HEADER SIGNALING PROTEIN 31-MAY-15 5BRJ TITLE STRUCTURE OF THE BACTERIOPHYTOCHROME RESPONSE REGULATOR ATBRR COMPND MOL_ID: 1; COMPND 2 MOLECULE: TWO COMPONENT RESPONSE REGULATOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AGROBACTERIUM TUMEFACIENS CCNWGS0286; SOURCE 3 ORGANISM_TAXID: 1082932; SOURCE 4 GENE: ATCR1_17512; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS BACTERIOPHYTOCHROME, RESPONSE REGULATOR, STABLE DIMER, TWO COMPONENT KEYWDS 2 SYSTEM, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.W.BAKER,K.A.SATYSHUR,K.T.FOREST REVDAT 6 06-MAR-24 5BRJ 1 REMARK REVDAT 5 27-NOV-19 5BRJ 1 REMARK REVDAT 4 01-NOV-17 5BRJ 1 REMARK REVDAT 3 06-SEP-17 5BRJ 1 JRNL REMARK REVDAT 2 13-APR-16 5BRJ 1 JRNL REVDAT 1 24-FEB-16 5BRJ 0 JRNL AUTH A.W.BAKER,K.A.SATYSHUR,N.MORENO MORALES,K.T.FOREST JRNL TITL ARM-IN-ARM RESPONSE REGULATOR DIMERS PROMOTE INTERMOLECULAR JRNL TITL 2 SIGNAL TRANSDUCTION. JRNL REF J.BACTERIOL. V. 198 1218 2016 JRNL REFN ESSN 1098-5530 JRNL PMID 26833410 JRNL DOI 10.1128/JB.00872-15 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 12959 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1296 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 30.8995 - 3.9958 0.98 1442 161 0.1730 0.2071 REMARK 3 2 3.9958 - 3.1726 1.00 1327 147 0.1746 0.1926 REMARK 3 3 3.1726 - 2.7719 0.99 1313 146 0.2069 0.2470 REMARK 3 4 2.7719 - 2.5186 0.99 1294 144 0.2190 0.2700 REMARK 3 5 2.5186 - 2.3381 0.99 1283 143 0.2143 0.2911 REMARK 3 6 2.3381 - 2.2003 0.99 1263 141 0.2133 0.2803 REMARK 3 7 2.2003 - 2.0901 0.98 1240 137 0.2225 0.3091 REMARK 3 8 2.0901 - 1.9992 0.98 1258 140 0.2185 0.2895 REMARK 3 9 1.9992 - 1.9222 0.97 1243 137 0.2171 0.2743 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.70 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 : 0.007 1130 REMARK 3 ANGLE : 1.029 1543 REMARK 3 CHIRALITY : 0.042 184 REMARK 3 PLANARITY : 0.005 201 REMARK 3 DIHEDRAL : 12.781 421 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 5BRJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000209181. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-AUG-14 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 : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13163 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 27.20 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 53.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 26.40 REMARK 200 R MERGE FOR SHELL (I) : 0.15500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 23.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.9_1692 REMARK 200 STARTING MODEL: RTBRR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM MAGNESIUM CHLORIDE, 100 MM TRIS REMARK 280 PH 8.5, 20% PEG 8000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 93.85650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 46.92825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 140.78475 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 93.85650 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 140.78475 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 46.92825 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 300 REMARK: DIMER CONFIRMED BY SIZE EXCLUSION CHROMATOGRAPHY AND REMARK 300 STRUCTURE PACKING 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: 3000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 187.71300 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 370 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 378 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 0 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 53 CG OD1 ND2 REMARK 470 ARG A 98 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS A 67 O HOH A 301 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 53 26.03 46.60 REMARK 500 PRO A 55 107.57 -53.10 REMARK 500 LYS A 70 -60.58 71.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 11 OD1 REMARK 620 2 ASP A 65 OD2 90.3 REMARK 620 3 LYS A 67 O 89.5 85.8 REMARK 620 4 HOH A 315 O 86.3 174.4 89.7 REMARK 620 5 HOH A 320 O 86.0 90.5 174.2 93.7 REMARK 620 6 HOH A 322 O 171.0 80.9 92.0 102.6 91.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 DBREF 5BRJ A 0 140 UNP G6XXW5 G6XXW5_RHIRD 1 141 SEQRES 1 A 141 MET PRO GLU LEU ARG PRO ILE LEU LEU VAL GLU ASP ASN SEQRES 2 A 141 PRO ARG ASP LEU GLU LEU THR LEU THR ALA LEU GLU LYS SEQRES 3 A 141 CYS GLN LEU ALA ASN GLU VAL VAL VAL ALA ARG ASP GLY SEQRES 4 A 141 THR GLU ALA LEU ASP TYR LEU ASN VAL THR GLY SER TYR SEQRES 5 A 141 HIS ASN ARG PRO GLY GLY ASP PRO ALA VAL VAL LEU LEU SEQRES 6 A 141 ASP LEU LYS LEU PRO LYS VAL ASP GLY LEU GLU VAL LEU SEQRES 7 A 141 GLN THR VAL LYS GLY SER ASP HIS LEU ARG HIS ILE PRO SEQRES 8 A 141 VAL VAL MET LEU THR SER SER ARG GLU GLU GLN ASP LEU SEQRES 9 A 141 VAL ARG SER TYR GLU LEU GLY VAL ASN ALA PHE VAL VAL SEQRES 10 A 141 LYS PRO VAL GLU PHE ASN GLN PHE PHE LYS ALA ILE GLN SEQRES 11 A 141 ASP LEU GLY VAL PHE TRP ALA LEU LEU ASN GLU HET MG A 201 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *135(H2 O) HELIX 1 AA1 ASN A 12 CYS A 26 1 15 HELIX 2 AA2 ASP A 37 ASN A 46 1 10 HELIX 3 AA3 THR A 48 HIS A 52 5 5 HELIX 4 AA4 ASP A 72 GLY A 82 1 11 HELIX 5 AA5 SER A 97 TYR A 107 1 11 HELIX 6 AA6 GLU A 120 GLY A 132 1 13 SHEET 1 AA1 5 VAL A 32 ALA A 35 0 SHEET 2 AA1 5 ILE A 6 VAL A 9 1 N ILE A 6 O VAL A 33 SHEET 3 AA1 5 VAL A 61 ASP A 65 1 O LEU A 63 N LEU A 7 SHEET 4 AA1 5 VAL A 91 THR A 95 1 O VAL A 92 N LEU A 64 SHEET 5 AA1 5 PHE A 114 VAL A 116 1 O VAL A 115 N THR A 95 LINK OD1 ASP A 11 MG MG A 201 1555 1555 1.95 LINK OD2 ASP A 65 MG MG A 201 1555 1555 1.94 LINK O LYS A 67 MG MG A 201 1555 1555 2.19 LINK MG MG A 201 O HOH A 315 1555 1555 2.15 LINK MG MG A 201 O HOH A 320 1555 1555 2.12 LINK MG MG A 201 O HOH A 322 1555 1555 2.13 CISPEP 1 LYS A 117 PRO A 118 0 1.54 SITE 1 AC1 6 ASP A 11 ASP A 65 LYS A 67 HOH A 315 SITE 2 AC1 6 HOH A 320 HOH A 322 CRYST1 41.046 41.046 187.713 90.00 90.00 90.00 P 41 2 2 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 0.024363 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024363 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005327 0.00000