PDB Short entry for 3G51 HEADER TRANSFERASE 04-FEB-09 3G51 TITLE STRUCTURAL DIVERSITY OF THE ACTIVE CONFORMATION OF THE N-TERMINAL TITLE 2 KINASE DOMAIN OF P90 RIBOSOMAL S6 KINASE 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL PROTEIN S6 KINASE ALPHA-3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: S6K-ALPHA 3, 90 KDA RIBOSOMAL PROTEIN S6 KINASE 3, P90-RSK COMPND 5 3, RIBOSOMAL S6 KINASE 2, RSK-2, PP90RSK2, MAP KINASE-ACTIVATED COMPND 6 PROTEIN KINASE 1B, MAPKAPK1B; COMPND 7 EC: 2.7.11.1; COMPND 8 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: MUS MUSCULUS RIBOSOMAL PROTEIN S6 KINASE 2, RPS6KA-RS1, SOURCE 6 RPS6KA3, RSK2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21-CODON PLUS (DE3)-RILP; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PET-28A KEYWDS N-TERMINAL KINASE DOMAIN OF P90 RIBOSOMAL S6 KINASE 2, ATP-BINDING, KEYWDS 2 KINASE, NUCLEOTIDE-BINDING, PHOSPHOPROTEIN, SERINE/THREONINE-PROTEIN KEYWDS 3 KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR I.KURINOV REVDAT 2 06-SEP-23 3G51 1 REMARK SEQADV REVDAT 1 15-DEC-09 3G51 0 JRNL AUTH M.MALAKHOVA,I.KURINOV,K.LIU,D.ZHENG,I.D'ANGELO,J.H.SHIM, JRNL AUTH 2 V.STEINMAN,A.M.BODE,Z.DONG JRNL TITL STRUCTURAL DIVERSITY OF THE ACTIVE N-TERMINAL KINASE DOMAIN JRNL TITL 2 OF P90 RIBOSOMAL S6 KINASE 2 JRNL REF PLOS ONE V. 4 E8044 2009 JRNL REFN ESSN 1932-6203 JRNL PMID 19956600 JRNL DOI 10.1371/JOURNAL.PONE.0008044 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 32826 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1637 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : 0.003 NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 3G51 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051431. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-08 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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI 111 DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : HFM, VFM, MICRODIFFRACTOMETER 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 : 35092 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 36.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.09100 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) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 1VZO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE DILUTED PROTEIN AT DIFFERENT REMARK 280 CONCENTRATIONS (2.5 MG/ML 10 MG/ML) WAS MIXED AT A 2:1 RATIO REMARK 280 WITH PRECIPITANT SOLUTION (6%-10% PEG 3350, 0.2 M PROLINE, 0.1 M REMARK 280 HEPES PH 7.5). , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 25.58350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.43650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.69050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.43650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.58350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.69050 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: 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 MET A 43 REMARK 465 GLU A 44 REMARK 465 GLY A 45 REMARK 465 SER A 46 REMARK 465 ASP A 111 REMARK 465 ARG A 112 REMARK 465 VAL A 113 REMARK 465 ARG A 114 REMARK 465 THR A 115 REMARK 465 LYS A 116 REMARK 465 MET A 117 REMARK 465 GLU A 118 REMARK 465 ARG A 119 REMARK 465 ASP A 220 REMARK 465 HIS A 221 REMARK 465 GLU A 222 REMARK 465 LYS A 223 REMARK 465 LYS A 224 REMARK 465 ALA A 225 REMARK 465 TYR A 226 REMARK 465 SER A 227 REMARK 465 PHE A 228 REMARK 465 CYS A 229 REMARK 465 GLY A 230 REMARK 465 ALA A 347 REMARK 465 THR A 348 REMARK 465 GLY A 349 REMARK 465 ARG A 350 REMARK 465 PRO A 351 REMARK 465 GLU A 352 REMARK 465 ASP A 353 REMARK 465 THR A 354 REMARK 465 PHE A 355 REMARK 465 TYR A 356 REMARK 465 PHE A 357 REMARK 465 ASP A 358 REMARK 465 PRO A 359 REMARK 465 GLU A 360 REMARK 465 PHE A 361 REMARK 465 THR A 362 REMARK 465 ALA A 363 REMARK 465 LYS A 364 REMARK 465 THR A 365 REMARK 465 PRO A 366 REMARK 465 LYS A 367 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 THR A 53 -31.96 -130.10 REMARK 500 ARG A 94 -10.88 85.18 REMARK 500 ARG A 192 -58.97 85.71 REMARK 500 PHE A 212 33.76 -140.68 REMARK 500 HIS A 245 117.51 -173.30 REMARK 500 PHE A 303 47.26 -88.35 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 ANP A 480 DBREF 3G51 A 44 367 UNP P18654 KS6A3_MOUSE 44 367 SEQADV 3G51 MET A 43 UNP P18654 EXPRESSION TAG SEQRES 1 A 325 MET GLU GLY SER ILE LYS GLU ILE ALA ILE THR HIS HIS SEQRES 2 A 325 VAL LYS GLU GLY HIS GLU LYS ALA ASP PRO SER GLN PHE SEQRES 3 A 325 GLU LEU LEU LYS VAL LEU GLY GLN GLY SER PHE GLY LYS SEQRES 4 A 325 VAL PHE LEU VAL LYS LYS ILE SER GLY SER ASP ALA ARG SEQRES 5 A 325 GLN LEU TYR ALA MET LYS VAL LEU LYS LYS ALA THR LEU SEQRES 6 A 325 LYS VAL ARG ASP ARG VAL ARG THR LYS MET GLU ARG ASP SEQRES 7 A 325 ILE LEU VAL GLU VAL ASN HIS PRO PHE ILE VAL LYS LEU SEQRES 8 A 325 HIS TYR ALA PHE GLN THR GLU GLY LYS LEU TYR LEU ILE SEQRES 9 A 325 LEU ASP PHE LEU ARG GLY GLY ASP LEU PHE THR ARG LEU SEQRES 10 A 325 SER LYS GLU VAL MET PHE THR GLU GLU ASP VAL LYS PHE SEQRES 11 A 325 TYR LEU ALA GLU LEU ALA LEU ALA LEU ASP HIS LEU HIS SEQRES 12 A 325 SER LEU GLY ILE ILE TYR ARG ASP LEU LYS PRO GLU ASN SEQRES 13 A 325 ILE LEU LEU ASP GLU GLU GLY HIS ILE LYS LEU THR ASP SEQRES 14 A 325 PHE GLY LEU SER LYS GLU SER ILE ASP HIS GLU LYS LYS SEQRES 15 A 325 ALA TYR SER PHE CYS GLY THR VAL GLU TYR MET ALA PRO SEQRES 16 A 325 GLU VAL VAL ASN ARG ARG GLY HIS THR GLN SER ALA ASP SEQRES 17 A 325 TRP TRP SER PHE GLY VAL LEU MET PHE GLU MET LEU THR SEQRES 18 A 325 GLY THR LEU PRO PHE GLN GLY LYS ASP ARG LYS GLU THR SEQRES 19 A 325 MET THR MET ILE LEU LYS ALA LYS LEU GLY MET PRO GLN SEQRES 20 A 325 PHE LEU SER PRO GLU ALA GLN SER LEU LEU ARG MET LEU SEQRES 21 A 325 PHE LYS ARG ASN PRO ALA ASN ARG LEU GLY ALA GLY PRO SEQRES 22 A 325 ASP GLY VAL GLU GLU ILE LYS ARG HIS SER PHE PHE SER SEQRES 23 A 325 THR ILE ASP TRP ASN LYS LEU TYR ARG ARG GLU ILE HIS SEQRES 24 A 325 PRO PRO PHE LYS PRO ALA THR GLY ARG PRO GLU ASP THR SEQRES 25 A 325 PHE TYR PHE ASP PRO GLU PHE THR ALA LYS THR PRO LYS HET ANP A 480 31 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 HOH *274(H2 O) HELIX 1 1 ASP A 64 SER A 66 5 3 HELIX 2 2 ASP A 120 VAL A 125 1 6 HELIX 3 3 ASP A 154 LYS A 161 1 8 HELIX 4 4 THR A 166 LEU A 187 1 22 HELIX 5 5 LYS A 195 GLU A 197 5 3 HELIX 6 6 THR A 231 MET A 235 5 5 HELIX 7 7 ALA A 236 ASN A 241 1 6 HELIX 8 8 GLN A 247 GLY A 264 1 18 HELIX 9 9 ASP A 272 ALA A 283 1 12 HELIX 10 10 SER A 292 PHE A 303 1 12 HELIX 11 11 ASN A 306 ARG A 310 5 5 HELIX 12 12 VAL A 318 ARG A 323 1 6 HELIX 13 13 HIS A 324 SER A 328 5 5 HELIX 14 14 ASP A 331 ARG A 337 1 7 SHEET 1 A 3 LYS A 48 ALA A 51 0 SHEET 2 A 3 LYS A 104 VAL A 109 -1 O LEU A 107 N ILE A 50 SHEET 3 A 3 LEU A 214 GLU A 217 -1 O SER A 215 N THR A 106 SHEET 1 B 6 HIS A 55 VAL A 56 0 SHEET 2 B 6 LEU A 133 GLN A 138 -1 O ALA A 136 N HIS A 55 SHEET 3 B 6 LEU A 143 ASP A 148 -1 O TYR A 144 N PHE A 137 SHEET 4 B 6 LEU A 96 LEU A 102 -1 N LEU A 102 O LEU A 143 SHEET 5 B 6 GLY A 80 LYS A 87 -1 N PHE A 83 O MET A 99 SHEET 6 B 6 PHE A 68 GLY A 77 -1 N GLY A 77 O GLY A 80 SHEET 1 C 2 ILE A 199 LEU A 201 0 SHEET 2 C 2 ILE A 207 LEU A 209 -1 O LYS A 208 N LEU A 200 SITE 1 AC1 22 LEU A 74 GLY A 75 GLN A 76 GLY A 77 SITE 2 AC1 22 SER A 78 PHE A 79 GLY A 80 VAL A 82 SITE 3 AC1 22 ALA A 98 LYS A 100 ASP A 148 LEU A 150 SITE 4 AC1 22 LYS A 195 GLU A 197 ASN A 198 LEU A 200 SITE 5 AC1 22 THR A 210 LYS A 216 HOH A 438 HOH A 457 SITE 6 AC1 22 HOH A 498 HOH A 556 CRYST1 51.167 51.381 140.873 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 0.019544 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019462 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007099 0.00000