HEADER SIGNALING PROTEIN 10-JAN-02 1J56 TITLE MINIMIZED AVERAGE STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER TITLE 2 DOMAIN: MODEL STRUCTURE INCORPORATING ACTIVE SITE CONTACTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITROGEN REGULATION PROTEIN NR(I); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN: RECEIVER DOMAIN, RESIDUES 1-124; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM; SOURCE 3 ORGANISM_TAXID: 602; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS TWO COMPONENT SIGNAL TRANSDUCTION, RECEIVER DOMAIN, BEF3, KEYWDS 2 PHOSPHORYLATION, BACTERIAL NITROGEN REGULATORY PROTEIN, SIGNALING KEYWDS 3 PROTEIN EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR C.A.HASTINGS,S.-Y.LEE,H.S.CHO,D.YAN,S.KUSTU,D.E.WEMMER REVDAT 4 27-DEC-23 1J56 1 REMARK REVDAT 3 23-FEB-22 1J56 1 REMARK REVDAT 2 24-FEB-09 1J56 1 VERSN REVDAT 1 19-AUG-03 1J56 0 JRNL AUTH C.A.HASTINGS,S.-Y.LEE,H.S.CHO,D.YAN,S.KUSTU,D.E.WEMMER JRNL TITL HIGH-RESOLUTION SOLUTION STRUCTURE OF THE JRNL TITL 2 BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER DOMAIN JRNL REF BIOCHEMISTRY V. 42 9081 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12885241 JRNL DOI 10.1021/BI0273866 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.S.CHO,S.-Y.LEE,D.YAN,X.PAN,J.S.PARKINSON,S.KUSTU, REMARK 1 AUTH 2 D.E.WEMMER,J.G.PELTON REMARK 1 TITL NMR STRUCTURE OF ACTIVATED CHEY REMARK 1 REF J.MOL.BIOL. V. 297 543 2000 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.2000.3595 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.-Y.LEE,H.S.CHO,J.G.PELTON,D.YAN,R.K.HENDERSON,D.S.KING, REMARK 1 AUTH 2 L.HUANG,S.KUSTU,E.A.BERRY,D.E.WEMMER REMARK 1 TITL CRYSTAL STRUCTURE OF AN ACTIVATED RESPONSE REGULATOR BOUND REMARK 1 TITL 2 TO ITS TARGET REMARK 1 REF NAT.STRUCT.BIOL. V. 8 52 2001 REMARK 1 REFN ISSN 1072-8368 REMARK 1 DOI 10.1038/NSB0901-789 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, CNS 1.0, MOLMOL REMARK 3 AUTHORS : GUNTERT (DYANA), BRUNGER ET. AL. (CNS 1.0) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 3 ADDITIONAL CONSTRAINTS FROM CRYSTAL REMARK 3 STRUCTURE OF BEF3-ACTIVATED CHEY WERE USED FOR STRUCTURE REMARK 3 CALCULATION. REMARK 4 REMARK 4 1J56 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-02. REMARK 100 THE DEPOSITION ID IS D_1000001626. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 303; 303; 303 REMARK 210 PH : 6.75; 6.75; 6.75; 6.75 REMARK 210 IONIC STRENGTH : 50MM NACL, 4.4MM BECL2, 7.2MM REMARK 210 MGCL2, 29MM NAF; 50MM NACL, REMARK 210 4.4MM BECL2, 7.2MM MGCL2, 29MM REMARK 210 NAF; 50MM NACL, 4.4MM BECL2, REMARK 210 7.2MM MGCL2, 29MM NAF; 50MM NACL, REMARK 210 4.4MM BECL2, 7.2MM MGCL2, 29MM REMARK 210 NAF REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT REMARK 210 SAMPLE CONTENTS : U-15N; 1.1-1.5MM NTRC RECEIVER REMARK 210 DOMAIN(1-124); 50MM SODIUM REMARK 210 PHOSPHATE BUFFER(PH6.75); 50MM REMARK 210 NACL; 4.4MM BECL2, 7.2MM MGCL2, REMARK 210 29MM NAF; 95% H2O, 5% D2O; U-15N, REMARK 210 13C;1.1-1.5MM NTRC RECEIVER REMARK 210 DOMAIN(1-124); 50MM SODIUM REMARK 210 PHOSPHATE BUFFER(PH6.75); 50MM REMARK 210 NACL; 4.4MM BECL2, 7.2MM MGCL2, REMARK 210 29MM NAF; 95% H2O, 5% D2O; 10% REMARK 210 13C;1.1-1.5MM NTRC RECEIVER REMARK 210 DOMAIN(1-124); 50MM SODIUM REMARK 210 PHOSPHATE BUFFER(PH6.75); 50MM REMARK 210 NACL; 4.4MM BECL2, 7.2MM MGCL2, REMARK 210 29MM NAF; 95% H2O, 5% D2O; U-15N; REMARK 210 1.1-1.5MM NTRC RECEIVER REMARK 210 DOMAIN(1-124); 50MM SODIUM REMARK 210 PHOSPHATE BUFFER(PH6.75); 50MM REMARK 210 NACL; 4.4MM BECL2, 7.2MM MGCL2, REMARK 210 29MM NAF; 95% H2O, 5% D2O; 30MG/ REMARK 210 ML PHAGE PF1 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; REMARK 210 4D_13C/15N-SEPARATED_NOESY; 4D_ REMARK 210 13C-SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY; HNCA-J; CBCA(CO) REMARK 210 NH; 13C,1H-HSQC; IPAP-HSQC; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.0, FELIX, NMRVIEW REMARK 210 METHOD USED : DISTANCE GEOMETRY, TORSION ANGLE REMARK 210 DYNAMICS, SIMULATED ANNEALING, REMARK 210 ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: MINIMIZED AVERAGE STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED REMARK 210 NTRC RECEIVER DOMAIN: MODEL STRUCTURE INCORPORATING ACTIVE 3 REMARK 210 SITE CONTACTS. 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 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 O ILE A 55 HE2 HIS A 84 1.44 REMARK 500 O ARG A 16 H GLU A 20 1.46 REMARK 500 OD1 ASP A 12 HG1 THR A 32 1.49 REMARK 500 O GLY A 4 H THR A 29 1.54 REMARK 500 O ASP A 12 H ARG A 16 1.55 REMARK 500 OD2 ASP A 10 HZ3 LYS A 104 1.55 REMARK 500 O ILE A 108 H VAL A 112 1.57 REMARK 500 O TRP A 7 H LEU A 52 1.59 REMARK 500 O ASP A 10 H ASP A 12 1.60 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 ASP A 10 109.87 -178.29 REMARK 500 ASP A 11 -53.89 68.47 REMARK 500 ASP A 12 -98.34 90.37 REMARK 500 ASN A 35 -35.90 -151.74 REMARK 500 LYS A 46 130.34 173.54 REMARK 500 ASP A 54 -168.14 -68.74 REMARK 500 ILE A 55 51.58 -157.32 REMARK 500 ARG A 56 74.54 -153.39 REMARK 500 MET A 57 -61.56 178.10 REMARK 500 PRO A 58 153.37 -48.79 REMARK 500 MET A 60 55.52 -105.95 REMARK 500 ASP A 61 -74.89 57.71 REMARK 500 PRO A 77 91.53 -67.85 REMARK 500 PHE A 99 -78.96 -64.25 REMARK 500 PHE A 106 -69.48 -143.10 REMARK 500 ASP A 107 -97.03 28.16 REMARK 500 ILE A 108 -56.61 -138.63 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 BEF A 125 BE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 54 OD1 REMARK 620 2 BEF A 125 F1 110.8 REMARK 620 3 BEF A 125 F2 109.8 109.6 REMARK 620 4 BEF A 125 F3 108.3 109.7 108.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEF A 125 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DC7 RELATED DB: PDB REMARK 900 INACTIVE CONFORMATION OF NTRC RECEIVER DOMAIN REMARK 900 RELATED ID: 1DC8 RELATED DB: PDB REMARK 900 TRANSIENTLY PHOSPHORYLATED FORM OF NTRC RECEIVER DOMAIN REMARK 900 RELATED ID: 1DJM RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF ACTIVE CHEY, THE HOMOLOG OF NTRC RECEIVER REMARK 900 DOMAIN REMARK 900 RELATED ID: 1F4V RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ACTIVE CHEY BOUND TO ITS DOWNSTREAM TARGET REMARK 900 DOMAIN REMARK 900 RELATED ID: 1KRW RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF BERYLLOFLUORIDE- REMARK 900 ACTIVATED NTRC RECEIVER DOMAIN REMARK 900 RELATED ID: 1KRX RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER REMARK 900 DOMAIN: MODEL STRUCTURES INCORPORATING ACTIVE SITE CONTACTS DBREF 1J56 A 1 124 UNP P41789 NTRC_SALTY 1 124 SEQRES 1 A 124 MET GLN ARG GLY ILE VAL TRP VAL VAL ASP ASP ASP SER SEQRES 2 A 124 SER ILE ARG TRP VAL LEU GLU ARG ALA LEU ALA GLY ALA SEQRES 3 A 124 GLY LEU THR CYS THR THR PHE GLU ASN GLY ASN GLU VAL SEQRES 4 A 124 LEU ALA ALA LEU ALA SER LYS THR PRO ASP VAL LEU LEU SEQRES 5 A 124 SER ASP ILE ARG MET PRO GLY MET ASP GLY LEU ALA LEU SEQRES 6 A 124 LEU LYS GLN ILE LYS GLN ARG HIS PRO MET LEU PRO VAL SEQRES 7 A 124 ILE ILE MET THR ALA HIS SER ASP LEU ASP ALA ALA VAL SEQRES 8 A 124 SER ALA TYR GLN GLN GLY ALA PHE ASP TYR LEU PRO LYS SEQRES 9 A 124 PRO PHE ASP ILE ASP GLU ALA VAL ALA LEU VAL GLU ARG SEQRES 10 A 124 ALA ILE SER HIS TYR GLN GLU HET BEF A 125 4 HETNAM BEF BERYLLIUM TRIFLUORIDE ION FORMUL 2 BEF BE F3 1- HELIX 1 1 ASP A 12 GLY A 27 1 16 HELIX 2 2 GLY A 36 LEU A 43 1 8 HELIX 3 3 LEU A 63 HIS A 73 1 11 HELIX 4 4 ASP A 86 GLY A 97 1 12 HELIX 5 5 ILE A 108 HIS A 121 1 14 SHEET 1 A 5 THR A 29 PHE A 33 0 SHEET 2 A 5 ILE A 5 VAL A 9 1 N VAL A 8 O THR A 31 SHEET 3 A 5 VAL A 50 SER A 53 1 O LEU A 52 N TRP A 7 SHEET 4 A 5 VAL A 78 ILE A 80 1 O ILE A 79 N SER A 53 SHEET 5 A 5 ASP A 100 TYR A 101 1 O ASP A 100 N ILE A 80 LINK OD1 ASP A 54 BE BEF A 125 1555 1555 1.61 SITE 1 AC1 6 ASP A 54 ILE A 55 ARG A 56 THR A 82 SITE 2 AC1 6 HIS A 84 LYS A 104 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