 640 644 PDB 5F2U 5F2U 640 644 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 B 149 SER ALA LYS ASP GLU ARG ALA ARG GLU ILE LEU ARG GLY SEQRES 2 B 149 PHE LYS LEU ASN TRP MET ASN LEU ARG ASP ALA GLU THR SEQRES 3 B 149 GLY LYS ILE LEU TRP GLN GLY THR GLU ASP LEU SER VAL SEQRES 4 B 149 PRO GLY VAL GLU HIS GLU ALA ARG VAL PRO LYS LYS ILE SEQRES 5 B 149 LEU LYS CYS LYS ALA VAL SER ARG GLU LEU ASN PHE SER SEQRES 6 B 149 SER THR GLU GLN MET GLU LYS PHE ARG LEU GLU GLN LYS SEQRES 7 B 149 VAL TYR PHE LYS GLY GLN CYS LEU GLU GLU TRP PHE PHE SEQRES 8 B 149 GLU PHE GLY PHE VAL ILE PRO ASN SER THR ASN THR TRP SEQRES 9 B 149 GLN SER LEU ILE GLU ALA ALA PRO GLU SER GLN MET MET SEQRES 10 B 149 PRO ALA SER VAL LEU THR GLY ASN VAL ILE ILE GLU THR SEQRES 11 B 149 LYS PHE PHE ASP ASP ASP LEU LEU VAL SER THR SER ARG SEQRES 12 B 149 VAL ARG LEU PHE TYR VAL SEQRES 1 C 5 SER SER THR ILE CMT SEQRES 1 D 5 SER SER THR ILE CMT HET CMT C 644 7 HET CMT D 644 7 HET FAR C 701 15 HET FAR D 701 15 HETNAM CMT O-METHYLCYSTEINE HETNAM FAR FARNESYL FORMUL 3 CMT 2(C4 H9 N O2 S) FORMUL 5 FAR 2(C15 H26) FORMUL 7 HOH *89(H2 O) HELIX 1 AA1 SER A 2 GLY A 14 1 13 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 LYS B 4 GLY B 14 1 11 HELIX 6 AA6 LYS B 52 CYS B 56 5 5 HELIX 7 AA7 PRO B 113 MET B 117 5 5 HELIX 8 AA8 PRO B 119 THR B 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 LEU A 31 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 SER A 107 N ARG A 61 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 VAL A 49 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 GLU A 77 O LYS A 132 SHEET 5 AA2 5 GLN A 85 VAL A 97 -1 O TRP A 90 N GLN A 78 SHEET 1 AA3 4 ILE B 30 GLY B 34 0 SHEET 2 AA3 4 PHE B 15 ASP B 24 -1 N LEU B 22 O LEU B 31 SHEET 3 AA3 4 ALA B 58 SER B 67 -1 O ASN B 64 N TRP B 19 SHEET 4 AA3 4 SER B 101 GLU B 110 -1 O SER B 107 N ARG B 61 SHEET 1 AA4 5 GLU B 44 PRO B 50 0 SHEET 2 AA4 5 LEU B 138 VAL B 150 1 O PHE B 148 N VAL B 49 SHEET 3 AA4 5 VAL B 127 ASP B 135 -1 N PHE B 133 O VAL B 140 SHEET 4 AA4 5 MET B 71 PHE B 82 -1 N GLU B 77 O LYS B 132 SHEET 5 AA4 5 GLN B 85 VAL B 97 -1 O TRP B 90 N GLN B 78 LINK C ILE C 643 N CMT C 644 1555 1555 1.54 LINK SG CMT C 644 C1 FAR C 701 1555 1555 1.82 LINK C ILE D 643 N CMT D 644 1555 1555 1.56 LINK SG CMT D 644 C1 FAR D 701 1555 1555 1.83 SITE 1 AC1 9 ILE A 53 LEU A 54 CYS A 56 VAL A 80 SITE 2 AC1 9 ALA A 111 TYR A 149 SER C 641 THR C 642 SITE 3 AC1 9 FAR C 701 SITE 1 AC2 8 ILE A 53 CYS A 56 GLN A 78 ALA A 111 SITE 2 AC2 8 THR A 131 TYR A 149 SER C 641 ILE C 643 SITE 1 AC3 7 ILE B 53 CYS B 56 VAL B 59 GLN B 78 SITE 2 AC3 7 THR B 131 SER D 641 ILE D 643 SITE 1 AC4 8 ILE B 53 LEU B 54 CYS B 56 VAL B 59 SITE 2 AC4 8 TYR B 149 SER D 641 THR D 642 FAR D 701 CRYST1 77.470 81.200 117.210 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 0.012908 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012315 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008532 0.00000