HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 28-FEB-06 2G7J TITLE SOLUTION NMR STRUCTURE OF THE PUTATIVE CYTOPLASMIC PROTEIN YGAC FROM TITLE 2 SALMONELLA TYPHIMURIUM. NORTHEAST STRUCTURAL GENOMICS TARGET STR72. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE CYTOPLASMIC PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM; SOURCE 3 ORGANISM_TAXID: 99287; SOURCE 4 STRAIN: LT2; SOURCE 5 GENE: YGAC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)MGK; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET21; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: STR72-21.1 KEYWDS STR72, AUTOSTRUCTURE, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, UNKNOWN KEYWDS 3 FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.M.ARAMINI,G.V.T.SWAPNA,T.A.RAMELOT,C.K.HO,K.CUNNINGHAM,L.-C.MA, AUTHOR 2 K.SHETTY,R.XIAO,T.B.ACTON,M.A.KENNEDY,G.T.MONTELIONE,NORTHEAST AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 3 13-JUL-11 2G7J 1 VERSN REVDAT 2 24-FEB-09 2G7J 1 VERSN REVDAT 1 02-MAY-06 2G7J 0 JRNL AUTH J.M.ARAMINI,G.V.T.SWAPNA,T.A.RAMELOT,C.K.HO,K.CUNNINGHAM, JRNL AUTH 2 L.-C.MA,K.SHETTY,R.XIAO,T.B.ACTON,M.A.KENNEDY,G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF THE PUTATIVE CYTOPLASMIC PROTEIN JRNL TITL 2 YGAC FROM SALMONELLA TYPHIMURIUM. NORTHEAST STRUCTURAL JRNL TITL 3 GENOMICS TARGET STR72. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AUTOSTRUCTURE 2.1.1, XPLOR-NIH 2.11.2, CNS 1.1 REMARK 3 AUTHORS : HUANG & MONTELIONE (AUTOSTRUCTURE), CLORE ET AL. REMARK 3 (XPLOR-NIH), BRUNGER ET AL. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 1759 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS, 219 DIHEDRAL ANGLE CONSTRAINTS, AND 58 HYDROGEN BOND REMARK 3 CONSTRAINTS (18.2 CONSTRAINTS PER RESIDUE, 6.7 LONG RANGE REMARK 3 CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 112 BY PSVS REMARK 3 1.2). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING REMARK 3 AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING REMARK 3 THE FINAL CONSTRAINTS DERIVED FROM AUTOSTRUCTURE, THE 20 LOWEST REMARK 3 ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED REMARK 3 MOLECULAR DYANMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). REMARK 3 THE UNSTRUCTURED C-TERMINUS OF THE PROTEIN (EKTD + LEHHHHHH TAG) REMARK 3 WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED REMARK 3 FROM THIS DEPOSITION. REMARK 4 REMARK 4 2G7J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAR-06. REMARK 100 THE RCSB ID CODE IS RCSB036786. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.12MM U-13C,15N STR72, 20MM REMARK 210 MES, 100MM NACL, 5MM CACL2, 10MM REMARK 210 DTT, 0.02% NAN3, PH 6.5, 5% D2O/ REMARK 210 95% H2O; 1.12MM U-13C,15N STR72, REMARK 210 20MM MES, 100MM NACL, 5MM CACL2, REMARK 210 10MM DTT, 0.02% NAN3, PH 6.5, REMARK 210 100% D2O; 1.07MM 5%-13C,U-15N REMARK 210 STR72, 20MM MES, 100MM NACL, 5MM REMARK 210 CACL2, 10MM DTT, 0.02% NAN3, PH REMARK 210 6.5, 5% D2O/95% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY; 4D_13C- REMARK 210 SEPARATED_NOESY; HNHA; HIGH REMARK 210 RESOLUTION CH-HSQC REMARK 210 (STEREOSPECIFIC ASSIGNMENT OF REMARK 210 VAL/LEU METHYLS); BACKBONE TR REMARK 210 EXPTS; 3D HCCH-COSY; 3D TOCSYS, REMARK 210 AROMATIC EXPTS REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5PL6, VNMR 6.1C, REMARK 210 SPARKY 3.110, AUTOASSIGN 1.17.0, REMARK 210 PDBSTAT 4.01, PSVS 1.2 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 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR REMARK 210 SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING REMARK 210 AUTOASSIGN, AND THE ASSIGNMENTS WERE COMPLETED MANUALLY. REMARK 210 AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND REMARK 210 CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE REMARK 210 CONSTRAINTS WERE DETERMINED USING HYPER AND TALOS. COMPLETENESS REMARK 210 OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 100%, REMARK 210 SIDE CHAIN, 94.6%, AROMATICS, 91.1%, STEREOSPECIFIC METHYL, 94.4% REMARK 210 . FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 112, PSVS REMARK 210 1.2), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE 3- REMARK 210 43,49-50,55-66,69-71,75-76,88-96,98-109: (A) RMSD (ORDERED REMARK 210 RESIDUES): BB, 0.6, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS REMARK 210 FOR ORDERED RESIDUES: MOST FAVORED, 87.4%, ADDITIONALLY ALLOWED, REMARK 210 12.4%, GENEROUSLY ALLOWED, 0.2%, DISALLOWED, 0.0%. (C) PROCHECK REMARK 210 SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.34/-1.02, ALL, REMARK 210 -0.32/-1.89. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 25.21/-2.80. REMARK 210 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (ALL RESIDUES): REMARK 210 RECALL, 0.971, PRECISION, 0.945, F-MEASURE, 0.958, DP-SCORE, REMARK 210 0.846. 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 GLU A 113 REMARK 465 LYS A 114 REMARK 465 THR A 115 REMARK 465 ASP A 116 REMARK 465 LEU A 117 REMARK 465 GLU A 118 REMARK 465 HIS A 119 REMARK 465 HIS A 120 REMARK 465 HIS A 121 REMARK 465 HIS A 122 REMARK 465 HIS A 123 REMARK 465 HIS A 124 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 HG13 ILE A 51 H HIS A 52 1.16 REMARK 500 HB2 CYS A 72 HB2 HIS A 89 1.45 REMARK 500 HZ3 LYS A 56 OD1 ASP A 68 1.58 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 ILE A 51 -86.40 -106.32 REMARK 500 1 PRO A 53 -168.14 -53.80 REMARK 500 1 ARG A 54 -50.38 74.50 REMARK 500 1 SER A 67 -111.93 -156.07 REMARK 500 1 ASP A 68 -69.29 -157.98 REMARK 500 1 ASN A 77 -29.53 66.41 REMARK 500 1 PHE A 78 -53.57 101.61 REMARK 500 1 PRO A 79 12.04 -68.51 REMARK 500 1 LEU A 80 106.33 -3.42 REMARK 500 1 SER A 97 18.97 -152.15 REMARK 500 2 ASP A 20 -69.31 -99.43 REMARK 500 2 PRO A 53 98.99 -60.56 REMARK 500 2 ARG A 54 -39.42 168.30 REMARK 500 2 SER A 67 -130.43 -162.46 REMARK 500 2 ASP A 68 -46.20 -157.27 REMARK 500 2 CYS A 72 123.11 175.29 REMARK 500 2 ASN A 77 -3.69 63.27 REMARK 500 2 PHE A 78 -60.68 101.98 REMARK 500 2 LEU A 80 118.86 66.49 REMARK 500 2 SER A 97 14.04 -152.64 REMARK 500 3 TYR A 2 165.83 67.27 REMARK 500 3 THR A 26 149.20 -171.53 REMARK 500 3 ALA A 48 -25.73 -160.59 REMARK 500 3 ILE A 51 -82.52 -72.72 REMARK 500 3 HIS A 52 138.34 -177.54 REMARK 500 3 PRO A 53 -172.11 -53.26 REMARK 500 3 ARG A 54 -44.68 70.36 REMARK 500 3 SER A 67 -130.16 -162.03 REMARK 500 3 ASP A 68 -46.20 -157.21 REMARK 500 3 CYS A 72 124.37 167.26 REMARK 500 3 ASN A 77 -85.24 60.87 REMARK 500 3 PHE A 78 -60.79 -174.63 REMARK 500 3 LEU A 80 116.85 45.68 REMARK 500 3 GLU A 85 -148.78 -79.29 REMARK 500 3 HIS A 87 13.44 -170.53 REMARK 500 3 SER A 97 17.12 -153.76 REMARK 500 4 ASP A 20 -62.03 -105.66 REMARK 500 4 ARG A 31 97.52 -173.51 REMARK 500 4 HIS A 52 144.84 73.27 REMARK 500 4 PRO A 53 -166.59 -59.31 REMARK 500 4 ARG A 54 -51.60 71.49 REMARK 500 4 LEU A 55 26.42 -79.16 REMARK 500 4 LYS A 56 -71.38 -60.23 REMARK 500 4 SER A 67 -116.99 -174.26 REMARK 500 4 ASP A 68 -66.83 -157.45 REMARK 500 4 TYR A 75 42.10 -80.57 REMARK 500 4 LEU A 80 133.36 76.28 REMARK 500 4 PHE A 96 -157.66 -137.24 REMARK 500 4 SER A 97 11.20 -152.57 REMARK 500 5 PRO A 53 -166.96 -57.47 REMARK 500 REMARK 500 THIS ENTRY HAS 256 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: STR72 RELATED DB: TARGETDB DBREF 2G7J A 1 116 GB 16421350 AAL21686 1 116 SEQADV 2G7J LEU A 117 GB 16421350 CLONING ARTIFACT SEQADV 2G7J GLU A 118 GB 16421350 CLONING ARTIFACT SEQADV 2G7J HIS A 119 GB 16421350 EXPRESSION TAG SEQADV 2G7J HIS A 120 GB 16421350 EXPRESSION TAG SEQADV 2G7J HIS A 121 GB 16421350 EXPRESSION TAG SEQADV 2G7J HIS A 122 GB 16421350 EXPRESSION TAG SEQADV 2G7J HIS A 123 GB 16421350 EXPRESSION TAG SEQADV 2G7J HIS A 124 GB 16421350 EXPRESSION TAG SEQRES 1 A 124 MET TYR LEU ARG PRO ASP GLU VAL ALA ARG VAL LEU GLU SEQRES 2 A 124 LYS ALA GLY PHE THR VAL ASP VAL VAL THR ASN LYS THR SEQRES 3 A 124 TYR GLY TYR ARG ARG GLY GLU ASN TYR VAL TYR VAL ASN SEQRES 4 A 124 ARG GLU ALA ARG MET GLY ARG THR ALA LEU ILE ILE HIS SEQRES 5 A 124 PRO ARG LEU LYS ASP ARG SER SER SER LEU ALA ASP PRO SEQRES 6 A 124 ALA SER ASP ILE LYS THR CYS ASP HIS TYR GLN ASN PHE SEQRES 7 A 124 PRO LEU TYR LEU GLY GLY GLU THR HIS GLU HIS TYR GLY SEQRES 8 A 124 ILE PRO HIS GLY PHE SER SER ARG ILE ALA LEU GLU ARG SEQRES 9 A 124 TYR LEU ASN GLY LEU PHE GLY ASP GLU LYS THR ASP LEU SEQRES 10 A 124 GLU HIS HIS HIS HIS HIS HIS HELIX 1 1 ARG A 4 ALA A 15 1 12 HELIX 2 2 LEU A 55 ALA A 63 1 9 HELIX 3 3 SER A 98 GLY A 111 1 14 SHEET 1 A 5 THR A 18 THR A 23 0 SHEET 2 A 5 THR A 26 ARG A 31 -1 O GLY A 28 N VAL A 21 SHEET 3 A 5 ASN A 34 ASN A 39 -1 O VAL A 36 N TYR A 29 SHEET 4 A 5 LEU A 49 ILE A 50 -1 O ILE A 50 N TYR A 37 SHEET 5 A 5 PRO A 93 HIS A 94 -1 O HIS A 94 N LEU A 49 SHEET 1 B 2 LYS A 70 CYS A 72 0 SHEET 2 B 2 HIS A 89 GLY A 91 -1 O GLY A 91 N LYS A 70 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