HEADER CIRCADIAN CLOCK PROTEIN 29-MAY-06 2DQL TITLE CRYSTAL STRUCTURE OF THE CIRCADIAN CLOCK ASSOCIATED PROTEIN PEX FROM TITLE 2 ANABAENA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEX PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANABAENA SP. PCC 7120; SOURCE 3 ORGANISM_TAXID: 103690; SOURCE 4 STRAIN: PCC7120; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CIRCADIAN CLOCK ASSOCIATED PROTEIN, CIRCADIAN CLOCK PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.KUROSAWA,T.KOUYAMA REVDAT 5 13-MAR-24 2DQL 1 REMARK REVDAT 4 21-DEC-16 2DQL 1 TITLE VERSN REVDAT 3 05-MAY-09 2DQL 1 AUTHOR REMARK REVDAT 2 20-JAN-09 2DQL 1 JRNL VERSN REVDAT 1 29-MAY-07 2DQL 0 JRNL AUTH S.KUROSAWA,R.MURAKAMI,K.ONAI,M.MORISHITA,D.HASEGAWA,R.IWASE, JRNL AUTH 2 T.UZUMAKI,F.HAYASHI,T.KITAJIMA-IHARA,S.SAKATA,M.MURAKAMI, JRNL AUTH 3 T.KOUYAMA,M.ISHIURA JRNL TITL FUNCTIONALLY IMPORTANT STRUCTURAL ELEMENTS OF THE JRNL TITL 2 CYANOBACTERIAL CLOCK-RELATED PROTEIN PEX. JRNL REF GENES CELLS V. 14 1 2009 JRNL REFN ISSN 1356-9597 JRNL PMID 19032344 JRNL DOI 10.1111/J.1365-2443.2008.01245.X REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 40593 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) : 0.234 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2028 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 1.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2907 REMARK 3 BIN FREE R VALUE : 0.2832 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 218 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 : 1958 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 386 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.21200 REMARK 3 B22 (A**2) : -3.51300 REMARK 3 B33 (A**2) : 1.30100 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) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL 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 : ANISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 2DQL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000025726. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-06; 23-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 4.8 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SPRING-8; SPRING-8 REMARK 200 BEAMLINE : BL38B1; BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.92; 0.8 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41503 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 38.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.48400 REMARK 200 R SYM FOR SHELL (I) : 0.48400 REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR 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 (%): 65.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M SODIUM PHOSPHATE, PH 4.8, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 282K 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 25.06300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.85250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.52000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.85250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.06300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.52000 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: 2180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 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 114 -10.50 -154.01 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 PO4 A 201 DBREF 2DQL A 1 115 UNP Q8YQ56 Q8YQ56_ANASP 1 115 DBREF 2DQL B 1 115 UNP Q8YQ56 Q8YQ56_ANASP 1 115 SEQRES 1 A 115 MET LYS ILE GLU ASP ILE TYR GLN PHE PHE GLU ASN PRO SEQRES 2 A 115 PRO PRO THR TYR LEU CYS GLN GLU VAL ALA ILE CYS TYR SEQRES 3 A 115 ILE LEU TYR VAL LEU LEU GLN GLY GLU SER TYR GLY THR SEQRES 4 A 115 GLU LEU ILE GLN GLN LEU GLU THR GLU HIS PRO THR TYR SEQRES 5 A 115 ARG LEU SER ASP THR VAL LEU TYR SER ALA ILE LYS PHE SEQRES 6 A 115 LEU GLU ASP ASN ARG ALA ILE THR GLY TYR TRP LYS LYS SEQRES 7 A 115 LEU GLU GLY ARG GLY ARG PRO ARG ARG MET TYR GLN VAL SEQRES 8 A 115 SER PRO GLU TRP GLN HIS GLN ALA GLU ASP LEU ALA ARG SEQRES 9 A 115 LEU TRP GLN ASN TYR ILE TYR VAL ARG THR ASN SEQRES 1 B 115 MET LYS ILE GLU ASP ILE TYR GLN PHE PHE GLU ASN PRO SEQRES 2 B 115 PRO PRO THR TYR LEU CYS GLN GLU VAL ALA ILE CYS TYR SEQRES 3 B 115 ILE LEU TYR VAL LEU LEU GLN GLY GLU SER TYR GLY THR SEQRES 4 B 115 GLU LEU ILE GLN GLN LEU GLU THR GLU HIS PRO THR TYR SEQRES 5 B 115 ARG LEU SER ASP THR VAL LEU TYR SER ALA ILE LYS PHE SEQRES 6 B 115 LEU GLU ASP ASN ARG ALA ILE THR GLY TYR TRP LYS LYS SEQRES 7 B 115 LEU GLU GLY ARG GLY ARG PRO ARG ARG MET TYR GLN VAL SEQRES 8 B 115 SER PRO GLU TRP GLN HIS GLN ALA GLU ASP LEU ALA ARG SEQRES 9 B 115 LEU TRP GLN ASN TYR ILE TYR VAL ARG THR ASN HET PO4 A 201 5 HETNAM PO4 PHOSPHATE ION FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *386(H2 O) HELIX 1 1 LYS A 2 ASN A 12 1 11 HELIX 2 2 CYS A 19 LEU A 32 1 14 HELIX 3 3 TYR A 37 HIS A 49 1 13 HELIX 4 4 SER A 55 ASN A 69 1 15 HELIX 5 5 TRP A 95 ARG A 113 1 19 HELIX 6 6 LYS B 2 ASN B 12 1 11 HELIX 7 7 CYS B 19 LEU B 32 1 14 HELIX 8 8 TYR B 37 HIS B 49 1 13 HELIX 9 9 SER B 55 ASN B 69 1 15 HELIX 10 10 TRP B 95 ASN B 115 1 21 SHEET 1 A 2 THR A 16 TYR A 17 0 SHEET 2 A 2 TYR A 52 ARG A 53 1 O ARG A 53 N THR A 16 SHEET 1 B 2 ILE A 72 LYS A 77 0 SHEET 2 B 2 ARG A 86 VAL A 91 -1 O ARG A 86 N LYS A 77 SHEET 1 C 2 THR B 16 TYR B 17 0 SHEET 2 C 2 TYR B 52 ARG B 53 1 O ARG B 53 N THR B 16 SHEET 1 D 2 ILE B 72 LYS B 77 0 SHEET 2 D 2 ARG B 86 VAL B 91 -1 O MET B 88 N TYR B 75 SITE 1 AC1 7 THR A 39 ARG A 82 ARG A 86 HOH A 311 SITE 2 AC1 7 HOH A 313 HOH A 341 HOH A 428 CRYST1 50.126 75.040 103.705 90.00 90.00 90.00 P 21 21 21 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 0.019950 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013326 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009643 0.00000