HEADER SIGNALING PROTEIN 20-JUN-16 5KJZ TITLE CO-CRYSTAL STRUCTURE OF PKA RI ALPHA CNB-B MUTANT (G316R/A336T) WITH TITLE 2 CGMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-DEPENDENT PROTEIN KINASE TYPE I-ALPHA REGULATORY COMPND 3 SUBUNIT; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: TISSUE-SPECIFIC EXTINGUISHER 1,TSE1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PRKAR1A, PKR1, PRKAR1, TSE1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TP2000 DELTA CYA KEYWDS CYCLIC NUCLEOTIDE, CAMP-DEPENDENT PROTEIN KINASE, NUCLEOTIDE KEYWDS 2 SELECTIVITY, CYCLIC NUCLEOTIDE BINDING DOMAIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.LORENZ,E.MOON,J.J.KIM,G.Y.HUANG,C.KIM,F.W.HERBERG REVDAT 7 06-MAR-24 5KJZ 1 REMARK REVDAT 6 25-DEC-19 5KJZ 1 REMARK REVDAT 5 01-NOV-17 5KJZ 1 REMARK REVDAT 4 20-SEP-17 5KJZ 1 REMARK REVDAT 3 02-AUG-17 5KJZ 1 TITLE REVDAT 2 19-JUL-17 5KJZ 1 JRNL REVDAT 1 28-JUN-17 5KJZ 0 JRNL AUTH R.LORENZ,E.W.MOON,J.J.KIM,S.H.SCHMIDT,B.SANKARAN, JRNL AUTH 2 I.V.PAVLIDIS,C.KIM,F.W.HERBERG JRNL TITL MUTATIONS OF PKA CYCLIC NUCLEOTIDE-BINDING DOMAINS REVEAL JRNL TITL 2 NOVEL ASPECTS OF CYCLIC NUCLEOTIDE SELECTIVITY. JRNL REF BIOCHEM. J. V. 474 2389 2017 JRNL REFN ESSN 1470-8728 JRNL PMID 28583991 JRNL DOI 10.1042/BCJ20160969 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 34711 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1741 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 24.2684 - 3.0829 0.99 2957 157 0.1578 0.1853 REMARK 3 2 3.0829 - 2.4477 1.00 2847 150 0.1688 0.1948 REMARK 3 3 2.4477 - 2.1385 1.00 2824 148 0.1528 0.1892 REMARK 3 4 2.1385 - 1.9431 1.00 2803 148 0.1443 0.1645 REMARK 3 5 1.9431 - 1.8039 1.00 2797 147 0.1467 0.1800 REMARK 3 6 1.8039 - 1.6975 1.00 2768 146 0.1433 0.1936 REMARK 3 7 1.6975 - 1.6125 1.00 2775 146 0.1285 0.1413 REMARK 3 8 1.6125 - 1.5424 1.00 2748 144 0.1205 0.1578 REMARK 3 9 1.5424 - 1.4830 1.00 2777 147 0.1242 0.1590 REMARK 3 10 1.4830 - 1.4318 1.00 2738 144 0.1323 0.1671 REMARK 3 11 1.4318 - 1.3871 0.97 2671 141 0.1325 0.1891 REMARK 3 12 1.3871 - 1.3474 0.83 2265 123 0.1415 0.1791 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1274 REMARK 3 ANGLE : 1.098 1728 REMARK 3 CHIRALITY : 0.085 193 REMARK 3 PLANARITY : 0.005 222 REMARK 3 DIHEDRAL : 22.113 505 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5KJZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000222329. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34711 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.347 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.21400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.04 M CRITIC ACID, 0.06 M BIS-TRIS REMARK 280 PROPANE, 24% W/V PEG 1500, 20% V/V GLYCEROL, PH 6.4, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 14.73050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.98000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.89000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.98000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.73050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.89000 REMARK 290 SMTRY3 4 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 300 REMARK: MONOMER ACCORDING TO GEL FILTRATION 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLY A 232 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 LYS A 244 CG CD CE NZ REMARK 470 LYS A 252 CD CE NZ REMARK 470 LYS A 346 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 692 O HOH A 720 4445 2.18 REMARK 500 O HOH A 517 O HOH A 617 1655 2.19 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 SER A 321 -2.28 76.78 REMARK 500 SER A 321 -1.95 76.66 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 GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues PCG A 401 and GOL A REMARK 800 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KJY RELATED DB: PDB REMARK 900 RELATED ID: 5KJX RELATED DB: PDB DBREF 5KJZ A 234 381 UNP P10644 KAP0_HUMAN 234 381 SEQADV 5KJZ GLY A 232 UNP P10644 EXPRESSION TAG SEQADV 5KJZ SER A 233 UNP P10644 EXPRESSION TAG SEQADV 5KJZ ARG A 316 UNP P10644 GLY 316 ENGINEERED MUTATION SEQADV 5KJZ THR A 336 UNP P10644 ALA 336 ENGINEERED MUTATION SEQRES 1 A 150 GLY SER ILE LEU MET GLY SER THR LEU ARG LYS ARG LYS SEQRES 2 A 150 MET TYR GLU GLU PHE LEU SER LYS VAL SER ILE LEU GLU SEQRES 3 A 150 SER LEU ASP LYS TRP GLU ARG LEU THR VAL ALA ASP ALA SEQRES 4 A 150 LEU GLU PRO VAL GLN PHE GLU ASP GLY GLN LYS ILE VAL SEQRES 5 A 150 VAL GLN GLY GLU PRO GLY ASP GLU PHE PHE ILE ILE LEU SEQRES 6 A 150 GLU GLY SER ALA ALA VAL LEU GLN ARG ARG SER GLU ASN SEQRES 7 A 150 GLU GLU PHE VAL GLU VAL ARG ARG LEU GLY PRO SER ASP SEQRES 8 A 150 TYR PHE GLY GLU ILE ALA LEU LEU MET ASN ARG PRO ARG SEQRES 9 A 150 THR ALA THR VAL VAL ALA ARG GLY PRO LEU LYS CYS VAL SEQRES 10 A 150 LYS LEU ASP ARG PRO ARG PHE GLU ARG VAL LEU GLY PRO SEQRES 11 A 150 CYS SER ASP ILE LEU LYS ARG ASN ILE GLN GLN TYR ASN SEQRES 12 A 150 SER PHE VAL SER LEU SER VAL HET PCG A 401 23 HET GOL A 402 6 HET GOL A 403 6 HETNAM PCG CYCLIC GUANOSINE MONOPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 PCG C10 H12 N5 O7 P FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *236(H2 O) HELIX 1 AA1 MET A 236 SER A 251 1 16 HELIX 2 AA2 LYS A 252 GLU A 257 5 6 HELIX 3 AA3 ASP A 260 LEU A 271 1 12 HELIX 4 AA4 GLY A 325 MET A 331 1 7 HELIX 5 AA5 ARG A 352 LEU A 359 1 8 HELIX 6 AA6 CYS A 362 GLN A 371 1 10 SHEET 1 AA1 4 GLU A 272 PHE A 276 0 SHEET 2 AA1 4 THR A 338 ASP A 351 -1 O CYS A 347 N VAL A 274 SHEET 3 AA1 4 GLU A 291 GLN A 304 -1 N LEU A 303 O THR A 338 SHEET 4 AA1 4 VAL A 313 LEU A 318 -1 O ARG A 316 N VAL A 302 SHEET 1 AA2 4 LYS A 281 VAL A 283 0 SHEET 2 AA2 4 THR A 338 ASP A 351 -1 O VAL A 339 N ILE A 282 SHEET 3 AA2 4 GLU A 291 GLN A 304 -1 N LEU A 303 O THR A 338 SHEET 4 AA2 4 TYR A 323 PHE A 324 -1 O PHE A 324 N PHE A 293 LINK N2 PCG A 401 O1 GOL A 402 1555 1555 1.31 SITE 1 AC1 9 ARG A 241 GLY A 360 PRO A 361 SER A 363 SITE 2 AC1 9 ASP A 364 HOH A 507 HOH A 523 HOH A 635 SITE 3 AC1 9 HOH A 648 SITE 1 AC2 20 GLN A 304 VAL A 315 ARG A 316 PHE A 324 SITE 2 AC2 20 GLY A 325 GLU A 326 ILE A 327 ALA A 328 SITE 3 AC2 20 ARG A 335 THR A 336 ALA A 337 ILE A 370 SITE 4 AC2 20 TYR A 373 ASN A 374 SER A 378 LEU A 379 SITE 5 AC2 20 SER A 380 VAL A 381 HOH A 543 HOH A 587 CRYST1 29.461 67.780 77.960 90.00 90.00 90.00 P 21 21 21 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 0.033943 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014754 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012827 0.00000