HEADER TRANSCRIPTION 18-JUN-13 4L9E TITLE STRUCTURE OF PPSR Q-PAS1 FROM RB. SPHAEROIDES COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR, PPSR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 123-257; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOBACTER SPHAEROIDES; SOURCE 3 ORGANISM_TAXID: 272943; SOURCE 4 STRAIN: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158; SOURCE 5 GENE: PPSR, RHOS4_18870, RSP_0282; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETM11 KEYWDS PAS DOMAIN, PER-ARNT-SIM, OLIGOMERIZATION, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR U.HEINTZ,A.MEINHART,I.SCHLICHTING,A.WINKLER REVDAT 4 20-SEP-23 4L9E 1 SEQADV REVDAT 3 15-NOV-17 4L9E 1 REMARK REVDAT 2 02-APR-14 4L9E 1 JRNL REVDAT 1 12-FEB-14 4L9E 0 JRNL AUTH U.HEINTZ,A.MEINHART,A.WINKLER JRNL TITL MULTI-PAS DOMAIN-MEDIATED PROTEIN OLIGOMERIZATION OF PPSR JRNL TITL 2 FROM RHODOBACTER SPHAEROIDES. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 863 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 24598755 JRNL DOI 10.1107/S1399004713033634 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 15633 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 798 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 43.6300 - 2.9981 1.00 2688 142 0.1845 0.2058 REMARK 3 2 2.9981 - 2.3797 1.00 2493 130 0.2144 0.2019 REMARK 3 3 2.3797 - 2.0789 1.00 2428 141 0.1972 0.2365 REMARK 3 4 2.0789 - 1.8889 1.00 2428 136 0.2093 0.2787 REMARK 3 5 1.8889 - 1.7535 1.00 2386 133 0.2319 0.2822 REMARK 3 6 1.7535 - 1.6500 1.00 2409 116 0.2490 0.3157 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.39 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 : 0.006 903 REMARK 3 ANGLE : 0.966 1220 REMARK 3 CHIRALITY : 0.068 145 REMARK 3 PLANARITY : 0.006 162 REMARK 3 DIHEDRAL : 10.749 355 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 157 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.2705 -1.5323 -4.0289 REMARK 3 T TENSOR REMARK 3 T11: 0.3799 T22: 0.4154 REMARK 3 T33: 0.4861 T12: 0.0874 REMARK 3 T13: 0.0826 T23: 0.0134 REMARK 3 L TENSOR REMARK 3 L11: 5.3038 L22: 7.5098 REMARK 3 L33: 4.1956 L12: 0.0207 REMARK 3 L13: 2.9449 L23: -1.0805 REMARK 3 S TENSOR REMARK 3 S11: 0.3191 S12: 0.9452 S13: -0.5153 REMARK 3 S21: -0.2383 S22: -0.3723 S23: -1.5653 REMARK 3 S31: 0.4322 S32: 1.3486 S33: -0.1179 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 158 THROUGH 257 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.3620 15.0536 -0.6997 REMARK 3 T TENSOR REMARK 3 T11: 0.2527 T22: 0.2330 REMARK 3 T33: 0.2514 T12: -0.0013 REMARK 3 T13: 0.0241 T23: -0.0150 REMARK 3 L TENSOR REMARK 3 L11: 4.6103 L22: 4.3634 REMARK 3 L33: 2.1459 L12: -0.7296 REMARK 3 L13: 0.7505 L23: 0.2530 REMARK 3 S TENSOR REMARK 3 S11: -0.0165 S12: -0.2612 S13: 0.2068 REMARK 3 S21: 0.1727 S22: 0.0023 S23: -0.1066 REMARK 3 S31: -0.1650 S32: -0.0561 S33: 0.0215 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 4L9E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000080346. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9765 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : DYNAMICALLY BENDABLE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15633 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.55800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.420 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: PDB ENTRY 4L9F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.9% (W/V) PEG 3000, 0.2 M MAGNESIUM REMARK 280 CHLORIDE, 0.1 M SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.43667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 108.87333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 81.65500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 136.09167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.21833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 54.43667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 108.87333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 136.09167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 81.65500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 27.21833 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: 2610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 377 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 GLY A 119 REMARK 465 ALA A 120 REMARK 465 MET A 121 REMARK 465 GLY A 122 REMARK 465 ILE A 123 REMARK 465 ALA A 124 REMARK 465 GLU A 125 REMARK 465 VAL A 126 REMARK 465 GLN A 127 REMARK 465 GLN A 128 REMARK 465 GLN A 129 REMARK 465 LEU A 130 REMARK 465 VAL A 131 REMARK 465 ALA A 132 REMARK 465 ALA A 133 REMARK 465 GLN A 134 REMARK 465 LEU A 135 REMARK 465 ALA A 136 REMARK 465 MET A 137 REMARK 465 GLU A 138 REMARK 465 ARG A 139 REMARK 465 ASP A 140 REMARK 465 TYR A 141 REMARK 465 GLU A 142 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HH2 RELATED DB: PDB REMARK 900 RELATED ID: 4HH3 RELATED DB: PDB REMARK 900 RELATED ID: 4HH0 RELATED DB: PDB REMARK 900 RELATED ID: 4L9F RELATED DB: PDB REMARK 900 RELATED ID: 4L9G RELATED DB: PDB DBREF 4L9E A 123 257 UNP Q3J179 Q3J179_RHOS4 123 257 SEQADV 4L9E GLY A 119 UNP Q3J179 EXPRESSION TAG SEQADV 4L9E ALA A 120 UNP Q3J179 EXPRESSION TAG SEQADV 4L9E MET A 121 UNP Q3J179 EXPRESSION TAG SEQADV 4L9E GLY A 122 UNP Q3J179 EXPRESSION TAG SEQRES 1 A 139 GLY ALA MET GLY ILE ALA GLU VAL GLN GLN GLN LEU VAL SEQRES 2 A 139 ALA ALA GLN LEU ALA MET GLU ARG ASP TYR GLU THR GLN SEQRES 3 A 139 ARG GLU MET GLU THR ARG TYR ARG VAL VAL LEU ASP VAL SEQRES 4 A 139 SER ARG ASP PRO MET VAL LEU VAL SER MET SER THR GLY SEQRES 5 A 139 ARG ILE VAL ASP LEU ASN SER ALA ALA GLY LEU LEU LEU SEQRES 6 A 139 GLY GLY VAL ARG GLN ASP LEU LEU GLY ALA ALA ILE ALA SEQRES 7 A 139 GLN GLU PHE GLU GLY ARG ARG ARG GLY GLU PHE MET GLU SEQRES 8 A 139 THR MET THR ASN LEU ALA ALA THR GLU SER ALA ALA PRO SEQRES 9 A 139 VAL GLU VAL LEU ALA ARG ARG SER GLN LYS ARG LEU LEU SEQRES 10 A 139 VAL VAL PRO ARG VAL PHE ARG ALA ALA GLY GLU ARG LEU SEQRES 11 A 139 LEU LEU CYS GLN ILE ASP PRO ALA ASP FORMUL 2 HOH *82(H2 O) HELIX 1 1 THR A 143 SER A 158 1 16 HELIX 2 2 ASN A 176 GLY A 184 1 9 HELIX 3 3 VAL A 186 LEU A 191 1 6 HELIX 4 4 ALA A 194 PHE A 199 5 6 HELIX 5 5 ARG A 203 ALA A 216 1 14 SHEET 1 A 5 ILE A 172 LEU A 175 0 SHEET 2 A 5 MET A 162 SER A 166 -1 N LEU A 164 O ASP A 174 SHEET 3 A 5 GLU A 246 PRO A 255 -1 O CYS A 251 N VAL A 163 SHEET 4 A 5 ARG A 233 ALA A 243 -1 N PHE A 241 O LEU A 248 SHEET 5 A 5 VAL A 223 LEU A 226 -1 N VAL A 225 O LEU A 234 CRYST1 50.380 50.380 163.310 90.00 90.00 120.00 P 61 2 2 12 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 0.019849 0.011460 0.000000 0.00000 SCALE2 0.000000 0.022920 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006123 0.00000