HEADER HYDROLASE 21-JAN-14 4OJX TITLE CRYSTAL STRUCTURE OF YEAST PHOSPHODIESTERASE-1 IN COMPLEX WITH GMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3',5'-CYCLIC-NUCLEOTIDE PHOSPHODIESTERASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PDEASE 1,3':5'-CNP,LOW-AFFINITY CAMP PHOSPHODIESTERASE; COMPND 5 EC: 3.1.4.17; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_TAXID: 559292; SOURCE 4 STRAIN: ATCC 204508 / S288C; SOURCE 5 GENE: PDE1, YGL248W, NRB369; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS PHOSPHODIESTERASE, CGMP AND CAMP, YEAST PDE, DUAL SPECIFICITY, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.TIAN,W.CUI,M.HUANG,H.ROBINSON,Y.WAN,Y.WANG,H.KE REVDAT 4 28-FEB-24 4OJX 1 REMARK REVDAT 3 20-APR-22 4OJX 1 COMPND SOURCE REMARK HET REVDAT 3 2 1 HETNAM FORMUL LINK SITE REVDAT 3 3 1 ATOM REVDAT 2 01-JUL-15 4OJX 1 JRNL REVDAT 1 03-DEC-14 4OJX 0 JRNL AUTH Y.TIAN,W.CUI,M.HUANG,H.ROBINSON,Y.WAN,Y.WANG,H.KE JRNL TITL DUAL SPECIFICITY AND NOVEL STRUCTURAL FOLDING OF YEAST JRNL TITL 2 PHOSPHODIESTERASE-1 FOR HYDROLYSIS OF SECOND MESSENGERS JRNL TITL 3 CYCLIC ADENOSINE AND GUANOSINE 3',5'-MONOPHOSPHATE. JRNL REF BIOCHEMISTRY V. 53 4938 2014 JRNL REFN ISSN 0006-2960 JRNL PMID 25050706 JRNL DOI 10.1021/BI500406H REMARK 2 REMARK 2 RESOLUTION. 1.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 93308 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4910 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) : 1.31 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.34 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6318 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE SET COUNT : 317 REMARK 3 BIN FREE R VALUE : 0.2990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2913 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 215 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.06000 REMARK 3 B33 (A**2) : -0.06000 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): 0.050 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.044 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.024 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.215 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.966 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3021 ; 0.008 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4087 ; 1.250 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 361 ; 6.431 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 135 ;36.912 ;24.444 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 537 ;10.344 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;18.110 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 460 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2242 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 3021 ; 2.588 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 60 ;14.527 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3103 ; 6.219 ; 5.000 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4OJX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084586. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-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 : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.05 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 98268 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.310 REMARK 200 RESOLUTION RANGE LOW (A) : 34.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: 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 (%): 49.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE NATIVE CRYSTAL OF YPDE1 (6 MG/ML) REMARK 280 WAS GROWN BY HANGING DROP AGAINST A BUFFER OF 20 MM HEPES PH 7.5, REMARK 280 5% PEG3350, 40 MM LI SULFATE, AND 12% MPD AT ROOM TEMPERATURE, REMARK 280 OR A SIMILAR BUFFER BUT 15% GLYCEROL AND 20% MPD, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 65.41800 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 65.41800 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 36.83700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.58100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.83700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.58100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 65.41800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.83700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 42.58100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 65.41800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.83700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 42.58100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: 6620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -65.41800 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 ARG A 55 REMARK 465 ASN A 56 REMARK 465 GLU A 57 REMARK 465 ASN A 58 REMARK 465 GLU A 59 REMARK 465 GLY A 60 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 A 569 O HOH A 708 2.14 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 HIS A 160 CG HIS A 160 CD2 0.054 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 ARG A 29 -35.56 75.87 REMARK 500 ASP A 39 176.90 64.69 REMARK 500 SER A 67 -66.29 -139.74 REMARK 500 PHE A 68 17.95 83.24 REMARK 500 TYR A 69 -114.84 -110.15 REMARK 500 LEU A 173 -59.80 -121.33 REMARK 500 HIS A 213 49.31 -147.07 REMARK 500 ARG A 250 -85.36 -18.14 REMARK 500 SER A 286 95.70 9.15 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 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 128 NE2 REMARK 620 2 HIS A 130 ND1 90.6 REMARK 620 3 HIS A 213 NE2 93.3 95.5 REMARK 620 4 ASP A 244 OD2 88.3 170.1 94.4 REMARK 620 5 5GP A 402 O2P 173.6 95.7 87.2 85.3 REMARK 620 6 HOH A 501 O 96.1 102.0 160.0 68.4 81.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 404 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 132 OD2 REMARK 620 2 HIS A 133 NE2 84.8 REMARK 620 3 ASP A 244 OD2 159.2 94.2 REMARK 620 4 HIS A 326 NE2 98.9 110.9 100.9 REMARK 620 5 5GP A 402 O3P 87.5 162.6 87.5 85.7 REMARK 620 6 HOH A 501 O 88.8 93.3 70.5 155.1 70.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5GP A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OJV RELATED DB: PDB DBREF 4OJX A 1 369 UNP P22434 PDE1_YEAST 1 369 SEQRES 1 A 369 MET VAL VAL PHE GLU ILE THR ILE LEU GLY ALA ASN GLY SEQRES 2 A 369 GLY PRO THR GLU TYR GLY THR GLN CYS PHE ILE LEU LYS SEQRES 3 A 369 PRO ALA ARG THR GLU ASP PRO GLU LEU ILE ALA VAL ASP SEQRES 4 A 369 GLY GLY ALA GLY MET TYR GLN LEU ARG GLU MET LEU VAL SEQRES 5 A 369 GLN GLY ARG ASN GLU ASN GLU GLY ASP ASP GLU LEU VAL SEQRES 6 A 369 PRO SER PHE TYR GLU HIS ASP ARG GLU PRO ILE GLU PHE SEQRES 7 A 369 PHE ILE ASP SER LYS LEU ASN ILE GLN LYS GLY LEU SER SEQRES 8 A 369 LYS SER LEU LEU GLN SER LEU LYS ARG GLN GLY GLU HIS SEQRES 9 A 369 PHE GLU SER ALA ASN THR MET LYS LYS THR TYR GLU VAL SEQRES 10 A 369 PHE GLN GLY ILE THR ASP TYR TYR ILE THR HIS PRO HIS SEQRES 11 A 369 LEU ASP HIS ILE SER GLY LEU VAL VAL ASN SER PRO SER SEQRES 12 A 369 ILE TYR GLU GLN GLU ASN SER LYS LYS LYS THR ILE TRP SEQRES 13 A 369 GLY LEU PRO HIS THR ILE ASP VAL LEU GLN LYS HIS VAL SEQRES 14 A 369 PHE ASN ASP LEU ILE TRP PRO ASP LEU THR ALA GLU ARG SEQRES 15 A 369 SER ARG LYS LEU LYS LEU LYS CYS LEU ASN PRO LYS GLU SEQRES 16 A 369 VAL GLN LYS CYS THR ILE PHE PRO TRP ASP VAL ILE PRO SEQRES 17 A 369 PHE LYS VAL HIS HIS GLY ILE GLY VAL LYS THR GLY ALA SEQRES 18 A 369 PRO VAL TYR SER THR PHE TYR ILE PHE ARG ASP ARG LYS SEQRES 19 A 369 SER LYS ASP CYS ILE ILE VAL CYS GLY ASP VAL GLU GLN SEQRES 20 A 369 ASP ARG ARG GLU SER GLU GLU SER LEU LEU GLU GLU PHE SEQRES 21 A 369 TRP SER TYR VAL ALA GLU ASN ILE PRO LEU VAL HIS LEU SEQRES 22 A 369 LYS GLY ILE LEU VAL GLU CYS SER CYS PRO LEU SER SER SEQRES 23 A 369 LYS PRO GLU GLN LEU TYR GLY HIS LEU SER PRO ILE TYR SEQRES 24 A 369 LEU ILE ASN GLU LEU SER ASN LEU ASN THR LEU TYR ASN SEQRES 25 A 369 SER SER LYS GLY LEU SER GLY LEU ASN VAL ILE VAL THR SEQRES 26 A 369 HIS VAL LYS SER THR PRO ALA LYS ARG ASP PRO ARG LEU SEQRES 27 A 369 THR ILE LEU GLU GLU LEU ARG PHE LEU ALA GLU GLU ARG SEQRES 28 A 369 ASN LEU GLY ASP LEU ARG ILE SER ILE ALA LEU GLU GLY SEQRES 29 A 369 HIS THR LEU PHE LEU HET MPD A 401 8 HET 5GP A 402 24 HET ZN A 403 1 HET ZN A 404 1 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION FORMUL 2 MPD C6 H14 O2 FORMUL 3 5GP C10 H14 N5 O8 P FORMUL 4 ZN 2(ZN 2+) FORMUL 6 HOH *215(H2 O) HELIX 1 1 GLY A 43 GLY A 54 1 12 HELIX 2 2 GLU A 77 ILE A 80 5 4 HELIX 3 3 SER A 91 SER A 97 1 7 HELIX 4 4 GLN A 101 ALA A 108 1 8 HELIX 5 5 ASN A 109 GLY A 120 1 12 HELIX 6 6 HIS A 130 HIS A 133 5 4 HELIX 7 7 ILE A 134 SER A 141 1 8 HELIX 8 8 PRO A 142 GLU A 146 5 5 HELIX 9 9 LEU A 158 VAL A 169 1 12 HELIX 10 10 ASP A 177 GLU A 181 5 5 HELIX 11 11 SER A 255 ILE A 268 1 14 HELIX 12 12 PRO A 269 VAL A 271 5 3 HELIX 13 13 LYS A 287 TYR A 292 1 6 HELIX 14 14 SER A 296 ASN A 312 1 17 HELIX 15 15 ASP A 335 ARG A 351 1 17 SHEET 1 A 8 ILE A 86 LYS A 88 0 SHEET 2 A 8 HIS A 365 PHE A 368 -1 O THR A 366 N GLN A 87 SHEET 3 A 8 PHE A 4 GLY A 10 -1 N ILE A 8 O HIS A 365 SHEET 4 A 8 CYS A 22 PRO A 27 -1 O ILE A 24 N THR A 7 SHEET 5 A 8 LEU A 35 VAL A 38 -1 O VAL A 38 N PHE A 23 SHEET 6 A 8 ILE A 121 TYR A 125 1 O ASP A 123 N ALA A 37 SHEET 7 A 8 LYS A 153 GLY A 157 1 O TRP A 156 N TYR A 124 SHEET 8 A 8 LEU A 186 CYS A 190 1 O LYS A 187 N ILE A 155 SHEET 1 B 2 LEU A 64 PRO A 66 0 SHEET 2 B 2 ARG A 73 PRO A 75 -1 O GLU A 74 N VAL A 65 SHEET 1 C 7 GLN A 197 LYS A 198 0 SHEET 2 C 7 TRP A 204 ILE A 215 -1 O VAL A 206 N GLN A 197 SHEET 3 C 7 PRO A 222 ASP A 232 -1 O VAL A 223 N HIS A 213 SHEET 4 C 7 CYS A 238 CYS A 242 -1 O VAL A 241 N TYR A 228 SHEET 5 C 7 LEU A 273 GLU A 279 1 O LEU A 277 N ILE A 240 SHEET 6 C 7 ASN A 321 THR A 325 1 O ILE A 323 N ILE A 276 SHEET 7 C 7 ARG A 357 ILE A 360 1 O SER A 359 N VAL A 324 LINK NE2 HIS A 128 ZN ZN A 403 1555 1555 2.18 LINK ND1 HIS A 130 ZN ZN A 403 1555 1555 2.17 LINK OD2 ASP A 132 ZN ZN A 404 1555 1555 2.15 LINK NE2 HIS A 133 ZN ZN A 404 1555 1555 2.11 LINK NE2 HIS A 213 ZN ZN A 403 1555 1555 2.14 LINK OD2 ASP A 244 ZN ZN A 403 1555 1555 2.24 LINK OD2 ASP A 244 ZN ZN A 404 1555 1555 2.12 LINK NE2 HIS A 326 ZN ZN A 404 1555 1555 2.10 LINK O2P 5GP A 402 ZN ZN A 403 1555 1555 2.21 LINK O3P 5GP A 402 ZN ZN A 404 1555 1555 2.31 LINK ZN ZN A 403 O HOH A 501 1555 1555 2.00 LINK ZN ZN A 404 O HOH A 501 1555 1555 2.01 CISPEP 1 GLY A 14 PRO A 15 0 6.60 SITE 1 AC1 7 ASN A 12 PRO A 66 SER A 67 TYR A 69 SITE 2 AC1 7 SER A 329 ARG A 337 HOH A 599 SITE 1 AC2 19 HIS A 130 ASP A 132 TYR A 145 TRP A 175 SITE 2 AC2 19 PRO A 176 HIS A 213 VAL A 217 ASP A 244 SITE 3 AC2 19 GLU A 289 HIS A 294 HIS A 326 LYS A 328 SITE 4 AC2 19 ZN A 403 ZN A 404 HOH A 501 HOH A 515 SITE 5 AC2 19 HOH A 541 HOH A 607 HOH A 706 SITE 1 AC3 7 HIS A 128 HIS A 130 HIS A 213 ASP A 244 SITE 2 AC3 7 5GP A 402 ZN A 404 HOH A 501 SITE 1 AC4 7 ASP A 132 HIS A 133 ASP A 244 HIS A 326 SITE 2 AC4 7 5GP A 402 ZN A 403 HOH A 501 CRYST1 73.674 85.162 130.836 90.00 90.00 90.00 C 2 2 21 8 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 0.013573 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011742 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007643 0.00000