PDB Short entry for 1OM1 HEADER TRANSFERASE 24-FEB-03 1OM1 TITLE CRYSTAL STRUCTURE OF MAIZE CK2 ALPHA IN COMPLEX WITH IQA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CASEIN KINASE II, ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CK II, CK2-ALPHA; COMPND 5 EC: 2.7.1.37 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ZEA MAYS; SOURCE 3 ORGANISM_TAXID: 4577 KEYWDS CK2, IQA, INHIBITOR, ZEA MAYS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.BATTISTUTTA,E.DE MOLINER,G.ZANOTTI REVDAT 3 11-OCT-17 1OM1 1 REMARK REVDAT 2 24-FEB-09 1OM1 1 VERSN REVDAT 1 24-FEB-04 1OM1 0 JRNL AUTH S.SARNO,E.DE MOLINER,M.RUZZENE,M.A.PAGANO,R.BATTISTUTTA, JRNL AUTH 2 J.BAIN,D.FABBRO,J.SCHOEPFER,M.ELLIOTT,P.FURET,F.MEGGIO, JRNL AUTH 3 G.ZANOTTI,L.A.PINNA JRNL TITL BIOCHEMICAL AND THREE-DIMENSIONAL-STRUCTURAL STUDY OF THE JRNL TITL 2 SPECIFIC INHIBITION OF PROTEIN KINASE CK2 BY JRNL TITL 3 [5-OXO-5,6-DIHYDROINDOLO-(1,2-A)QUINAZOLIN-7-YL]ACETIC ACID JRNL TITL 4 (IQA). JRNL REF BIOCHEM.J. V. 374 639 2003 JRNL REFN ISSN 0264-6021 JRNL PMID 12816539 JRNL DOI 10.1042/BJ20030674 REMARK 2 REMARK 2 RESOLUTION. 1.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.80 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) (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 40418 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) : 0.206 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3277 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.68 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5618 REMARK 3 BIN R VALUE (WORKING SET) : 0.3470 REMARK 3 BIN FREE R VALUE : 0.3780 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 533 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2713 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 252 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.03000 REMARK 3 B22 (A**2) : 12.19000 REMARK 3 B33 (A**2) : -5.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.400 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.960 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.310 ; 2.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.320 ; 3.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 39.33 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : IQA.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : IQA.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OM1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018434. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40418 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 34.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACETATE, TRIS, PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 70.76200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.13800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 70.76200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.13800 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 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 6 REMARK 465 ASN A 332 REMARK 465 SER A 333 REMARK 465 ARG A 334 REMARK 465 THR A 335 REMARK 465 ARG A 336 REMARK 465 ALA A 337 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 156 40.99 -153.83 REMARK 500 ASP A 175 79.40 47.92 REMARK 500 ALA A 193 179.01 61.82 REMARK 500 ARG A 195 -57.29 -29.72 REMARK 500 ASP A 210 -158.67 -148.24 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 IQA A 338 DBREF 1OM1 A 6 337 UNP P28523 CSK2A_MAIZE 1 332 SEQRES 1 A 332 MET SER LYS ALA ARG VAL TYR ALA ASP VAL ASN VAL LEU SEQRES 2 A 332 ARG PRO LYS GLU TYR TRP ASP TYR GLU ALA LEU THR VAL SEQRES 3 A 332 GLN TRP GLY GLU GLN ASP ASP TYR GLU VAL VAL ARG LYS SEQRES 4 A 332 VAL GLY ARG GLY LYS TYR SER GLU VAL PHE GLU GLY ILE SEQRES 5 A 332 ASN VAL ASN ASN ASN GLU LYS CYS ILE ILE LYS ILE LEU SEQRES 6 A 332 LYS PRO VAL LYS LYS LYS LYS ILE LYS ARG GLU ILE LYS SEQRES 7 A 332 ILE LEU GLN ASN LEU CYS GLY GLY PRO ASN ILE VAL LYS SEQRES 8 A 332 LEU LEU ASP ILE VAL ARG ASP GLN HIS SER LYS THR PRO SEQRES 9 A 332 SER LEU ILE PHE GLU TYR VAL ASN ASN THR ASP PHE LYS SEQRES 10 A 332 VAL LEU TYR PRO THR LEU THR ASP TYR ASP ILE ARG TYR SEQRES 11 A 332 TYR ILE TYR GLU LEU LEU LYS ALA LEU ASP TYR CYS HIS SEQRES 12 A 332 SER GLN GLY ILE MET HIS ARG ASP VAL LYS PRO HIS ASN SEQRES 13 A 332 VAL MET ILE ASP HIS GLU LEU ARG LYS LEU ARG LEU ILE SEQRES 14 A 332 ASP TRP GLY LEU ALA GLU PHE TYR HIS PRO GLY LYS GLU SEQRES 15 A 332 TYR ASN VAL ARG VAL ALA SER ARG TYR PHE LYS GLY PRO SEQRES 16 A 332 GLU LEU LEU VAL ASP LEU GLN ASP TYR ASP TYR SER LEU SEQRES 17 A 332 ASP MET TRP SER LEU GLY CYS MET PHE ALA GLY MET ILE SEQRES 18 A 332 PHE ARG LYS GLU PRO PHE PHE TYR GLY HIS ASP ASN HIS SEQRES 19 A 332 ASP GLN LEU VAL LYS ILE ALA LYS VAL LEU GLY THR ASP SEQRES 20 A 332 GLY LEU ASN VAL TYR LEU ASN LYS TYR ARG ILE GLU LEU SEQRES 21 A 332 ASP PRO GLN LEU GLU ALA LEU VAL GLY ARG HIS SER ARG SEQRES 22 A 332 LYS PRO TRP LEU LYS PHE MET ASN ALA ASP ASN GLN HIS SEQRES 23 A 332 LEU VAL SER PRO GLU ALA ILE ASP PHE LEU ASP LYS LEU SEQRES 24 A 332 LEU ARG TYR ASP HIS GLN GLU ARG LEU THR ALA LEU GLU SEQRES 25 A 332 ALA MET THR HIS PRO TYR PHE GLN GLN VAL ARG ALA ALA SEQRES 26 A 332 GLU ASN SER ARG THR ARG ALA HET IQA A 338 44 HETNAM IQA (5-OXO-5,6-DIHYDRO-INDOLO[1,2-A]QUINAZOLIN-7-YL)-ACETIC HETNAM 2 IQA ACID FORMUL 2 IQA C17 H12 N2 O3 FORMUL 3 HOH *252(H2 O) HELIX 1 1 ASP A 14 ARG A 19 1 6 HELIX 2 2 PRO A 20 ASP A 25 1 6 HELIX 3 3 TYR A 26 LEU A 29 5 4 HELIX 4 4 GLU A 35 ASP A 37 5 3 HELIX 5 5 LYS A 74 CYS A 89 1 16 HELIX 6 6 ASP A 120 TYR A 125 1 6 HELIX 7 7 PRO A 126 LEU A 128 5 3 HELIX 8 8 THR A 129 GLN A 150 1 22 HELIX 9 9 LYS A 158 HIS A 160 5 3 HELIX 10 10 SER A 194 LYS A 198 5 5 HELIX 11 11 GLY A 199 VAL A 204 1 6 HELIX 12 12 TYR A 211 PHE A 227 1 17 HELIX 13 13 ASP A 237 GLY A 250 1 14 HELIX 14 14 GLY A 250 TYR A 261 1 12 HELIX 15 15 ASP A 266 GLY A 274 1 9 HELIX 16 16 PRO A 280 MET A 285 5 6 HELIX 17 17 SER A 294 LYS A 303 1 10 HELIX 18 18 ASP A 308 ARG A 312 5 5 HELIX 19 19 THR A 314 HIS A 321 1 8 HELIX 20 20 PHE A 324 GLU A 331 1 8 SHEET 1 A 5 TYR A 39 GLY A 48 0 SHEET 2 A 5 SER A 51 ASN A 58 -1 O GLU A 55 N ARG A 43 SHEET 3 A 5 LYS A 64 LEU A 70 -1 O CYS A 65 N GLY A 56 SHEET 4 A 5 PRO A 109 GLU A 114 -1 O PHE A 113 N ILE A 66 SHEET 5 A 5 LEU A 97 ARG A 102 -1 N VAL A 101 O SER A 110 SHEET 1 B 2 ILE A 152 MET A 153 0 SHEET 2 B 2 GLU A 180 PHE A 181 -1 O GLU A 180 N MET A 153 SHEET 1 C 2 VAL A 162 ASP A 165 0 SHEET 2 C 2 LYS A 170 LEU A 173 -1 O LYS A 170 N ASP A 165 CISPEP 1 GLU A 230 PRO A 231 0 -0.20 SITE 1 AC1 13 VAL A 45 GLY A 46 SER A 51 VAL A 53 SITE 2 AC1 13 ILE A 66 LYS A 68 VAL A 95 PHE A 113 SITE 3 AC1 13 VAL A 116 MET A 163 ILE A 174 ASP A 175 SITE 4 AC1 13 HOH A 377 CRYST1 141.524 60.276 44.546 90.00 102.63 90.00 C 1 2 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 0.007066 0.000000 0.001583 0.00000 SCALE2 0.000000 0.016590 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023005 0.00000