HEADER C-DI-GMP BINDING PROTEIN 02-DEC-10 2L74 TITLE SOLUTION STRUCTURE OF THE PILZ DOMAIN PROTEIN PA4608 COMPLEX WITH C- TITLE 2 DI-GMP IDENTIFIES CHARGE CLUSTERING AS MOLECULAR READOUT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN PA4608; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: PA4608; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET15 KEYWDS PILZ, PA4608, C-DI-GMP, UNKNOWN FUNCTION, C-DI-GMP BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.HABAZETTL,M.ALLAN,U.JENAL,S.GRZESIEK REVDAT 4 01-MAY-24 2L74 1 REMARK SEQADV HETSYN REVDAT 3 28-DEC-11 2L74 1 JRNL VERSN REVDAT 2 23-FEB-11 2L74 1 JRNL REVDAT 1 09-FEB-11 2L74 0 JRNL AUTH J.HABAZETTL,M.G.ALLAN,U.JENAL,S.GRZESIEK JRNL TITL SOLUTION STRUCTURE OF THE PILZ DOMAIN PROTEIN PA4608 COMPLEX JRNL TITL 2 WITH CYCLIC DI-GMP IDENTIFIES CHARGE CLUSTERING AS MOLECULAR JRNL TITL 3 READOUT JRNL REF J.BIOL.CHEM. V. 286 14304 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21310957 JRNL DOI 10.1074/JBC.M110.209007 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, X-PLOR NIH, SPARKY REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR NIH), GODDARD (SPARKY) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L74 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000102040. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 313; 303 REMARK 210 PH : 6.7; 6.7; 6.7 REMARK 210 IONIC STRENGTH : NULL; NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 250 MM SODIUM CHLORIDE-1; 10 MM REMARK 210 TRIS-2; 0.01 % SODIUM AZIDE-3; REMARK 210 95% H2O/5% D2O; 250 MM SODIUM REMARK 210 CHLORIDE-4; 10 MM TRIS-5; 0.01 % REMARK 210 SODIUM AZIDE-6; 95% H2O/5% D2O; REMARK 210 250 MM SODIUM CHLORIDE-7; 10 MM REMARK 210 TRIS-8; 0.01 % SODIUM AZIDE-9; REMARK 210 100% D2O; 250 MM SODIUM CHLORIDE- REMARK 210 10; 10 MM TRIS-11; 0.01 % SODIUM REMARK 210 AZIDE-12; 100% D2O; 250 MM REMARK 210 SODIUM CHLORIDE-13; 10 MM TRIS- REMARK 210 14; 0.01 % SODIUM AZIDE-15, 93% REMARK 210 H2O/7% D2O; 250 MM SODIUM REMARK 210 CHLORIDE-16; 10 MM TRIS-17; 0.01 REMARK 210 % SODIUM AZIDE-18; 95% H2O/5% REMARK 210 D2O; 250 MM SODIUM CHLORIDE-19; REMARK 210 10 MM TRIS-20; 0.01 % SODIUM REMARK 210 AZIDE-21; 95% H2O/5% D2O; 250 MM REMARK 210 SODIUM CHLORIDE-22; 10 MM TRIS- REMARK 210 23; 0.01 % SODIUM AZIDE-24; 95% REMARK 210 H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D H(CCO)NH; 3D HCCH- REMARK 210 TOCSY; 3D HCCH-TOCSY (RIBOSE); REMARK 210 3D HCCH-COSY (RIBOSE); HAHB; REMARK 210 HAHB (RIBOSE); 13C-{13CG}SPIN- REMARK 210 ECHO DIFFERENCE H-15N HSQC; 15N-{ REMARK 210 13CG} SPIN-ECHO DIFERENCE H-15N REMARK 210 HAQC; METHYL C; METHYL N; 3D 1H- REMARK 210 15N ROESY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D 1H-13C REMARK 210 NOESY(RIBOSE); 4D 13C-13C NOESY; REMARK 210 2D 1H-1H NOESY; 2D 1H-1H NOESY REMARK 210 (FILTERED AGAINST H BOUND TO 13C, REMARK 210 15N); IPAP 1H-15N HSQC; J- REMARK 210 RESOLVED CT 13C-HSQC; 2D H- REMARK 210 RESOLVED 15N EXSY; 3D H-15N-15N REMARK 210 EXSY; 2D 1H RESOLVED 15N EXSY; REMARK 210 2D 1H-RESOLVED 15N EXSY; 15N REMARK 210 RELAXATION REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DPX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PIPP, SPARKY, X-PLOR NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 H MET A 1 H SER A 2 1.26 REMARK 500 H SER A 2 OE1 GLN A 4 1.47 REMARK 500 H MET A 1 OE1 GLN A 4 1.48 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 1 SER A 2 -119.45 -101.97 REMARK 500 1 HIS A 5 27.77 31.43 REMARK 500 1 ASP A 6 74.57 43.43 REMARK 500 1 ARG A 10 -71.28 8.79 REMARK 500 1 HIS A 12 -172.38 -54.48 REMARK 500 1 ILE A 14 100.06 -46.50 REMARK 500 1 HIS A 39 40.17 -159.72 REMARK 500 1 TRP A 49 69.62 -59.30 REMARK 500 1 LEU A 63 -85.87 -106.17 REMARK 500 1 LEU A 111 -130.79 -114.09 REMARK 500 1 LEU A 112 -1.07 59.17 REMARK 500 1 GLU A 113 -83.22 36.06 REMARK 500 1 ARG A 114 -68.43 -24.00 REMARK 500 1 ALA A 122 -86.90 -111.02 REMARK 500 1 HIS A 123 -154.55 -127.58 REMARK 500 1 ASP A 124 51.66 27.90 REMARK 500 2 SER A 2 43.59 -166.76 REMARK 500 2 HIS A 5 7.33 117.28 REMARK 500 2 ASP A 6 158.29 -37.96 REMARK 500 2 ARG A 10 -73.75 17.76 REMARK 500 2 ILE A 14 86.04 -48.80 REMARK 500 2 ALA A 18 176.75 179.57 REMARK 500 2 LEU A 38 1.40 -62.42 REMARK 500 2 HIS A 39 44.89 -168.34 REMARK 500 2 TRP A 49 69.57 -59.51 REMARK 500 2 LEU A 63 -85.37 -104.53 REMARK 500 2 ASP A 108 123.42 -170.46 REMARK 500 2 GLU A 110 -74.28 57.49 REMARK 500 2 LEU A 111 114.15 66.07 REMARK 500 2 LEU A 112 129.12 60.04 REMARK 500 2 ARG A 114 172.35 63.45 REMARK 500 2 GLU A 115 -92.01 56.50 REMARK 500 3 SER A 2 153.53 129.21 REMARK 500 3 HIS A 5 103.66 50.47 REMARK 500 3 ARG A 10 -84.56 29.17 REMARK 500 3 HIS A 12 155.28 -36.25 REMARK 500 3 HIS A 39 38.98 -161.32 REMARK 500 3 TRP A 49 67.40 -61.56 REMARK 500 3 LEU A 63 -83.35 -105.94 REMARK 500 3 LEU A 112 -113.45 -78.07 REMARK 500 3 GLU A 113 -119.15 -90.99 REMARK 500 3 ARG A 114 110.64 55.13 REMARK 500 3 VAL A 120 0.18 -56.85 REMARK 500 3 ALA A 122 112.35 -166.61 REMARK 500 3 ASP A 124 -1.82 55.62 REMARK 500 4 SER A 2 35.54 -78.60 REMARK 500 4 HIS A 5 73.30 -14.48 REMARK 500 4 ASP A 6 91.87 19.98 REMARK 500 4 ARG A 10 -91.18 17.33 REMARK 500 4 HIS A 39 43.16 -162.25 REMARK 500 REMARK 500 THIS ENTRY HAS 299 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE NOMENCLATURE OF C2E IN PDB FOLLOWS THE PDB'S CHEMICAL COMPONENT REMARK 600 DICTIONARY. THEREFORE DISCREPANCY OF NOMENCLATURE WILL APPEAR REMARK 600 BETWEEN PDB AND THE REFERENCE ARTICLE. 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: 1YWU RELATED DB: PDB REMARK 900 APO PA4608 REMARK 900 RELATED ID: 3KYF RELATED DB: PDB REMARK 900 HOLO PP4397 DBREF 2L74 A 1 125 UNP Q9HVI1 Q9HVI1_PSEAE 1 125 SEQADV 2L74 MET A -19 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 GLY A -18 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 SER A -17 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 SER A -16 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 HIS A -15 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 HIS A -14 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 HIS A -13 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 HIS A -12 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 HIS A -11 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 HIS A -10 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 SER A -9 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 SER A -8 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 GLY A -7 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 LEU A -6 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 VAL A -5 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 PRO A -4 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 ARG A -3 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 GLY A -2 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 SER A -1 UNP Q9HVI1 EXPRESSION TAG SEQADV 2L74 HIS A 0 UNP Q9HVI1 EXPRESSION TAG SEQRES 1 A 145 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 145 LEU VAL PRO ARG GLY SER HIS MET SER ASP GLN HIS ASP SEQRES 3 A 145 GLU ARG ARG ARG PHE HIS ARG ILE ALA PHE ASP ALA ASP SEQRES 4 A 145 SER GLU ILE LEU GLN GLY GLU ARG ARG TRP GLU VAL LEU SEQRES 5 A 145 LEU HIS ASP VAL SER LEU HIS GLY ILE LEU VAL GLY GLN SEQRES 6 A 145 PRO GLN ASP TRP ASN GLY ASP PRO GLN ARG PRO PHE GLU SEQRES 7 A 145 ALA ARG LEU TYR LEU GLY LEU ASP VAL LEU ILE ARG MET SEQRES 8 A 145 GLU ILE SER LEU ALA TRP ALA ARG ASP GLY LEU LEU GLY SEQRES 9 A 145 PHE GLU CYS GLN HIS ILE ASP LEU ASP SER ILE SER HIS SEQRES 10 A 145 LEU ARG ARG LEU VAL GLU LEU ASN LEU GLY ASP GLU GLU SEQRES 11 A 145 LEU LEU GLU ARG GLU LEU ALA LEU LEU VAL SER ALA HIS SEQRES 12 A 145 ASP ASP 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 1 ASP A 91 GLY A 107 1 17 HELIX 2 2 GLU A 113 LEU A 118 1 6 HELIX 3 3 LEU A 119 ALA A 122 5 4 SHEET 1 A 7 ALA A 18 GLN A 24 0 SHEET 2 A 7 ARG A 27 SER A 37 -1 O VAL A 31 N SER A 20 SHEET 3 A 7 GLY A 40 GLY A 44 -1 O GLY A 40 N SER A 37 SHEET 4 A 7 LEU A 82 ILE A 90 -1 O LEU A 83 N VAL A 43 SHEET 5 A 7 LEU A 68 ARG A 79 -1 N GLU A 72 O HIS A 89 SHEET 6 A 7 PHE A 57 TYR A 62 -1 N ALA A 59 O MET A 71 SHEET 7 A 7 ALA A 18 GLN A 24 -1 N GLU A 21 O ARG A 60 SITE 1 AC1 15 ARG A 8 ARG A 9 ARG A 10 ARG A 13 SITE 2 AC1 15 ASP A 35 VAL A 36 SER A 37 HIS A 39 SITE 3 AC1 15 GLY A 40 ILE A 41 LEU A 42 TRP A 77 SITE 4 AC1 15 PHE A 85 GLU A 86 C2E A 502 SITE 1 AC2 9 HIS A 5 ASP A 6 GLU A 7 ARG A 8 SITE 2 AC2 9 ARG A 9 HIS A 12 ARG A 13 TRP A 77 SITE 3 AC2 9 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