HEADER TRANSFERASE 19-OCT-17 6ERV TITLE CRYSTAL STRUCTURE OF THE PROTEIN-KINASE A CATALYTIC SUBUNIT FROM TITLE 2 CRITECULUS GRISEUS IN COMPLEX WITH COMPOUNDS RKP013 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 INHIBITOR; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: PKI5-22 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CRICETULUS GRISEUS; SOURCE 3 ORGANISM_COMMON: CHINESE HAMSTER; SOURCE 4 ORGANISM_TAXID: 10029; SOURCE 5 ORGAN: OVARY; SOURCE 6 TISSUE: OVARY; SOURCE 7 GENE: PRKACA; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_VARIANT: GOLD PLYSS AG; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: CRICETULUS GRISEUS; SOURCE 14 ORGANISM_COMMON: CHINESE HAMSTER; SOURCE 15 ORGANISM_TAXID: 10029 KEYWDS COMPLEX, PEPTIDIC LIGAND, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.MUELLER,A.HEINE,G.KLEBE REVDAT 2 15-MAY-19 6ERV 1 JRNL REVDAT 1 31-OCT-18 6ERV 0 JRNL AUTH J.M.MUELLER,R.KIRSCHNER,A.GEYER,G.KLEBE JRNL TITL CONCEPTIONAL DESIGN OF SELF-ASSEMBLING BISUBSTRATE-LIKE JRNL TITL 2 INHIBITORS OF PROTEIN KINASE A RESULTING IN A BORONIC ACID JRNL TITL 3 GLUTAMATE LINKAGE JRNL REF ACS OMEGA 2019 JRNL REFN ESSN 2470-1343 JRNL DOI 10.1021/ACSOMEGA.8B02364 REMARK 2 REMARK 2 RESOLUTION. 2.06 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 29607 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1481 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 43.7826 - 4.5765 0.97 2671 141 0.1727 0.1828 REMARK 3 2 4.5765 - 3.6331 0.98 2594 137 0.1523 0.2139 REMARK 3 3 3.6331 - 3.1740 0.99 2586 136 0.1784 0.2111 REMARK 3 4 3.1740 - 2.8838 0.99 2553 134 0.1861 0.2211 REMARK 3 5 2.8838 - 2.6772 0.99 2535 133 0.1895 0.2404 REMARK 3 6 2.6772 - 2.5193 0.99 2560 135 0.1899 0.2159 REMARK 3 7 2.5193 - 2.3932 0.99 2535 134 0.1790 0.2150 REMARK 3 8 2.3932 - 2.2890 0.99 2523 132 0.1943 0.2513 REMARK 3 9 2.2890 - 2.2009 1.00 2549 135 0.1968 0.2301 REMARK 3 10 2.2009 - 2.1250 0.99 2524 132 0.2201 0.3039 REMARK 3 11 2.1250 - 2.0585 0.98 2496 132 0.2539 0.2936 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.810 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 : 0.012 2948 REMARK 3 ANGLE : 1.083 4007 REMARK 3 CHIRALITY : 0.062 432 REMARK 3 PLANARITY : 0.007 514 REMARK 3 DIHEDRAL : 15.108 1723 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -2 THROUGH 54 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.0973 -12.7495 12.4905 REMARK 3 T TENSOR REMARK 3 T11: 0.3932 T22: 0.4834 REMARK 3 T33: 0.4918 T12: 0.1503 REMARK 3 T13: -0.0223 T23: -0.0227 REMARK 3 L TENSOR REMARK 3 L11: 0.7750 L22: 1.0698 REMARK 3 L33: 1.2149 L12: 0.3514 REMARK 3 L13: 0.8728 L23: -0.0622 REMARK 3 S TENSOR REMARK 3 S11: -0.0064 S12: 0.0088 S13: -0.0528 REMARK 3 S21: 0.0670 S22: -0.0696 S23: 0.3243 REMARK 3 S31: -0.1499 S32: -0.1932 S33: 0.0003 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 55 THROUGH 160 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.5911 -20.1890 23.0230 REMARK 3 T TENSOR REMARK 3 T11: 0.3307 T22: 0.4115 REMARK 3 T33: 0.3822 T12: -0.0319 REMARK 3 T13: 0.0356 T23: -0.0678 REMARK 3 L TENSOR REMARK 3 L11: 0.7067 L22: 1.4212 REMARK 3 L33: 1.2296 L12: -0.2109 REMARK 3 L13: -0.1538 L23: -0.5117 REMARK 3 S TENSOR REMARK 3 S11: 0.0693 S12: -0.0057 S13: -0.1965 REMARK 3 S21: 0.2542 S22: -0.1004 S23: 0.4216 REMARK 3 S31: 0.0269 S32: -0.4649 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 161 THROUGH 316 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.2024 -17.6743 16.6507 REMARK 3 T TENSOR REMARK 3 T11: 0.1903 T22: 0.1975 REMARK 3 T33: 0.2201 T12: -0.0083 REMARK 3 T13: -0.0041 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 1.7595 L22: 3.0335 REMARK 3 L33: 2.5255 L12: -0.0047 REMARK 3 L13: -0.4167 L23: 0.1728 REMARK 3 S TENSOR REMARK 3 S11: 0.0806 S12: 0.0075 S13: -0.0063 REMARK 3 S21: 0.0439 S22: -0.1437 S23: -0.1619 REMARK 3 S31: -0.1271 S32: 0.0184 S33: -0.0004 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 317 THROUGH 350 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.9424 -16.1019 34.8172 REMARK 3 T TENSOR REMARK 3 T11: 0.6779 T22: 0.7016 REMARK 3 T33: 0.6668 T12: -0.0848 REMARK 3 T13: 0.1970 T23: -0.1492 REMARK 3 L TENSOR REMARK 3 L11: 0.0741 L22: 0.2702 REMARK 3 L33: 0.0759 L12: 0.1418 REMARK 3 L13: -0.0733 L23: -0.1362 REMARK 3 S TENSOR REMARK 3 S11: 0.3319 S12: -0.1754 S13: 0.2176 REMARK 3 S21: 0.7632 S22: -0.4494 S23: 0.4273 REMARK 3 S31: -0.0014 S32: -0.7437 S33: 0.0008 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 10 THROUGH 17 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4052 -33.1074 27.2026 REMARK 3 T TENSOR REMARK 3 T11: 0.4734 T22: 0.4695 REMARK 3 T33: 0.5109 T12: -0.0744 REMARK 3 T13: -0.0797 T23: 0.1533 REMARK 3 L TENSOR REMARK 3 L11: 0.0428 L22: 0.0382 REMARK 3 L33: 0.0118 L12: -0.0400 REMARK 3 L13: 0.0003 L23: 0.0028 REMARK 3 S TENSOR REMARK 3 S11: 0.0349 S12: 0.0475 S13: -0.1476 REMARK 3 S21: -0.0229 S22: 0.1250 S23: -0.5397 REMARK 3 S31: 0.0348 S32: 0.3315 S33: 0.0005 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 18 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.6474 -24.3528 31.6472 REMARK 3 T TENSOR REMARK 3 T11: 0.5975 T22: 0.3159 REMARK 3 T33: 0.3089 T12: -0.0965 REMARK 3 T13: 0.0165 T23: 0.0078 REMARK 3 L TENSOR REMARK 3 L11: 0.0346 L22: 0.1706 REMARK 3 L33: 0.0748 L12: -0.0152 REMARK 3 L13: 0.0210 L23: -0.0236 REMARK 3 S TENSOR REMARK 3 S11: 0.2684 S12: -0.6207 S13: 0.1748 REMARK 3 S21: 0.7533 S22: -0.2893 S23: -0.4033 REMARK 3 S31: -0.0902 S32: 0.1215 S33: 0.0002 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 6ERV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1200007155. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29607 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 REMARK 200 RESOLUTION RANGE LOW (A) : 43.773 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.420 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.58 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.49400 REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 58.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES-BIS-TRIS, 75 MM LITHIUM REMARK 280 CHLORIDE, 1 MM DTT, 0.1 MM SODIUM EDTA, 0.25 MM MEGA 8, 0.7 MM REMARK 280 PEPTIDIC LIGAND, 20% V/V METHANOL/WATER IN RESERVOIR, PH 6.9, REMARK 280 VAPOR DIFFUSION, SITTING 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 29.48800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.73550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.45400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.73550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.48800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.45400 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 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: 1920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 LYS A 319 REMARK 465 GLY A 320 REMARK 465 PHE A 327 REMARK 465 ASP A 328 REMARK 465 ASP A 329 REMARK 465 TYR A 330 REMARK 465 GLU A 331 REMARK 465 GLU A 332 REMARK 465 GLU A 333 REMARK 465 GLU A 334 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 ASN A 2 CG OD1 ND2 REMARK 470 LYS A 7 CD CE NZ REMARK 470 LYS A 8 CE NZ REMARK 470 LYS A 16 CD CE NZ REMARK 470 LYS A 21 CG CD CE NZ REMARK 470 GLU A 25 CD OE1 OE2 REMARK 470 LYS A 28 CD CE NZ REMARK 470 LYS A 29 NZ REMARK 470 ARG A 45 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 47 CD CE NZ REMARK 470 SER A 53 OG REMARK 470 PHE A 54 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 56 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 61 CD CE NZ REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 LYS A 72 NZ REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 LYS A 81 CG CD CE NZ REMARK 470 LYS A 83 CG CD CE NZ REMARK 470 LYS A 192 CG CD CE NZ REMARK 470 LYS A 254 CD CE NZ REMARK 470 LYS A 285 CD CE NZ REMARK 470 LYS A 295 CD CE NZ REMARK 470 LYS A 317 CG CD CE NZ REMARK 470 PHE A 318 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 323 CG OD1 OD2 REMARK 470 THR A 324 OG1 CG2 REMARK 470 SER A 325 OG REMARK 470 ASN A 326 CG OD1 ND2 REMARK 470 ILE A 335 CG1 CG2 CD1 REMARK 470 ARG A 336 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 339 CG1 CG2 CD1 REMARK 470 ASN A 340 CG OD1 ND2 REMARK 470 LYS A 342 CG CD CE NZ REMARK 470 LYS A 345 CG CD CE NZ 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 ARG A 144 NE - CZ - NH2 ANGL. DEV. = 3.2 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 ASP A 166 41.93 -145.28 REMARK 500 ASP A 184 86.88 78.53 REMARK 500 SER A 325 -72.80 -101.93 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 MPD A 401 DBREF 6ERV A 0 350 UNP P25321 KAPCA_CRIGR 1 351 DBREF1 6ERV B 10 27 UNP A0A061IH64_CRIGR DBREF2 6ERV B A0A061IH64 6 23 SEQADV 6ERV GLY A -2 UNP P25321 EXPRESSION TAG SEQADV 6ERV HIS A -1 UNP P25321 EXPRESSION TAG SEQRES 1 A 353 GLY HIS MET GLY ASN ALA ALA ALA ALA LYS LYS GLY SEP SEQRES 2 A 353 GLU GLN GLU SER VAL LYS GLU PHE LEU ALA LYS ALA LYS SEQRES 3 A 353 GLU GLU PHE LEU LYS LYS TRP GLU SER PRO SER GLN ASN SEQRES 4 A 353 THR ALA GLN LEU ASP HIS PHE ASP ARG ILE LYS THR LEU SEQRES 5 A 353 GLY THR GLY SER PHE GLY ARG VAL MET LEU VAL LYS HIS SEQRES 6 A 353 LYS GLU THR GLY ASN HIS TYR ALA MET LYS ILE LEU ASP SEQRES 7 A 353 LYS GLN LYS VAL VAL LYS LEU LYS GLN ILE GLU HIS THR SEQRES 8 A 353 LEU ASN GLU LYS ARG ILE LEU GLN ALA VAL ASN PHE PRO SEQRES 9 A 353 PHE LEU VAL LYS LEU GLU PHE SER PHE LYS ASP ASN SER SEQRES 10 A 353 ASN LEU TYR MET VAL MET GLU TYR VAL PRO GLY GLY GLU SEQRES 11 A 353 MET PHE SER HIS LEU ARG ARG ILE GLY ARG PHE SEP GLU SEQRES 12 A 353 PRO HIS ALA ARG PHE TYR ALA ALA GLN ILE VAL LEU THR SEQRES 13 A 353 PHE GLU TYR LEU HIS SER LEU ASP LEU ILE TYR ARG ASP SEQRES 14 A 353 LEU LYS PRO GLU ASN LEU LEU ILE ASP GLN GLN GLY TYR SEQRES 15 A 353 ILE GLN VAL THR ASP PHE GLY PHE ALA LYS ARG VAL LYS SEQRES 16 A 353 GLY ARG THR TRP TPO LEU CYS GLY THR PRO GLU TYR LEU SEQRES 17 A 353 ALA PRO GLU ILE ILE LEU SER LYS GLY TYR ASN LYS ALA SEQRES 18 A 353 VAL ASP TRP TRP ALA LEU GLY VAL LEU ILE TYR GLU MET SEQRES 19 A 353 ALA ALA GLY TYR PRO PRO PHE PHE ALA ASP GLN PRO ILE SEQRES 20 A 353 GLN ILE TYR GLU LYS ILE VAL SER GLY LYS VAL ARG PHE SEQRES 21 A 353 PRO SER HIS PHE SER SER ASP LEU LYS ASP LEU LEU ARG SEQRES 22 A 353 ASN LEU LEU GLN VAL ASP LEU THR LYS ARG PHE GLY ASN SEQRES 23 A 353 LEU LYS ASN GLY VAL ASN ASP ILE LYS ASN HIS LYS TRP SEQRES 24 A 353 PHE ALA THR THR ASP TRP ILE ALA ILE TYR GLN ARG LYS SEQRES 25 A 353 VAL GLU ALA PRO PHE ILE PRO LYS PHE LYS GLY PRO GLY SEQRES 26 A 353 ASP THR SER ASN PHE ASP ASP TYR GLU GLU GLU GLU ILE SEQRES 27 A 353 ARG VAL SEP ILE ASN GLU LYS CYS GLY LYS GLU PHE THR SEQRES 28 A 353 GLU PHE SEQRES 1 B 18 THR THR TYR ALA ASP PHE ILE ALA SER GLY ARG THR GLY SEQRES 2 B 18 ARG ARG ASN ALA ILE MODRES 6ERV SEP A 10 SER MODIFIED RESIDUE MODRES 6ERV SEP A 139 SER MODIFIED RESIDUE MODRES 6ERV TPO A 197 THR MODIFIED RESIDUE MODRES 6ERV SEP A 338 SER MODIFIED RESIDUE HET SEP A 10 10 HET SEP A 139 10 HET TPO A 197 11 HET SEP A 338 10 HET MPD A 401 8 HETNAM SEP PHOSPHOSERINE HETNAM TPO PHOSPHOTHREONINE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETSYN SEP PHOSPHONOSERINE HETSYN TPO PHOSPHONOTHREONINE FORMUL 1 SEP 3(C3 H8 N O6 P) FORMUL 1 TPO C4 H10 N O6 P FORMUL 3 MPD C6 H14 O2 FORMUL 4 HOH *177(H2 O) HELIX 1 AA1 GLY A 1 SER A 32 1 32 HELIX 2 AA2 GLN A 39 ASP A 41 5 3 HELIX 3 AA3 LYS A 76 LEU A 82 1 7 HELIX 4 AA4 GLN A 84 VAL A 98 1 15 HELIX 5 AA5 GLU A 127 GLY A 136 1 10 HELIX 6 AA6 SEP A 139 LEU A 160 1 22 HELIX 7 AA7 LYS A 168 GLU A 170 5 3 HELIX 8 AA8 THR A 201 LEU A 205 5 5 HELIX 9 AA9 ALA A 206 LEU A 211 1 6 HELIX 10 AB1 LYS A 217 GLY A 234 1 18 HELIX 11 AB2 GLN A 242 SER A 252 1 11 HELIX 12 AB3 SER A 262 LEU A 273 1 12 HELIX 13 AB4 VAL A 288 ASN A 293 1 6 HELIX 14 AB5 HIS A 294 ALA A 298 5 5 HELIX 15 AB6 ASP A 301 GLN A 307 1 7 HELIX 16 AB7 GLY A 344 THR A 348 5 5 HELIX 17 AB8 THR B 11 SER B 18 1 8 SHEET 1 AA1 5 PHE A 43 THR A 51 0 SHEET 2 AA1 5 GLY A 55 HIS A 62 -1 O LYS A 61 N ASP A 44 SHEET 3 AA1 5 HIS A 68 ASP A 75 -1 O ILE A 73 N ARG A 56 SHEET 4 AA1 5 ASN A 115 GLU A 121 -1 O MET A 118 N LYS A 72 SHEET 5 AA1 5 LEU A 106 LYS A 111 -1 N PHE A 108 O VAL A 119 SHEET 1 AA2 2 LEU A 162 ILE A 163 0 SHEET 2 AA2 2 LYS A 189 ARG A 190 -1 O LYS A 189 N ILE A 163 SHEET 1 AA3 2 LEU A 172 ILE A 174 0 SHEET 2 AA3 2 ILE A 180 VAL A 182 -1 O GLN A 181 N LEU A 173 LINK C GLY A 9 N SEP A 10 1555 1555 1.32 LINK C SEP A 10 N GLU A 11 1555 1555 1.33 LINK C PHE A 138 N SEP A 139 1555 1555 1.33 LINK C SEP A 139 N GLU A 140 1555 1555 1.34 LINK C TRP A 196 N TPO A 197 1555 1555 1.33 LINK C TPO A 197 N LEU A 198 1555 1555 1.32 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 SITE 1 AC1 7 VAL A 15 PHE A 18 LEU A 152 GLU A 155 SITE 2 AC1 7 LYS A 292 TYR A 306 HOH A 529 CRYST1 58.976 72.908 109.471 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 0.016956 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013716 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009135 0.00000