HEADER SIGNALING PROTEIN 23-MAR-17 6SFT TITLE SOLUTION STRUCTURE OF PROTEIN ARR_CLED IN COMPLEX WITH C-DI-GMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TWO-COMPONENT RECEIVER PROTEIN CLED; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: ARR_CLED IS THE ARGININE RICH REGION OF CLED, RANGING COMPND 6 FROM K140 TO S174. IT BINDS INTERCALATED DIMERIC C-DI-GMP SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAULOBACTER VIBRIOIDES (STRAIN NA1000 / CB15N); SOURCE 3 ORGANISM_TAXID: 565050; SOURCE 4 STRAIN: NA1000 / CB15N; SOURCE 5 ATCC: 19089; SOURCE 6 GENE: CLED, CCNA_03198; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS C-DI-GMP, CLED, CHEY, RESPONSE REGULATOR, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.HABAZETTL,C.S.HEE,U.JENAL,T.SCHIRMER,S.GRZESIEK REVDAT 4 19-JUN-24 6SFT 1 REMARK REVDAT 3 14-JUN-23 6SFT 1 REMARK REVDAT 2 13-JAN-21 6SFT 1 JRNL REVDAT 1 10-JUN-20 6SFT 0 JRNL AUTH C.S.HEE,J.HABAZETTL,C.SCHMUTZ,T.SCHIRMER,U.JENAL,S.GRZESIEK JRNL TITL INTERCEPTING SECOND-MESSENGER SIGNALING BY RATIONALLY JRNL TITL 2 DESIGNED PEPTIDES SEQUESTERING C-DI-GMP. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 17211 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 32611811 JRNL DOI 10.1073/PNAS.2001232117 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.34 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6SFT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1292103582. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 0.47; 0.31 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-99% 15N] ARR_CLED, 3.0 REMARK 210 MM C2E, 100 MM SODIUM CHLORIDE, REMARK 210 2 MM MAGNESIM CHLORIDE, 20 MM REMARK 210 SODIUM PHOSPHATE, 0.02 % SODIUM REMARK 210 AZIDE, 95% H2O/5% D2O; 0.9 MM [U- REMARK 210 99% 13C; U-99% 15N] ARR_CLED, REMARK 210 2.7 MM C2E, 100 MM SODIUM REMARK 210 CHLORIDE, 2 MM MAGNESIUM REMARK 210 CHLORIDE, 20 MM SODIUM PHOSPHATE, REMARK 210 0.02 % SODIUM AZIDE, 95% H2O/5% REMARK 210 D2O; 0.6 MM [U-99% 13C; U-99% REMARK 210 15N] ARR_CLED, 1.8 MM C2E, 66.6 REMARK 210 MM SODIUM CHLORIDE, 1.33 MM REMARK 210 MAGNESIUM CHLORIDE, 13.33 MM REMARK 210 SODIUM PHOSPHATE, 9 MG/ML PF1 REMARK 210 PHAGE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D 1H-15N TOCSY; 3D 1H-15N NH2 REMARK 210 NOESY; 3D 1H-15N NH2 TOCSY; 2D REMARK 210 1H-1H NOESY; 3D HNCA; 3D HNCO; REMARK 210 3D CBCA(CO)NH; 3D HBHA(CO)NH; 3D REMARK 210 CBCANH; 3D C(CO)NH; 2D 1H-1H REMARK 210 NOESY ISOTPE FILTERED; 3D 15N T1 REMARK 210 INTERLEAVED; 3D 15N T2 REMARK 210 INTERLEAVED; 2D 1H-15N NOE REMARK 210 WITHOUT STURATION; 2D 1H-15N NOE REMARK 210 WITH STURATION; 3D HN(CO)CA; 3D REMARK 210 HN(CO)CA WITHOUT DECOUPLING; 2D REMARK 210 1H-15N HSQC IPAP REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH 2.34, SPARKY 3.115, REMARK 210 NMRPIPE 8.9, MODELFREE 4, PIPP, REMARK 210 TOPSPIN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 9.0 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 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 1 LYS A 140 75.14 -161.71 REMARK 500 1 ARG A 142 -136.04 -70.55 REMARK 500 1 ARG A 157 -13.03 -155.41 REMARK 500 1 LYS A 168 14.55 -144.12 REMARK 500 2 PRO A 141 -124.73 -78.64 REMARK 500 2 ARG A 142 47.60 -146.87 REMARK 500 2 ARG A 157 -10.45 -155.61 REMARK 500 2 LYS A 168 15.12 -143.86 REMARK 500 3 LYS A 140 59.62 -165.24 REMARK 500 3 ARG A 142 -138.84 -69.73 REMARK 500 3 GLU A 143 72.51 53.24 REMARK 500 3 ARG A 157 -7.57 -155.74 REMARK 500 3 LYS A 168 14.63 -141.24 REMARK 500 4 LYS A 140 67.00 -165.39 REMARK 500 4 PRO A 141 -121.19 -81.73 REMARK 500 4 ARG A 157 -9.53 -155.95 REMARK 500 4 LYS A 168 14.24 -141.08 REMARK 500 5 LYS A 140 76.82 53.64 REMARK 500 5 PRO A 141 171.80 -55.31 REMARK 500 5 ARG A 157 -11.91 -150.36 REMARK 500 5 LYS A 168 15.35 -143.02 REMARK 500 6 ARG A 142 -134.89 -72.69 REMARK 500 6 ARG A 157 -9.84 -155.80 REMARK 500 7 ARG A 142 -137.62 -66.25 REMARK 500 7 ARG A 157 -14.90 -154.99 REMARK 500 7 LYS A 168 16.91 -145.13 REMARK 500 8 LYS A 140 -42.75 -163.34 REMARK 500 8 PRO A 141 -112.37 -94.75 REMARK 500 8 ARG A 142 -130.83 -135.48 REMARK 500 8 LYS A 168 14.20 -141.58 REMARK 500 9 ARG A 142 -132.17 -65.83 REMARK 500 9 ARG A 157 -8.69 -155.95 REMARK 500 9 LYS A 168 15.00 -142.69 REMARK 500 10 ARG A 142 -136.00 -71.45 REMARK 500 10 ARG A 157 -11.41 -155.53 REMARK 500 10 LYS A 168 15.40 -144.27 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 C2E A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C2E A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 27990 RELATED DB: BMRB REMARK 900 APO ARR_CLED ASSIGNMENTS REMARK 900 RELATED ID: 50001 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF PROTEIN ARR_CLED IN COMPLEX WITH C-DI-GMP DBREF1 6SFT A 140 174 UNP A0A0H3CCM2_CAUVN DBREF2 6SFT A A0A0H3CCM2 140 174 SEQADV 6SFT SER A 139 UNP A0A0H3CCM EXPRESSION TAG SEQRES 1 A 36 SER LYS PRO ARG GLU TRP VAL GLU ALA VAL ALA TYR VAL SEQRES 2 A 36 GLY PRO ASP ARG ARG ARG PHE ASN SER ALA ASP TYR LYS SEQRES 3 A 36 GLY PRO ARG LYS ARG LYS ALA ASP ALA SER HET C2E A 501 68 HET C2E A 502 68 HETNAM C2E 9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10, HETNAM 2 C2E 12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3, HETNAM 3 C2E 2-D:3',2'-J][1,3,7,9,2, HETNAM 4 C2E 8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO- HETNAM 5 C2E 1,9-DIHYDRO-6H-PURIN-6-ONE) HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE FORMUL 2 C2E 2(C20 H24 N10 O14 P2) HELIX 1 AA1 ARG A 169 ALA A 173 5 5 SHEET 1 AA1 2 VAL A 145 GLU A 146 0 SHEET 2 AA1 2 VAL A 151 GLY A 152 -1 O GLY A 152 N VAL A 145 SITE 1 AC1 8 TYR A 150 ASP A 154 ARG A 155 ARG A 156 SITE 2 AC1 8 LYS A 168 ARG A 169 LYS A 170 C2E A 502 SITE 1 AC2 7 ARG A 155 ARG A 156 PHE A 158 TYR A 163 SITE 2 AC2 7 LYS A 168 ARG A 169 C2E A 501 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1