HEADER GENE REGULATION 12-OCT-03 1R5P TITLE CRYSTAL STRUCTURE ANALYSIS OF KAIB FROM PCC7120 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CIRCADIAN OSCILLATION REGULATOR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: KAIB; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOSTOC SP.; SOURCE 3 ORGANISM_TAXID: 103690; SOURCE 4 STRAIN: PCC 7120; SOURCE 5 GENE: KAIB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET32 KEYWDS ALPHA-BETA MEANDER, PROTEIN DIMER, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR R.G.GARCES,N.WU,W.GILLON,E.F.PAI REVDAT 4 14-FEB-24 1R5P 1 REMARK REVDAT 3 13-JUL-11 1R5P 1 VERSN REVDAT 2 24-FEB-09 1R5P 1 VERSN REVDAT 1 04-MAY-04 1R5P 0 JRNL AUTH R.G.GARCES,N.WU,W.GILLON,E.F.PAI JRNL TITL ANABAENA CIRCADIAN CLOCK PROTEINS KAIA AND KAIB REVEAL A JRNL TITL 2 POTENTIAL COMMON BINDING SITE TO THEIR PARTNER KAIC JRNL REF EMBO J. V. 23 1688 2004 JRNL REFN ISSN 0261-4189 JRNL PMID 15071498 JRNL DOI 10.1038/SJ.EMBOJ.7600190 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 554402.370 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 10159 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) : 0.212 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.900 REMARK 3 FREE R VALUE TEST SET COUNT : 602 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1506 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 138 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1452 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 67 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.26000 REMARK 3 B22 (A**2) : 19.25000 REMARK 3 B33 (A**2) : -12.99000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.08000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.16 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.100 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) : 1.290 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.170 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.720 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.720 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.42 REMARK 3 BSOL : 81.84 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.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1R5P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020469. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-FEB-03; NULL REMARK 200 TEMPERATURE (KELVIN) : 200; 200 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 14-ID-B; 14-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0; 0.95705, 0.97943, 0.97971 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10484 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 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) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 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: NULL; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298.0K 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 52.37750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.19350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.37750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.19350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 96.44433 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 53.49834 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 123 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 135 LIES ON A SPECIAL POSITION. 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 1 REMARK 465 ASN A 2 REMARK 465 LYS A 3 REMARK 465 ALA A 4 REMARK 465 ARG A 5 REMARK 465 LYS A 6 REMARK 465 LEU A 97 REMARK 465 THR A 98 REMARK 465 GLU A 99 REMARK 465 GLU A 100 REMARK 465 ASP A 101 REMARK 465 TRP A 102 REMARK 465 GLU A 103 REMARK 465 ALA A 104 REMARK 465 GLN A 105 REMARK 465 SER A 106 REMARK 465 ASN A 107 REMARK 465 LEU A 108 REMARK 465 MET B 1001 REMARK 465 ASN B 1002 REMARK 465 LYS B 1003 REMARK 465 ALA B 1004 REMARK 465 ARG B 1005 REMARK 465 GLU B 1099 REMARK 465 GLU B 1100 REMARK 465 ASP B 1101 REMARK 465 TRP B 1102 REMARK 465 GLU B 1103 REMARK 465 ALA B 1104 REMARK 465 GLN B 1105 REMARK 465 SER B 1106 REMARK 465 ASN B 1107 REMARK 465 LEU B 1108 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 37 44.66 38.70 REMARK 500 GLU A 55 -61.49 -29.97 REMARK 500 THR A 64 -74.18 -68.54 REMARK 500 ALA B1015 79.92 -103.12 REMARK 500 ARG B1083 -64.31 -99.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1R5Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF KAI A FROM PCC7120 DBREF 1R5P A 1 108 UNP Q8YT41 KAIB_ANASP 1 108 DBREF 1R5P B 1001 1108 UNP Q8YT41 KAIB_ANASP 1 108 SEQRES 1 A 108 MET ASN LYS ALA ARG LYS THR TYR VAL LEU LYS LEU TYR SEQRES 2 A 108 VAL ALA GLY ASN THR PRO ASN SER VAL ARG ALA LEU LYS SEQRES 3 A 108 THR LEU LYS ASN ILE LEU GLU GLN GLU PHE GLN GLY ILE SEQRES 4 A 108 TYR ALA LEU LYS VAL ILE ASP VAL LEU LYS ASN PRO GLN SEQRES 5 A 108 LEU ALA GLU GLU ASP LYS ILE LEU ALA THR PRO THR LEU SEQRES 6 A 108 SER LYS ILE LEU PRO PRO PRO VAL ARG LYS ILE ILE GLY SEQRES 7 A 108 ASP LEU SER ASP ARG GLU ARG VAL LEU ILE GLY LEU ASP SEQRES 8 A 108 LEU LEU TYR GLU GLU LEU THR GLU GLU ASP TRP GLU ALA SEQRES 9 A 108 GLN SER ASN LEU SEQRES 1 B 108 MET ASN LYS ALA ARG LYS THR TYR VAL LEU LYS LEU TYR SEQRES 2 B 108 VAL ALA GLY ASN THR PRO ASN SER VAL ARG ALA LEU LYS SEQRES 3 B 108 THR LEU LYS ASN ILE LEU GLU GLN GLU PHE GLN GLY ILE SEQRES 4 B 108 TYR ALA LEU LYS VAL ILE ASP VAL LEU LYS ASN PRO GLN SEQRES 5 B 108 LEU ALA GLU GLU ASP LYS ILE LEU ALA THR PRO THR LEU SEQRES 6 B 108 SER LYS ILE LEU PRO PRO PRO VAL ARG LYS ILE ILE GLY SEQRES 7 B 108 ASP LEU SER ASP ARG GLU ARG VAL LEU ILE GLY LEU ASP SEQRES 8 B 108 LEU LEU TYR GLU GLU LEU THR GLU GLU ASP TRP GLU ALA SEQRES 9 B 108 GLN SER ASN LEU FORMUL 3 HOH *67(H2 O) HELIX 1 1 THR A 18 GLN A 37 1 20 HELIX 2 2 ALA A 61 SER A 66 1 6 HELIX 3 3 LYS A 67 LEU A 69 5 3 HELIX 4 4 PRO A 70 ARG A 83 1 14 HELIX 5 5 THR B 1018 PHE B 1036 1 19 HELIX 6 6 ALA B 1061 LYS B 1067 1 7 HELIX 7 7 PRO B 1070 ARG B 1083 1 14 SHEET 1 A 3 TYR A 40 ASP A 46 0 SHEET 2 A 3 TYR A 8 VAL A 14 1 N LEU A 12 O ILE A 45 SHEET 3 A 3 LEU A 87 TYR A 94 -1 O LEU A 93 N VAL A 9 SHEET 1 B 2 ILE A 59 LEU A 60 0 SHEET 2 B 2 LYS B1058 ILE B1059 -1 O ILE B1059 N ILE A 59 SHEET 1 C 3 TYR B1040 ASP B1046 0 SHEET 2 C 3 THR B1007 VAL B1014 1 N LEU B1010 O ALA B1041 SHEET 3 C 3 LEU B1087 GLU B1095 -1 O GLU B1095 N THR B1007 CRYST1 104.755 36.387 54.140 90.00 98.83 90.00 C 1 2 1 8 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 0.009546 0.000000 0.001483 0.00000 SCALE2 0.000000 0.027482 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018692 0.00000