HEADER MEMBRANE PROTEIN 23-MAY-03 1PF0 OBSLTE 26-OCT-04 1PF0 1VP6 TITLE M. LOTI ION CHANNEL CYLIC NUCLEOTIDE BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CNBD; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MESORHIZOBIUM LOTI; SOURCE 3 ORGANISM_COMMON: BACTERIA; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21-RP; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS DIMER HELICAL BUNDLE BETA BARREL CORE WITH CYCLIC AMP BOUND EXPDTA X-RAY DIFFRACTION AUTHOR G.M.CLAYTON,W.SILVERMAN,L.HEGINBOTHAM,J.M.CABRAL REVDAT 2 26-OCT-04 1PF0 1 OBSLTE REVDAT 1 28-SEP-04 1PF0 0 JRNL AUTH G.M.CLAYTON,W.SILVERMAN,L.HEGINBOTHAM,J.M.CABRAL JRNL TITL M. LOTI ION CHANNEL CYLIC NUCLEOTIDE BINDING DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 45010 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 SET) : 0.190 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2211 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5326 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 267 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1996 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 262 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.28000 REMARK 3 B22 (A**2) : 4.17000 REMARK 3 B33 (A**2) : -2.90000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.46000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.11 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : CNS BULK SOLVENT MODEL USED REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 39.27 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PF0 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAY-2003. REMARK 100 THE RCSB ID CODE IS RCSB019282. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-2002 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90590 REMARK 200 MONOCHROMATOR : SI(111) CRYSTALS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58881 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 33.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.17700 REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE/RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA ACETATE, LICL, AMMONIUM REMARK 280 SULPHATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,1/2+Y,-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 40.14600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 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 ALA A 351 REMARK 465 ALA A 352 REMARK 465 ALA A 353 REMARK 465 SER A 354 REMARK 465 ALA A 355 REMARK 465 ALA C 351 REMARK 465 ALA C 352 REMARK 465 ALA C 353 REMARK 465 SER C 354 REMARK 465 ALA C 355 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET C 272 CG MET C 272 SD -0.047 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASN A 286 N - CA - C ANGL. DEV. =-11.0 DEGREES REMARK 500 THR A 315 N - CA - C ANGL. DEV. = -9.9 DEGREES REMARK 500 THR A 316 N - CA - C ANGL. DEV. =-10.3 DEGREES REMARK 500 ASN C 286 N - CA - C ANGL. DEV. =-10.6 DEGREES REMARK 500 THR C 315 N - CA - C ANGL. DEV. = -8.4 DEGREES REMARK 500 THR C 316 N - CA - C ANGL. DEV. = -9.6 DEGREES REMARK 500 LEU C 320 N - CA - C ANGL. DEV. = -8.6 DEGREES DBREF 1PF0 A 218 355 GB 13472825 NP_104392 218 355 DBREF 1PF0 C 218 355 GB 13472825 NP_104392 218 355 SEQRES 1 A 138 VAL ARG ARG GLY ASP PHE VAL ARG ASN TRP GLN LEU VAL SEQRES 2 A 138 ALA ALA VAL PRO LEU PHE GLN LYS LEU GLY PRO ALA VAL SEQRES 3 A 138 LEU VAL GLU ILE VAL ARG ALA LEU ARG ALA ARG THR VAL SEQRES 4 A 138 PRO ALA GLY ALA VAL ILE CYS ARG ILE GLY GLU PRO GLY SEQRES 5 A 138 ASP ARG MET PHE PHE VAL VAL GLU GLY SER VAL SER VAL SEQRES 6 A 138 ALA THR PRO ASN PRO VAL GLU LEU GLY PRO GLY ALA PHE SEQRES 7 A 138 PHE GLY GLU MET ALA LEU ILE SER GLY GLU PRO ARG SER SEQRES 8 A 138 ALA THR VAL SER ALA ALA THR THR VAL SER LEU LEU SER SEQRES 9 A 138 LEU HIS SER ALA ASP PHE GLN MET LEU CYS SER SER SER SEQRES 10 A 138 PRO GLU ILE ALA GLU ILE PHE ARG LYS THR ALA LEU GLU SEQRES 11 A 138 ARG ARG GLY ALA ALA ALA SER ALA SEQRES 1 C 138 VAL ARG ARG GLY ASP PHE VAL ARG ASN TRP GLN LEU VAL SEQRES 2 C 138 ALA ALA VAL PRO LEU PHE GLN LYS LEU GLY PRO ALA VAL SEQRES 3 C 138 LEU VAL GLU ILE VAL ARG ALA LEU ARG ALA ARG THR VAL SEQRES 4 C 138 PRO ALA GLY ALA VAL ILE CYS ARG ILE GLY GLU PRO GLY SEQRES 5 C 138 ASP ARG MET PHE PHE VAL VAL GLU GLY SER VAL SER VAL SEQRES 6 C 138 ALA THR PRO ASN PRO VAL GLU LEU GLY PRO GLY ALA PHE SEQRES 7 C 138 PHE GLY GLU MET ALA LEU ILE SER GLY GLU PRO ARG SER SEQRES 8 C 138 ALA THR VAL SER ALA ALA THR THR VAL SER LEU LEU SER SEQRES 9 C 138 LEU HIS SER ALA ASP PHE GLN MET LEU CYS SER SER SER SEQRES 10 C 138 PRO GLU ILE ALA GLU ILE PHE ARG LYS THR ALA LEU GLU SEQRES 11 C 138 ARG ARG GLY ALA ALA ALA SER ALA HET BR 263 1 HET BR 264 1 HET BR 265 1 HET BR 266 1 HET BR 267 1 HET BR 268 1 HET BR 269 1 HET BR 270 1 HET BR 271 1 HET BR 272 1 HET BR 273 1 HET BR 274 1 HET BR 275 1 HET BR 276 1 HET BR 277 1 HET BR 278 1 HET AMP 301 22 HET AMP 302 22 HETNAM BR BROMIDE ION HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 3 BR 16(BR 1-) FORMUL 19 AMP 2(C10 H14 N5 O7 P) FORMUL 21 HOH *262(H2 O1) HELIX 1 1 ARG A 219 ALA A 231 1 13 HELIX 2 2 ALA A 232 LEU A 239 5 8 HELIX 3 3 GLY A 240 LEU A 251 1 12 HELIX 4 4 GLY A 297 GLY A 304 1 8 HELIX 5 5 SER A 324 SER A 334 1 11 HELIX 6 6 SER A 334 ARG A 349 1 16 HELIX 7 7 ARG C 219 ALA C 231 1 13 HELIX 8 8 ALA C 232 LEU C 239 5 8 HELIX 9 9 GLY C 240 LEU C 251 1 12 HELIX 10 10 GLY C 297 GLY C 304 1 8 HELIX 11 11 SER C 324 SER C 334 1 11 HELIX 12 12 SER C 334 GLY C 350 1 17 SHEET 1 A 4 ARG A 252 VAL A 256 0 SHEET 2 A 4 VAL A 317 HIS A 323 -1 O LEU A 319 N ARG A 254 SHEET 3 A 4 ARG A 271 GLU A 277 -1 N MET A 272 O LEU A 322 SHEET 4 A 4 PHE A 295 PHE A 296 -1 O PHE A 296 N PHE A 273 SHEET 1 B 4 VAL A 261 CYS A 263 0 SHEET 2 B 4 VAL A 311 ALA A 313 -1 O VAL A 311 N CYS A 263 SHEET 3 B 4 VAL A 280 VAL A 282 -1 N SER A 281 O SER A 312 SHEET 4 B 4 VAL A 288 LEU A 290 -1 O VAL A 288 N VAL A 282 SHEET 1 C 4 ARG C 252 VAL C 256 0 SHEET 2 C 4 VAL C 317 HIS C 323 -1 O LEU C 319 N ARG C 254 SHEET 3 C 4 ARG C 271 GLU C 277 -1 N GLU C 277 O SER C 318 SHEET 4 C 4 PHE C 295 PHE C 296 -1 O PHE C 296 N PHE C 273 SHEET 1 D 4 VAL C 261 CYS C 263 0 SHEET 2 D 4 VAL C 311 ALA C 313 -1 O VAL C 311 N CYS C 263 SHEET 3 D 4 VAL C 280 VAL C 282 -1 N SER C 281 O SER C 312 SHEET 4 D 4 VAL C 288 LEU C 290 -1 O VAL C 288 N VAL C 282 CRYST1 34.324 80.292 50.419 90.00 99.16 90.00 P 1 21 1 4 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 0.029134 0.000000 0.004698 0.00000 SCALE2 0.000000 0.012455 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020090 0.00000