HEADER PROTEIN BINDING 11-AUG-17 5Y6F TITLE CRYSTAL STRUCTURE OF YCGR IN COMPLEX WITH C-DI-GMP FROM ESCHERICHIA TITLE 2 COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAGELLAR BRAKE PROTEIN YCGR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYCLIC DI-GMP BINDING PROTEIN YCGR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: YCGR, B1194, JW1183; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); 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: PET-22B KEYWDS C-DI-GMP BINDING, FLAGELLAR BRAKE PROTEIN, MOTOR PROTEIN BINDING, KEYWDS 2 PILZ DOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.J.HOU,D.C.WANG,D.F.LI REVDAT 3 27-MAR-24 5Y6F 1 REMARK REVDAT 2 05-FEB-20 5Y6F 1 JRNL HETSYN REVDAT 1 18-JUL-18 5Y6F 0 JRNL AUTH Y.J.HOU,W.S.YANG,Y.HONG,Y.ZHANG,D.C.WANG,D.F.LI JRNL TITL STRUCTURAL INSIGHTS INTO THE MECHANISM OF C-DI-GMP-BOUND JRNL TITL 2 YCGR REGULATING FLAGELLAR MOTILITY INESCHERICHIA COLI. JRNL REF J.BIOL.CHEM. V. 295 808 2020 JRNL REFN ESSN 1083-351X JRNL PMID 31836667 JRNL DOI 10.1074/JBC.RA119.009739 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.060 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 15972 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 774 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 46.9998 - 4.1787 0.97 2471 126 0.1685 0.2121 REMARK 3 2 4.1787 - 3.3170 1.00 2525 146 0.1738 0.2208 REMARK 3 3 3.3170 - 2.8978 1.00 2550 143 0.1979 0.2715 REMARK 3 4 2.8978 - 2.6329 1.00 2553 115 0.2168 0.2648 REMARK 3 5 2.6329 - 2.4442 1.00 2535 130 0.2004 0.2510 REMARK 3 6 2.4442 - 2.3001 1.00 2564 114 0.2250 0.2895 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.90 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 : 0.012 1973 REMARK 3 ANGLE : 1.380 2691 REMARK 3 CHIRALITY : 0.065 300 REMARK 3 PLANARITY : 0.008 327 REMARK 3 DIHEDRAL : 17.236 1136 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 108 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.2627 -0.9547 9.6136 REMARK 3 T TENSOR REMARK 3 T11: 0.4710 T22: 0.4111 REMARK 3 T33: 0.4776 T12: -0.0102 REMARK 3 T13: -0.0702 T23: -0.0198 REMARK 3 L TENSOR REMARK 3 L11: 7.8329 L22: 3.4975 REMARK 3 L33: 6.2585 L12: 1.4732 REMARK 3 L13: 3.9124 L23: 2.0440 REMARK 3 S TENSOR REMARK 3 S11: -0.3157 S12: 0.2633 S13: 0.4511 REMARK 3 S21: -0.7508 S22: -0.0906 S23: 0.6458 REMARK 3 S31: -0.4807 S32: -0.6126 S33: 0.3352 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 109 THROUGH 127 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.3566 -13.3811 25.6318 REMARK 3 T TENSOR REMARK 3 T11: 0.4086 T22: 0.3472 REMARK 3 T33: 0.4615 T12: -0.0472 REMARK 3 T13: 0.1120 T23: 0.0153 REMARK 3 L TENSOR REMARK 3 L11: 4.7045 L22: 4.0394 REMARK 3 L33: 5.4325 L12: 0.4133 REMARK 3 L13: 1.5350 L23: 0.8617 REMARK 3 S TENSOR REMARK 3 S11: -0.0429 S12: -0.2502 S13: -0.8743 REMARK 3 S21: 0.4166 S22: 0.0218 S23: 0.1497 REMARK 3 S31: 0.7795 S32: -0.0819 S33: -0.0660 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 128 THROUGH 154 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.1871 -19.9614 39.0982 REMARK 3 T TENSOR REMARK 3 T11: 0.9298 T22: 1.1910 REMARK 3 T33: 0.9667 T12: -0.1534 REMARK 3 T13: 0.1816 T23: 0.3604 REMARK 3 L TENSOR REMARK 3 L11: 4.7707 L22: 6.9582 REMARK 3 L33: 2.2993 L12: 2.4958 REMARK 3 L13: -3.2874 L23: -1.4658 REMARK 3 S TENSOR REMARK 3 S11: -0.4968 S12: -1.3377 S13: -1.5429 REMARK 3 S21: 1.1425 S22: 0.0222 S23: 1.0907 REMARK 3 S31: 0.3146 S32: -0.9936 S33: 0.6209 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 155 THROUGH 206 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.9293 -17.2502 38.3145 REMARK 3 T TENSOR REMARK 3 T11: 0.8230 T22: 1.0296 REMARK 3 T33: 1.0154 T12: -0.0296 REMARK 3 T13: 0.3349 T23: 0.2934 REMARK 3 L TENSOR REMARK 3 L11: 6.6660 L22: 8.4913 REMARK 3 L33: 5.4216 L12: -0.8894 REMARK 3 L13: -1.8507 L23: 1.0907 REMARK 3 S TENSOR REMARK 3 S11: -0.2310 S12: -1.2140 S13: -1.4159 REMARK 3 S21: 1.4171 S22: -0.7898 S23: 0.4777 REMARK 3 S31: 0.5521 S32: 0.3852 S33: 0.7471 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 207 THROUGH 243 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.5798 -22.5186 30.2389 REMARK 3 T TENSOR REMARK 3 T11: 0.6832 T22: 0.4891 REMARK 3 T33: 0.5468 T12: -0.1240 REMARK 3 T13: -0.0136 T23: 0.2492 REMARK 3 L TENSOR REMARK 3 L11: 7.4668 L22: 6.3389 REMARK 3 L33: 5.2244 L12: -2.2610 REMARK 3 L13: -1.7892 L23: 1.6243 REMARK 3 S TENSOR REMARK 3 S11: -0.0086 S12: -0.4263 S13: -0.7782 REMARK 3 S21: 0.7198 S22: 0.1294 S23: -0.2657 REMARK 3 S31: 0.8470 S32: -0.0903 S33: -0.0456 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 5Y6F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1300004700. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM V.7.0.4 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15972 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 46.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.49300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M POTASSIUM THIOCYANATE, 0.1M BIS REMARK 280 -TRIS PH 6.0, 20% (W/V) PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.99000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.12969 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.54667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 46.99000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 27.12969 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 36.54667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 46.99000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 27.12969 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 36.54667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 54.25938 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 73.09333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 54.25938 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 73.09333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 54.25938 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 73.09333 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 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 LEU A 123 REMARK 465 HIS A 124 REMARK 465 GLU A 156 REMARK 465 THR A 157 REMARK 465 ALA A 158 REMARK 465 LYS A 159 REMARK 465 PRO A 160 REMARK 465 LYS A 195 REMARK 465 VAL A 196 REMARK 465 ILE A 197 REMARK 465 ASP A 198 REMARK 465 GLY A 199 REMARK 465 LYS A 200 REMARK 465 ASN A 201 REMARK 465 GLU A 202 REMARK 465 THR A 203 REMARK 465 ASP A 244 REMARK 465 LYS A 245 REMARK 465 LEU A 246 REMARK 465 ALA A 247 REMARK 465 ALA A 248 REMARK 465 ALA A 249 REMARK 465 LEU A 250 REMARK 465 GLU A 251 REMARK 465 HIS A 252 REMARK 465 HIS A 253 REMARK 465 HIS A 254 REMARK 465 HIS A 255 REMARK 465 HIS A 256 REMARK 465 HIS A 257 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 O ASP A 185 N LEU A 214 2.18 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 GLN A 96 3.94 83.10 REMARK 500 ALA A 170 -50.59 -120.61 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 SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C2E A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C2E A 303 DBREF 5Y6F A 1 244 UNP P76010 YCGR_ECOLI 1 244 SEQADV 5Y6F LYS A 245 UNP P76010 EXPRESSION TAG SEQADV 5Y6F LEU A 246 UNP P76010 EXPRESSION TAG SEQADV 5Y6F ALA A 247 UNP P76010 EXPRESSION TAG SEQADV 5Y6F ALA A 248 UNP P76010 EXPRESSION TAG SEQADV 5Y6F ALA A 249 UNP P76010 EXPRESSION TAG SEQADV 5Y6F LEU A 250 UNP P76010 EXPRESSION TAG SEQADV 5Y6F GLU A 251 UNP P76010 EXPRESSION TAG SEQADV 5Y6F HIS A 252 UNP P76010 EXPRESSION TAG SEQADV 5Y6F HIS A 253 UNP P76010 EXPRESSION TAG SEQADV 5Y6F HIS A 254 UNP P76010 EXPRESSION TAG SEQADV 5Y6F HIS A 255 UNP P76010 EXPRESSION TAG SEQADV 5Y6F HIS A 256 UNP P76010 EXPRESSION TAG SEQADV 5Y6F HIS A 257 UNP P76010 EXPRESSION TAG SEQRES 1 A 257 MET SER HIS TYR HIS GLU GLN PHE LEU LYS GLN ASN PRO SEQRES 2 A 257 LEU ALA VAL LEU GLY VAL LEU ARG ASP LEU HIS LYS ALA SEQRES 3 A 257 ALA ILE PRO LEU ARG LEU SER TRP ASN GLY GLY GLN LEU SEQRES 4 A 257 ILE SER LYS LEU LEU ALA ILE THR PRO ASP LYS LEU VAL SEQRES 5 A 257 LEU ASP PHE GLY SER GLN ALA GLU ASP ASN ILE ALA VAL SEQRES 6 A 257 LEU LYS ALA GLN HIS ILE THR ILE THR ALA GLU THR GLN SEQRES 7 A 257 GLY ALA LYS VAL GLU PHE THR VAL GLU GLN LEU GLN GLN SEQRES 8 A 257 SER GLU TYR LEU GLN LEU PRO ALA PHE ILE THR VAL PRO SEQRES 9 A 257 PRO PRO THR LEU TRP PHE VAL GLN ARG ARG ARG TYR PHE SEQRES 10 A 257 ARG ILE SER ALA PRO LEU HIS PRO PRO TYR PHE CYS GLN SEQRES 11 A 257 THR LYS LEU ALA ASP ASN SER THR LEU ARG PHE ARG LEU SEQRES 12 A 257 TYR ASP LEU SER LEU GLY GLY MET GLY ALA LEU LEU GLU SEQRES 13 A 257 THR ALA LYS PRO ALA GLU LEU GLN GLU GLY MET ARG PHE SEQRES 14 A 257 ALA GLN ILE GLU VAL ASN MET GLY GLN TRP GLY VAL PHE SEQRES 15 A 257 HIS PHE ASP ALA GLN LEU ILE SER ILE SER GLU ARG LYS SEQRES 16 A 257 VAL ILE ASP GLY LYS ASN GLU THR ILE THR THR PRO ARG SEQRES 17 A 257 LEU SER PHE ARG PHE LEU ASN VAL SER PRO THR VAL GLU SEQRES 18 A 257 ARG GLN LEU GLN ARG ILE ILE PHE SER LEU GLU ARG GLU SEQRES 19 A 257 ALA ARG GLU LYS ALA ASP LYS VAL ARG ASP LYS LEU ALA SEQRES 20 A 257 ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS HET SO4 A 301 5 HET C2E A 302 68 HET C2E A 303 68 HETNAM SO4 SULFATE ION 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 SO4 O4 S 2- FORMUL 3 C2E 2(C20 H24 N10 O14 P2) FORMUL 5 HOH *42(H2 O) HELIX 1 AA1 HIS A 5 GLN A 7 5 3 HELIX 2 AA2 ASN A 12 ALA A 26 1 15 HELIX 3 AA3 GLN A 58 LYS A 67 1 10 HELIX 4 AA4 SER A 217 LYS A 241 1 25 SHEET 1 AA1 9 LEU A 9 LYS A 10 0 SHEET 2 AA1 9 LEU A 108 VAL A 111 -1 O LEU A 108 N LYS A 10 SHEET 3 AA1 9 ALA A 80 VAL A 86 -1 N LYS A 81 O VAL A 111 SHEET 4 AA1 9 ILE A 71 THR A 77 -1 N ILE A 73 O PHE A 84 SHEET 5 AA1 9 PRO A 29 TRP A 34 -1 N SER A 33 O THR A 72 SHEET 6 AA1 9 GLY A 37 THR A 47 -1 O LEU A 39 N LEU A 32 SHEET 7 AA1 9 LYS A 50 ASP A 54 -1 O LYS A 50 N THR A 47 SHEET 8 AA1 9 LEU A 97 THR A 102 -1 O PHE A 100 N LEU A 53 SHEET 9 AA1 9 GLN A 90 TYR A 94 -1 N SER A 92 O ALA A 99 SHEET 1 AA2 8 ILE A 119 SER A 120 0 SHEET 2 AA2 8 THR A 138 SER A 147 -1 O LEU A 146 N ILE A 119 SHEET 3 AA2 8 GLY A 150 LEU A 154 -1 O LEU A 154 N ARG A 142 SHEET 4 AA2 8 PRO A 207 LEU A 214 -1 O LEU A 209 N ALA A 153 SHEET 5 AA2 8 VAL A 181 GLU A 193 -1 N ASP A 185 O LEU A 214 SHEET 6 AA2 8 ILE A 172 ASN A 175 -1 N VAL A 174 O PHE A 182 SHEET 7 AA2 8 PHE A 128 LYS A 132 -1 N PHE A 128 O ASN A 175 SHEET 8 AA2 8 THR A 138 SER A 147 -1 O LEU A 139 N THR A 131 SITE 1 AC1 5 GLU A 6 ARG A 114 TYR A 116 PHE A 117 SITE 2 AC1 5 ARG A 118 SITE 1 AC2 19 ARG A 113 ARG A 114 ARG A 115 TYR A 116 SITE 2 AC2 19 ARG A 118 ASP A 145 LEU A 146 SER A 147 SITE 3 AC2 19 GLY A 149 GLY A 150 MET A 151 GLY A 152 SITE 4 AC2 19 ILE A 189 ARG A 208 SER A 210 PHE A 211 SITE 5 AC2 19 ARG A 212 C2E A 303 HOH A 402 SITE 1 AC3 21 GLU A 6 GLU A 76 GLY A 79 ALA A 80 SITE 2 AC3 21 LYS A 81 VAL A 111 ARG A 113 ARG A 114 SITE 3 AC3 21 ARG A 118 ILE A 189 SER A 190 SER A 192 SITE 4 AC3 21 ARG A 208 SER A 210 C2E A 302 HOH A 407 SITE 5 AC3 21 HOH A 408 HOH A 409 HOH A 413 HOH A 417 SITE 6 AC3 21 HOH A 424 CRYST1 93.980 93.980 109.640 90.00 90.00 120.00 H 3 9 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 0.010641 0.006143 0.000000 0.00000 SCALE2 0.000000 0.012287 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009121 0.00000