HEADER TRANSFERASE/TRANSPORT PROTEIN 31-JAN-12 4DIN TITLE NOVEL LOCALIZATION AND QUATERNARY STRUCTURE OF THE PKA RI BETA TITLE 2 HOLOENZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PKA C-ALPHA; COMPND 5 EC: 2.7.11.11; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CAMP-DEPENDENT PROTEIN KINASE TYPE I-BETA REGULATORY COMPND 9 SUBUNIT; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PRKACA, PKACA; 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: PRKAR1B; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOFORM DIVERSITY, RIB2:C2 TETRAMERIC COMPLEX, TRANSFERASE-TRANSPORT KEYWDS 2 PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.ILOUZ,J.BUBIS,J.WU,Y.Y.YIM,M.S.DEAL,A.P.KORNEV,Y.MA,D.K.BLUMENTHAL, AUTHOR 2 S.S.TAYLOR REVDAT 3 13-SEP-23 4DIN 1 REMARK LINK REVDAT 2 12-DEC-12 4DIN 1 JRNL REVDAT 1 04-JUL-12 4DIN 0 JRNL AUTH R.ILOUZ,J.BUBIS,J.WU,Y.Y.YIM,M.S.DEAL,A.P.KORNEV,Y.MA, JRNL AUTH 2 D.K.BLUMENTHAL,S.S.TAYLOR JRNL TITL LOCALIZATION AND QUATERNARY STRUCTURE OF THE PKA RI BETA JRNL TITL 2 HOLOENZYME JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 12443 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22797896 JRNL DOI 10.1073/PNAS.1209538109 REMARK 2 REMARK 2 RESOLUTION. 3.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 WITH DEN REFINEMENT REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2517.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 67.7 REMARK 3 NUMBER OF REFLECTIONS : 9613 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.500 REMARK 3 FREE R VALUE TEST SET COUNT : 495 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.83 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 30.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 406 REMARK 3 BIN R VALUE (WORKING SET) : 0.3676 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 22 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5393 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 156.4 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 44.26900 REMARK 3 B22 (A**2) : 44.26900 REMARK 3 B33 (A**2) : -88.53900 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.003 REMARK 3 BOND ANGLES (DEGREES) : NULL 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) : 11.521; 15.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 17.819; 20.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 16.915; 20.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 23.637; 25.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 143.4 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4DIN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070376. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : GRAPHITE 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16198 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: PDB ENTRY 2QCS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 ACETATE PH 5.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.88200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 97.76400 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 48.88200 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 97.76400 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.88200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 97.76400 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 48.88200 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 97.76400 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: 5690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 1 REMARK 465 ASN A 2 REMARK 465 ALA A 3 REMARK 465 ALA A 4 REMARK 465 ALA A 5 REMARK 465 ALA A 6 REMARK 465 LYS A 7 REMARK 465 LYS A 8 REMARK 465 MET B -1 REMARK 465 ALA B 0 REMARK 465 SER B 1 REMARK 465 PRO B 2 REMARK 465 PRO B 3 REMARK 465 ALA B 4 REMARK 465 CYS B 5 REMARK 465 PRO B 6 REMARK 465 SER B 7 REMARK 465 GLU B 8 REMARK 465 GLU B 9 REMARK 465 ASP B 10 REMARK 465 GLU B 11 REMARK 465 GLU B 59 REMARK 465 ASN B 60 REMARK 465 ARG B 61 REMARK 465 GLN B 62 REMARK 465 ILE B 63 REMARK 465 LEU B 64 REMARK 465 ALA B 65 REMARK 465 ARG B 66 REMARK 465 GLN B 67 REMARK 465 LYS B 68 REMARK 465 SER B 69 REMARK 465 ASN B 70 REMARK 465 SER B 71 REMARK 465 GLN B 72 REMARK 465 SER B 73 REMARK 465 ASP B 74 REMARK 465 SER B 75 REMARK 465 HIS B 76 REMARK 465 ASP B 77 REMARK 465 GLU B 78 REMARK 465 GLU B 79 REMARK 465 VAL B 80 REMARK 465 VAL B 379 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 SER A 10 OG REMARK 470 GLU A 11 CG CD OE1 OE2 REMARK 470 LYS A 16 CG CD CE NZ REMARK 470 GLU A 17 CG CD OE1 OE2 REMARK 470 LYS A 21 CG CD CE NZ REMARK 470 GLU A 24 CG CD OE1 OE2 REMARK 470 ASP A 25 CG OD1 OD2 REMARK 470 LYS A 81 CD CE NZ REMARK 470 ARG A 93 CZ NH1 NH2 REMARK 470 LYS A 105 CD CE NZ REMARK 470 LYS A 254 CG CD CE NZ REMARK 470 ARG A 256 CD NE CZ NH1 NH2 REMARK 470 LYS A 309 CE NZ REMARK 470 LYS A 317 CG CD CE NZ REMARK 470 PHE A 318 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 319 CG CD CE NZ REMARK 470 GLU A 331 CG CD OE1 OE2 REMARK 470 GLU A 333 CG CD OE1 OE2 REMARK 470 GLU A 334 CG CD OE1 REMARK 470 LYS A 345 CG CD CE NZ REMARK 470 LYS B 14 CG CD CE NZ REMARK 470 LEU B 18 CG CD1 CD2 REMARK 470 TYR B 19 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 VAL B 20 CG1 CG2 REMARK 470 HIS B 23 CG ND1 CD2 CE1 NE2 REMARK 470 ILE B 25 CG1 CG2 CD1 REMARK 470 GLN B 26 CG CD OE1 NE2 REMARK 470 GLN B 27 CG CD OE1 NE2 REMARK 470 VAL B 28 CG1 CG2 REMARK 470 LEU B 29 CG CD1 CD2 REMARK 470 LYS B 30 CG CD CE NZ REMARK 470 ASP B 31 CG OD1 OD2 REMARK 470 CYS B 32 SG REMARK 470 CYS B 37 SG REMARK 470 ILE B 38 CG1 CG2 CD1 REMARK 470 SER B 39 OG REMARK 470 LYS B 40 CG CD CE NZ REMARK 470 GLU B 42 CG CD OE1 OE2 REMARK 470 ARG B 43 CG CD NE CZ NH1 NH2 REMARK 470 PRO B 44 CG CD REMARK 470 MET B 45 CG SD CE REMARK 470 LYS B 46 CG CD CE NZ REMARK 470 SER B 81 OG REMARK 470 THR B 83 OG1 CG2 REMARK 470 ASN B 86 CG OD1 ND2 REMARK 470 LYS B 90 CG CD CE NZ REMARK 470 LYS B 114 CD CE NZ REMARK 470 TYR B 120 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 121 CD CE NZ REMARK 470 LYS B 128 CE NZ REMARK 470 GLN B 177 CD OE1 NE2 REMARK 470 LYS B 279 CE NZ REMARK 470 THR B 378 OG1 CG2 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 PRO B 271 O CYS B 345 2.13 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 VAL B 272 CB - CA - C ANGL. DEV. = 14.2 DEGREES REMARK 500 GLN B 273 N - CA - CB ANGL. DEV. = 11.8 DEGREES REMARK 500 SER B 305 CB - CA - C ANGL. DEV. = 13.0 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 GLN A 12 -31.96 178.77 REMARK 500 SER A 14 -39.28 -34.41 REMARK 500 PRO A 33 -156.94 -65.85 REMARK 500 SER A 34 -80.50 -115.93 REMARK 500 GLN A 35 -173.89 80.87 REMARK 500 ASN A 36 -120.51 38.53 REMARK 500 THR A 37 -18.36 81.33 REMARK 500 ALA A 38 -162.57 158.74 REMARK 500 ASP A 41 -12.50 -49.35 REMARK 500 ILE A 46 -87.19 -58.98 REMARK 500 PHE A 54 -86.03 -116.19 REMARK 500 HIS A 62 130.27 -34.90 REMARK 500 GLU A 64 -77.89 -69.22 REMARK 500 ASN A 67 -172.70 -61.69 REMARK 500 ALA A 70 78.49 -117.59 REMARK 500 GLN A 96 0.36 -68.33 REMARK 500 PHE A 102 39.22 -96.60 REMARK 500 GLU A 107 -72.06 -72.12 REMARK 500 PHE A 110 -166.50 -167.14 REMARK 500 ASP A 112 -116.84 -131.37 REMARK 500 TYR A 164 -78.02 -64.69 REMARK 500 ARG A 165 51.46 71.93 REMARK 500 ASP A 166 23.84 -179.57 REMARK 500 ASP A 175 -138.18 -70.82 REMARK 500 GLN A 177 2.92 -65.19 REMARK 500 TYR A 179 -154.58 -103.68 REMARK 500 ASP A 184 102.02 51.22 REMARK 500 LYS A 189 146.28 -170.75 REMARK 500 LYS A 192 59.63 -101.75 REMARK 500 TRP A 196 -37.61 -131.34 REMARK 500 ASN A 216 -157.88 -132.34 REMARK 500 VAL A 255 126.36 -176.46 REMARK 500 ARG A 256 54.31 -100.46 REMARK 500 HIS A 260 -15.27 -143.60 REMARK 500 ARG A 270 -70.63 -57.93 REMARK 500 LEU A 273 32.17 -72.83 REMARK 500 THR A 278 -9.33 -57.88 REMARK 500 ASN A 283 -33.67 -140.32 REMARK 500 LEU A 284 -174.57 -59.37 REMARK 500 PRO A 316 -178.96 -60.07 REMARK 500 LYS A 319 57.79 -104.98 REMARK 500 ASN A 326 -7.95 -56.54 REMARK 500 PHE A 327 -149.68 -98.81 REMARK 500 GLU A 334 106.29 -42.87 REMARK 500 CYS A 343 83.54 55.05 REMARK 500 LYS B 14 -87.60 -173.83 REMARK 500 GLU B 17 -6.45 -157.80 REMARK 500 LEU B 18 100.79 -55.52 REMARK 500 HIS B 23 29.95 174.16 REMARK 500 ILE B 25 -106.27 -108.37 REMARK 500 REMARK 500 THIS ENTRY HAS 107 RAMACHANDRAN OUTLIERS. 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 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 171 OD1 REMARK 620 2 ASP A 184 OD2 71.5 REMARK 620 3 ATP A 400 O2A 100.3 101.3 REMARK 620 4 ATP A 400 O3G 125.6 60.9 112.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 184 OD1 REMARK 620 2 ASP A 184 OD2 53.2 REMARK 620 3 ATP A 400 O3G 122.2 71.2 REMARK 620 4 ATP A 400 O2B 76.0 84.9 85.6 REMARK 620 5 ATP A 400 O2G 151.1 125.0 56.9 75.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QCS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RIA:C HOLOENZYME OF CAMP-DEPENDENT PROTEIN REMARK 900 KINASE DBREF 4DIN A 1 350 UNP P05132 KAPCA_MOUSE 2 351 DBREF 4DIN B -1 379 UNP P31321 KAP1_HUMAN 1 381 SEQRES 1 A 350 GLY ASN ALA ALA ALA ALA LYS LYS GLY SER GLU GLN GLU SEQRES 2 A 350 SER VAL LYS GLU PHE LEU ALA LYS ALA LYS GLU ASP PHE SEQRES 3 A 350 LEU LYS LYS TRP GLU THR PRO SER GLN ASN THR ALA GLN SEQRES 4 A 350 LEU ASP GLN PHE ASP ARG ILE LYS THR LEU GLY THR GLY SEQRES 5 A 350 SER PHE GLY ARG VAL MET LEU VAL LYS HIS LYS GLU SER SEQRES 6 A 350 GLY ASN HIS TYR ALA MET LYS ILE LEU ASP LYS GLN LYS SEQRES 7 A 350 VAL VAL LYS LEU LYS GLN ILE GLU HIS THR LEU ASN GLU SEQRES 8 A 350 LYS ARG ILE LEU GLN ALA VAL ASN PHE PRO PHE LEU VAL SEQRES 9 A 350 LYS LEU GLU PHE SER PHE LYS ASP ASN SER ASN LEU TYR SEQRES 10 A 350 MET VAL MET GLU TYR VAL ALA GLY GLY GLU MET PHE SER SEQRES 11 A 350 HIS LEU ARG ARG ILE GLY ARG PHE SER GLU PRO HIS ALA SEQRES 12 A 350 ARG PHE TYR ALA ALA GLN ILE VAL LEU THR PHE GLU TYR SEQRES 13 A 350 LEU HIS SER LEU ASP LEU ILE TYR ARG ASP LEU LYS PRO SEQRES 14 A 350 GLU ASN LEU LEU ILE ASP GLN GLN GLY TYR ILE GLN VAL SEQRES 15 A 350 THR ASP PHE GLY PHE ALA LYS ARG VAL LYS GLY ARG THR SEQRES 16 A 350 TRP TPO LEU CYS GLY THR PRO GLU TYR LEU ALA PRO GLU SEQRES 17 A 350 ILE ILE LEU SER LYS GLY TYR ASN LYS ALA VAL ASP TRP SEQRES 18 A 350 TRP ALA LEU GLY VAL LEU ILE TYR GLU MET ALA ALA GLY SEQRES 19 A 350 TYR PRO PRO PHE PHE ALA ASP GLN PRO ILE GLN ILE TYR SEQRES 20 A 350 GLU LYS ILE VAL SER GLY LYS VAL ARG PHE PRO SER HIS SEQRES 21 A 350 PHE SER SER ASP LEU LYS ASP LEU LEU ARG ASN LEU LEU SEQRES 22 A 350 GLN VAL ASP LEU THR LYS ARG PHE GLY ASN LEU LYS ASN SEQRES 23 A 350 GLY VAL ASN ASP ILE LYS ASN HIS LYS TRP PHE ALA THR SEQRES 24 A 350 THR ASP TRP ILE ALA ILE TYR GLN ARG LYS VAL GLU ALA SEQRES 25 A 350 PRO PHE ILE PRO LYS PHE LYS GLY PRO GLY ASP THR SER SEQRES 26 A 350 ASN PHE ASP ASP TYR GLU GLU GLU GLU ILE ARG VAL SEP SEQRES 27 A 350 ILE ASN GLU LYS CYS GLY LYS GLU PHE THR GLU PHE SEQRES 1 B 381 MET ALA SER PRO PRO ALA CYS PRO SER GLU GLU ASP GLU SEQRES 2 B 381 SER LEU LYS GLY CYS GLU LEU TYR VAL GLN LEU HIS GLY SEQRES 3 B 381 ILE GLN GLN VAL LEU LYS ASP CYS ILE VAL HIS LEU CYS SEQRES 4 B 381 ILE SER LYS PRO GLU ARG PRO MET LYS PHE LEU ARG GLU SEQRES 5 B 381 HIS PHE GLU LYS LEU GLU LYS GLU GLU ASN ARG GLN ILE SEQRES 6 B 381 LEU ALA ARG GLN LYS SER ASN SER GLN SER ASP SER HIS SEQRES 7 B 381 ASP GLU GLU VAL SER PRO THR PRO PRO ASN PRO VAL VAL SEQRES 8 B 381 LYS ALA ARG ARG ARG ARG GLY GLY VAL SER ALA GLU VAL SEQRES 9 B 381 TYR THR GLU GLU ASP ALA VAL SER TYR VAL ARG LYS VAL SEQRES 10 B 381 ILE PRO LYS ASP TYR LYS THR MET THR ALA LEU ALA LYS SEQRES 11 B 381 ALA ILE SER LYS ASN VAL LEU PHE ALA HIS LEU ASP ASP SEQRES 12 B 381 ASN GLU ARG SER ASP ILE PHE ASP ALA MET PHE PRO VAL SEQRES 13 B 381 THR HIS ILE ALA GLY GLU THR VAL ILE GLN GLN GLY ASN SEQRES 14 B 381 GLU GLY ASP ASN PHE TYR VAL VAL ASP GLN GLY GLU VAL SEQRES 15 B 381 ASP VAL TYR VAL ASN GLY GLU TRP VAL THR ASN ILE SER SEQRES 16 B 381 GLU GLY GLY SER PHE GLY GLU LEU ALA LEU ILE TYR GLY SEQRES 17 B 381 THR PRO ARG ALA ALA THR VAL LYS ALA LYS THR ASP LEU SEQRES 18 B 381 LYS LEU TRP GLY ILE ASP ARG ASP SER TYR ARG ARG ILE SEQRES 19 B 381 LEU MET GLY SER THR LEU ARG LYS ARG LYS MET TYR GLU SEQRES 20 B 381 GLU PHE LEU SER LYS VAL SER ILE LEU GLU SER LEU GLU SEQRES 21 B 381 LYS TRP GLU ARG LEU THR VAL ALA ASP ALA LEU GLU PRO SEQRES 22 B 381 VAL GLN PHE GLU ASP GLY GLU LYS ILE VAL VAL GLN GLY SEQRES 23 B 381 GLU PRO GLY ASP ASP PHE TYR ILE ILE THR GLU GLY THR SEQRES 24 B 381 ALA SER VAL LEU GLN ARG ARG SER PRO ASN GLU GLU TYR SEQRES 25 B 381 VAL GLU VAL GLY ARG LEU GLY PRO SER ASP TYR PHE GLY SEQRES 26 B 381 GLU ILE ALA LEU LEU LEU ASN ARG PRO ARG ALA ALA THR SEQRES 27 B 381 VAL VAL ALA ARG GLY PRO LEU LYS CYS VAL LYS LEU ASP SEQRES 28 B 381 ARG PRO ARG PHE GLU ARG VAL LEU GLY PRO CYS SER GLU SEQRES 29 B 381 ILE LEU LYS ARG ASN ILE GLN ARG TYR ASN SER PHE ILE SEQRES 30 B 381 SER LEU THR VAL MODRES 4DIN TPO A 197 THR PHOSPHOTHREONINE MODRES 4DIN SEP A 338 SER PHOSPHOSERINE HET TPO A 197 11 HET SEP A 338 10 HET ATP A 400 31 HET MG A 401 1 HET MG A 402 1 HETNAM TPO PHOSPHOTHREONINE HETNAM SEP PHOSPHOSERINE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN TPO PHOSPHONOTHREONINE HETSYN SEP PHOSPHONOSERINE FORMUL 1 TPO C4 H10 N O6 P FORMUL 1 SEP C3 H8 N O6 P FORMUL 3 ATP C10 H16 N5 O13 P3 FORMUL 4 MG 2(MG 2+) HELIX 1 1 GLU A 13 THR A 32 1 20 HELIX 2 2 LYS A 76 VAL A 80 1 5 HELIX 3 3 GLN A 84 GLN A 96 1 13 HELIX 4 4 GLU A 127 ILE A 135 1 9 HELIX 5 5 SER A 139 LEU A 160 1 22 HELIX 6 6 LYS A 168 GLU A 170 5 3 HELIX 7 7 ALA A 206 LEU A 211 1 6 HELIX 8 8 LYS A 217 GLY A 234 1 18 HELIX 9 9 GLN A 242 VAL A 251 1 10 HELIX 10 10 SER A 262 LEU A 273 1 12 HELIX 11 11 ASP A 276 ARG A 280 5 5 HELIX 12 12 VAL A 288 ASN A 293 1 6 HELIX 13 13 HIS A 294 ALA A 298 5 5 HELIX 14 14 ASP A 301 GLN A 307 1 7 HELIX 15 15 GLY A 344 THR A 348 5 5 HELIX 16 16 THR B 104 SER B 110 1 7 HELIX 17 17 ASP B 119 SER B 131 1 13 HELIX 18 18 ASP B 140 MET B 151 1 12 HELIX 19 19 GLY B 199 ILE B 204 5 6 HELIX 20 20 ARG B 226 VAL B 251 1 26 HELIX 21 21 TRP B 260 ASP B 267 1 8 HELIX 22 22 ILE B 325 LEU B 329 5 5 HELIX 23 23 ARG B 350 GLY B 358 1 9 HELIX 24 24 PRO B 359 ARG B 366 1 8 HELIX 25 25 ASN B 367 SER B 376 1 10 SHEET 1 A 5 PHE A 43 THR A 51 0 SHEET 2 A 5 ARG A 56 HIS A 62 -1 O LEU A 59 N LYS A 47 SHEET 3 A 5 TYR A 69 ASP A 75 -1 O ILE A 73 N ARG A 56 SHEET 4 A 5 ASN A 115 GLU A 121 -1 O MET A 120 N ALA A 70 SHEET 5 A 5 PHE A 110 LYS A 111 -1 N PHE A 110 O TYR A 117 SHEET 1 B 2 LEU A 172 LEU A 173 0 SHEET 2 B 2 GLN A 181 VAL A 182 -1 O GLN A 181 N LEU A 173 SHEET 1 C 3 PHE B 152 THR B 155 0 SHEET 2 C 3 LYS B 220 ASP B 225 -1 O GLY B 223 N PHE B 152 SHEET 3 C 3 ASN B 171 VAL B 174 -1 N VAL B 174 O TRP B 222 SHEET 1 D 3 GLU B 187 SER B 193 0 SHEET 2 D 3 GLU B 179 VAL B 184 -1 N VAL B 182 O THR B 190 SHEET 3 D 3 THR B 212 ALA B 215 -1 O LYS B 214 N ASP B 181 SHEET 1 E 3 TYR B 321 PHE B 322 0 SHEET 2 E 3 ASP B 289 GLU B 295 -1 N TYR B 291 O PHE B 322 SHEET 3 E 3 LYS B 344 ASP B 349 -1 O LEU B 348 N PHE B 290 SHEET 1 F 3 GLU B 312 LEU B 316 0 SHEET 2 F 3 ALA B 298 LEU B 301 -1 N VAL B 300 O GLY B 314 SHEET 3 F 3 THR B 336 ALA B 339 -1 O VAL B 338 N SER B 299 LINK C TRP A 196 N TPO A 197 1555 1555 1.33 LINK C TPO A 197 N LEU A 198 1555 1555 1.33 LINK C VAL A 337 N SEP A 338 1555 1555 1.33 LINK C SEP A 338 N ILE A 339 1555 1555 1.33 LINK OD1 ASN A 171 MG MG A 401 1555 1555 1.98 LINK OD2 ASP A 184 MG MG A 401 1555 1555 2.58 LINK OD1 ASP A 184 MG MG A 402 1555 1555 2.25 LINK OD2 ASP A 184 MG MG A 402 1555 1555 2.60 LINK O2A ATP A 400 MG MG A 401 1555 1555 2.22 LINK O3G ATP A 400 MG MG A 401 1555 1555 2.85 LINK O3G ATP A 400 MG MG A 402 1555 1555 2.10 LINK O2B ATP A 400 MG MG A 402 1555 1555 2.22 LINK O2G ATP A 400 MG MG A 402 1555 1555 2.90 SITE 1 AC1 26 LEU A 49 GLY A 50 THR A 51 GLY A 52 SITE 2 AC1 26 SER A 53 PHE A 54 VAL A 57 ALA A 70 SITE 3 AC1 26 LYS A 72 MET A 120 GLU A 121 VAL A 123 SITE 4 AC1 26 GLU A 127 ASP A 166 LYS A 168 GLU A 170 SITE 5 AC1 26 ASN A 171 LEU A 173 THR A 183 ASP A 184 SITE 6 AC1 26 PHE A 327 MG A 401 MG A 402 ARG B 94 SITE 7 AC1 26 GLY B 96 GLY B 97 SITE 1 AC2 4 LYS A 168 ASN A 171 ASP A 184 ATP A 400 SITE 1 AC3 3 ASP A 166 ASP A 184 ATP A 400 CRYST1 172.194 172.194 146.646 90.00 90.00 120.00 P 64 2 2 12 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 0.005807 0.003353 0.000000 0.00000 SCALE2 0.000000 0.006706 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006819 0.00000