HEADER TRANSCRIPTION 17-JUL-07 2JT1 TITLE SOLUTION NMR STRUCTURE OF PEFI (PLASMID-ENCODED FIMBRIAE REGULATORY) TITLE 2 PROTEIN FROM SALMONELLA TYPHIMURIUM. NORTHEAST STRUCTURAL GENOMICS TITLE 3 TARGET STR82 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEFI PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM LT2; SOURCE 3 ORGANISM_TAXID: 99287; SOURCE 4 STRAIN: LT2, SGSC1412; SOURCE 5 ATCC: 700720; SOURCE 6 GENE: PEFI, PSLT013; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)MGK; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: STR82-21.1; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS SOLUTION NMR STRUCTURE, WINGED HELIX-TURN-HELIX, TRANSCRIPTION KEYWDS 2 REGULATORY PROTEIN, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, KEYWDS 4 TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.M.ARAMINI,P.ROSSI,H.WANG,C.NWOSU,K.CUNNINGHAM,L.-C.MA,R.XIAO,J.LIU, AUTHOR 2 M.C.BARAN,G.V.T.SWAPNA,T.B.ACTON,B.ROST,G.T.MONTELIONE,NORTHEAST AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 6 14-JUN-23 2JT1 1 REMARK REVDAT 5 19-FEB-20 2JT1 1 REMARK SEQADV REVDAT 4 24-JAN-18 2JT1 1 AUTHOR REVDAT 3 23-FEB-11 2JT1 1 JRNL REVDAT 2 24-FEB-09 2JT1 1 VERSN REVDAT 1 09-OCT-07 2JT1 0 JRNL AUTH J.M.ARAMINI,P.ROSSI,J.R.CORT,L.C.MA,R.XIAO,T.B.ACTON, JRNL AUTH 2 G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF THE PLASMID-ENCODED FIMBRIAE JRNL TITL 2 REGULATORY PROTEIN PEFI FROM SALMONELLA ENTERICA SEROVAR JRNL TITL 3 TYPHIMURIUM. JRNL REF PROTEINS V. 79 335 2011 JRNL REFN ISSN 0887-3585 JRNL PMID 20979070 JRNL DOI 10.1002/PROT.22869 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 1.3, CNS 1.1 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FINAL STRUCTURES ARE BASED ON A REMARK 3 TOTAL OF 1155 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS, 92 DIHEDRAL ANGLE CONSTRAINTS, AND 52 HYDROGEN BOND REMARK 3 CONSTRAINTS (19.1 CONSTRAINTS PER RESIDUE, 4.5 LONG RANGE REMARK 3 CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 71 BY PSVS REMARK 3 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING REMARK 3 CYANA 2.1. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET REMARK 3 FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ REMARK 3 ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19. REMARK 4 REMARK 4 2JT1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000100253. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 450 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.72 MM [U-100% 13C; U-100% 15N] REMARK 210 STR82, 20 MM AMMONIUM ACETATE, REMARK 210 450 MM SODIUM CHLORIDE, 10 MM REMARK 210 DTT, 5 MM CALCIUM CHLORIDE, 0.02 REMARK 210 % SODIUM AZIDE, 95% H2O/5% D2O; REMARK 210 0.46 MM [U-5% 13C; U-100% 15N] REMARK 210 STR82, 20 MM AMMONIUM ACETATE, REMARK 210 450 MM SODIUM CHLORIDE, 10 MM REMARK 210 DTT, 5 MM CALCIUM CHLORIDE, 0.02 REMARK 210 % SODIUM AZIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HN(CA)CO; 3D HNCACB; REMARK 210 3D HN(COCA)CB; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-COSY; 3D CCH-TOCSY; 3D REMARK 210 SIMULTANEOUS CN-NOESY; 3D HNHA; REMARK 210 3D 1H-13C NOESY AROMATIC; 2D 1H- REMARK 210 13C HSQC STEREOSPECIFIC LEU/VAL REMARK 210 METHYL REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AUTOASSIGN 2.4.0, CYANA 2.1, REMARK 210 NMRPIPE 2.3, AUTOSTRUCTURE 2.1.1, REMARK 210 PSVS 1.3, PDBSTAT 5.0, PROCHECK, REMARK 210 MOLPROBITY, MOLMOL 2K-2, SPARKY REMARK 210 3.110 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY REMARK 210 AND STATIC LIGHT SCATTERING. THE STRUCTURE WAS DETERMINED USING REMARK 210 TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE REMARK 210 ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN REMARK 210 ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS REMARK 210 WERE DETERMINED USING CYANA 2.1. DIHEDRAL ANGLE CONSTRAINTS WERE REMARK 210 OBTAINED FROM TALOS. HYDROGEN BOND CONSTRAINTS WERE DETERMINED REMARK 210 USING BOTH AUTOSTRUCTURE AND CYANA, AND WERE APPLIED ONLY IN THE REMARK 210 FINAL REFINEMENT STAGE (CNS) OF THE STRUCTURE DETERMINATION. REMARK 210 COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): REMARK 210 BACKBONE, 97.8%, SIDE CHAIN, 95.8%, AROMATICS, 100%, REMARK 210 STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100% REMARK 210 . FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 71, PSVS REMARK 210 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 5- REMARK 210 19,23-57,66-69: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, REMARK 210 1.0. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST REMARK 210 FAVORED, 95.9%, ADDITIONALLY ALLOWED, 4.1%, GENEROUSLY ALLOWED, REMARK 210 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES REMARK 210 (RAW/Z-): PHI-PSI, 0.16/0.94, ALL, 0.11/0.65. (D) MOLPROBITY REMARK 210 CLASH SCORE (RAW/Z-): 21.29/-2.13. (E) RPF SCORES FOR GOODNESS REMARK 210 OF FIT TO NOESY DATA (RESIDUES 1-71): RECALL, 0.983, PRECISION, REMARK 210 0.930, F-MEASURE, 0.956, DP-SCORE, 0.789. (F) NUMBER OF CLOSE REMARK 210 CONTACTS PER 20 MODELS: 2. THE C-TERMINAL HIS TAG RESIDUES OF REMARK 210 THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE REMARK 210 CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. REMARK 210 COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED REMARK 210 (S(PHI) + S(PSI) < 1.8): 1-4,20-22,58-65,70-71. 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 HIS A 72 REMARK 465 HIS A 73 REMARK 465 HIS A 74 REMARK 465 HIS A 75 REMARK 465 HIS A 76 REMARK 465 HIS A 77 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 -22.71 -155.68 REMARK 500 1 SER A 4 -79.71 47.15 REMARK 500 1 ASP A 21 -74.75 64.10 REMARK 500 1 LEU A 70 -49.82 -143.40 REMARK 500 2 ASP A 21 -72.57 69.14 REMARK 500 2 VAL A 53 -56.88 -124.77 REMARK 500 2 ASN A 58 -176.93 -173.00 REMARK 500 2 LEU A 70 90.67 -59.92 REMARK 500 3 ASP A 21 -74.58 63.26 REMARK 500 3 ALA A 59 96.80 -69.16 REMARK 500 3 LYS A 61 -36.58 -175.33 REMARK 500 4 ASP A 21 104.96 67.26 REMARK 500 4 VAL A 53 -51.94 -131.77 REMARK 500 4 LEU A 70 92.90 -68.12 REMARK 500 5 ASP A 21 95.57 -51.11 REMARK 500 6 ASN A 58 -80.16 177.50 REMARK 500 6 ALA A 59 126.36 -174.08 REMARK 500 6 PRO A 64 99.77 -55.26 REMARK 500 7 GLU A 3 44.31 -86.69 REMARK 500 7 MET A 19 -74.19 -91.50 REMARK 500 7 VAL A 53 -58.51 -129.71 REMARK 500 7 ASN A 58 131.28 77.05 REMARK 500 7 ALA A 59 -80.96 -67.22 REMARK 500 8 SER A 2 -68.31 -99.79 REMARK 500 8 VAL A 53 -60.15 -96.46 REMARK 500 8 LEU A 70 93.15 -69.12 REMARK 500 9 LYS A 61 97.29 -61.38 REMARK 500 9 ARG A 68 117.55 -165.30 REMARK 500 10 ASP A 21 -69.08 68.47 REMARK 500 10 VAL A 53 -60.92 -141.36 REMARK 500 10 ASN A 58 -177.86 162.40 REMARK 500 10 ALA A 59 -172.04 -67.83 REMARK 500 11 PRO A 24 177.39 -48.34 REMARK 500 11 PRO A 64 95.25 -67.75 REMARK 500 12 SER A 2 99.61 -57.59 REMARK 500 12 ASP A 21 97.24 54.73 REMARK 500 12 ASN A 58 163.34 76.44 REMARK 500 13 ASN A 58 93.79 60.74 REMARK 500 13 LEU A 70 78.53 -69.71 REMARK 500 14 SER A 4 111.56 -176.56 REMARK 500 14 VAL A 53 -60.69 -107.65 REMARK 500 14 ASN A 58 -167.38 -161.93 REMARK 500 14 LEU A 70 92.25 -67.32 REMARK 500 15 MET A 19 -69.64 -102.79 REMARK 500 15 ASP A 21 -60.87 69.30 REMARK 500 16 SER A 2 72.70 57.59 REMARK 500 16 ASP A 21 94.08 -63.01 REMARK 500 17 ASP A 21 -88.19 59.22 REMARK 500 18 GLU A 3 -171.89 -176.25 REMARK 500 18 ASN A 58 87.09 49.37 REMARK 500 REMARK 500 THIS ENTRY HAS 54 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: STR82 RELATED DB: TARGETDB REMARK 900 RELATED ID: 15386 RELATED DB: BMRB DBREF 2JT1 A 1 70 UNP Q04822 Q04822_SALTY 1 70 SEQADV 2JT1 GLU A 71 UNP Q04822 EXPRESSION TAG SEQADV 2JT1 HIS A 72 UNP Q04822 EXPRESSION TAG SEQADV 2JT1 HIS A 73 UNP Q04822 EXPRESSION TAG SEQADV 2JT1 HIS A 74 UNP Q04822 EXPRESSION TAG SEQADV 2JT1 HIS A 75 UNP Q04822 EXPRESSION TAG SEQADV 2JT1 HIS A 76 UNP Q04822 EXPRESSION TAG SEQADV 2JT1 HIS A 77 UNP Q04822 EXPRESSION TAG SEQRES 1 A 77 MET SER GLU SER ILE VAL THR LYS ILE ILE SER ILE VAL SEQRES 2 A 77 GLN GLU ARG GLN ASN MET ASP ASP GLY ALA PRO VAL LYS SEQRES 3 A 77 THR ARG ASP ILE ALA ASP ALA ALA GLY LEU SER ILE TYR SEQRES 4 A 77 GLN VAL ARG LEU TYR LEU GLU GLN LEU HIS ASP VAL GLY SEQRES 5 A 77 VAL LEU GLU LYS VAL ASN ALA GLY LYS GLY VAL PRO GLY SEQRES 6 A 77 LEU TRP ARG LEU LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 1 SER A 4 ASP A 21 1 18 HELIX 2 2 THR A 27 GLY A 35 1 9 HELIX 3 3 SER A 37 VAL A 51 1 15 SHEET 1 A 3 VAL A 25 LYS A 26 0 SHEET 2 A 3 LEU A 66 LEU A 69 -1 O TRP A 67 N VAL A 25 SHEET 3 A 3 LEU A 54 VAL A 57 -1 N GLU A 55 O ARG A 68 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