HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 21-SEP-05 2B3W TITLE NMR STRUCTURE OF THE E.COLI PROTEIN YBIA, NORTHEAST STRUCTURAL TITLE 2 GENOMICS TARGET ET24. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN YBIA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: YBIA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (LAMDA DE3) PMGK; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: P11 KEYWDS ET24, NESG, STRUCTURAL GENOMICS, YBIA, COG 3236, PSI, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, KEYWDS 3 UNKNOWN FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.A.RAMELOT,J.R.CORT,R.XIAO,L.Y.SHIH,T.B.ACTON,G.T.MONTELIONE, AUTHOR 2 M.A.KENNEDY,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 3 09-MAR-22 2B3W 1 REMARK SEQADV REVDAT 2 24-FEB-09 2B3W 1 VERSN REVDAT 1 01-NOV-05 2B3W 0 JRNL AUTH T.A.RAMELOT,J.R.CORT,R.XIAO,L.Y.SHIH,T.B.ACTON, JRNL AUTH 2 G.T.MONTELIONE,M.A.KENNEDY JRNL TITL NMR STRUCTURE OF THE E.COLI PROTEIN YBIA, NORTHEAST JRNL TITL 2 STRUCTURAL GENOMICS TARGET ET24. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SPARKY 3.1, CNS 1.1 REMARK 3 AUTHORS : T.D. GODDARD, D.G. KNELLER (SPARKY), A. BRUNGER, REMARK 3 G.L. WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 1598 RESTRAINTS. 1298 ARE NOE-DERIVED; SEQUENTIAL [(I-J)=1] = 1; REMARK 3 MEDIUM RANGE [1<(I-J)<5] = 498; LONG RANGE [(I-J)>=5] = 632; REMARK 3 HYDROGEN BOND RESTRAINTS = 94 (2 PER H-BOND); NUMBER OF NOE REMARK 3 RESTRAINTS PER RESIDUE = 8.1 (RESIDES 2-164); DIHEDRAL-ANGLE REMARK 3 RESTRAINTS = 206 (103 PHI, 103 PSI); TOTAL NUMBER OF RESTRAINTS REMARK 3 PER RESIDUE = 10.0 (RESIDES 2-164); NUMBER OF LONG RANGE REMARK 3 RESTRAINTS PER RESIDUE = 4.0; NUMBER OF STRUCTURES COMPUTED = 25; REMARK 3 NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS > REMARK 3 0.1 ANG = 0; AVERAGE R.M.S. DISTANCE VIOLATION = 0.002 ANG. REMARK 3 AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0 DEG = 5.1; MAX NUMBER OF REMARK 3 DIHEDRAL ANGLE VIOLATIONS = 10; AVERAGE R.M.S. ANGLE VIOLATION = REMARK 3 0.06 DEG. RMSD VALUES: BACKBONE ATOMS (N,C,C', RESIDUES 15-162) = REMARK 3 0.87 ANG; ALL HEAVY ATOMS = 1.29 ANG; PROCHECK (RESIDUES 15-162) REMARK 3 : MOST FAVORED REGIONS = 87%; ADDITIONAL ALLOWED REGIONS = 10%; REMARK 3 GENEROUSLY ALLOWED REGIONS = 2%; DISALLOWED REGIONS = 1%. REMARK 4 REMARK 4 2B3W COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034642. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM YBIA, U-15N, 13C; 20 MM MES, REMARK 210 100MM NACL, 10 MM DTT, 5MM CACL2, REMARK 210 0.02% NAN3; 95% H2O, 5% D2O; REMARK 210 1MM YBIA, U-15N, 13C; 20 MM MES, REMARK 210 100MM NACL, 10 MM DTT, 5MM CACL2, REMARK 210 0.02% NAN3; 100 % D2O; 1MM YBIA, REMARK 210 U-15N, 5%-13C; 20 MM MES, 100MM REMARK 210 NACL, 10 MM DTT, 5MM CACL2, 0.02% REMARK 210 NAN3; 95% H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 4D_13C- REMARK 210 SEPARATED_NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE LINUX9, AUTOSTRUCTURE REMARK 210 2.1.1, X-PLOR XPLOR-NIH-2.10, REMARK 210 VNMR 6.1C REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING CNS WATER REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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 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 TYR A 20 HG SER A 21 1.58 REMARK 500 HE ARG A 7 OD2 ASP A 25 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 1 GLN A 6 69.41 66.97 REMARK 500 1 GLN A 9 94.12 -61.25 REMARK 500 1 HIS A 10 98.70 60.64 REMARK 500 1 MET A 12 -85.50 -64.09 REMARK 500 1 GLN A 13 120.49 169.89 REMARK 500 1 SER A 21 88.83 177.89 REMARK 500 1 GLU A 128 41.32 -82.17 REMARK 500 1 ASN A 129 -75.79 -143.06 REMARK 500 1 TRP A 133 -10.34 74.73 REMARK 500 1 ASP A 135 1.77 -68.82 REMARK 500 1 LYS A 140 65.13 176.84 REMARK 500 1 ASN A 143 5.10 -57.15 REMARK 500 1 HIS A 163 106.70 -53.81 REMARK 500 1 HIS A 164 86.36 -154.80 REMARK 500 1 HIS A 167 -39.65 -160.08 REMARK 500 2 VAL A 3 -65.93 -137.95 REMARK 500 2 ARG A 7 171.10 64.82 REMARK 500 2 GLN A 13 102.56 63.83 REMARK 500 2 ASP A 14 79.84 49.95 REMARK 500 2 SER A 21 159.52 62.48 REMARK 500 2 SER A 23 -78.88 61.41 REMARK 500 2 ASP A 24 -169.08 -105.90 REMARK 500 2 THR A 46 -179.93 -170.76 REMARK 500 2 PRO A 84 108.36 -56.31 REMARK 500 2 TYR A 132 118.79 -170.03 REMARK 500 2 HIS A 138 -24.79 -168.10 REMARK 500 2 LYS A 142 63.67 62.48 REMARK 500 2 GLU A 162 6.56 -67.01 REMARK 500 3 ARG A 4 -81.13 65.89 REMARK 500 3 ALA A 5 90.77 61.10 REMARK 500 3 GLN A 9 80.75 62.85 REMARK 500 3 HIS A 10 -179.53 66.67 REMARK 500 3 MET A 12 -74.26 -93.71 REMARK 500 3 GLN A 13 121.83 -176.48 REMARK 500 3 SER A 21 84.82 71.30 REMARK 500 3 ASP A 24 -84.83 -93.35 REMARK 500 3 ASP A 25 -46.60 -171.81 REMARK 500 3 LEU A 57 34.60 -85.30 REMARK 500 3 ASN A 88 36.38 -97.38 REMARK 500 3 TYR A 132 140.32 178.07 REMARK 500 3 HIS A 138 24.91 -168.60 REMARK 500 3 LYS A 142 80.87 72.55 REMARK 500 3 ASN A 143 4.79 -67.49 REMARK 500 3 HIS A 164 -41.42 164.99 REMARK 500 3 HIS A 166 75.22 -111.07 REMARK 500 3 HIS A 167 -43.70 73.44 REMARK 500 4 PRO A 2 -167.50 -78.24 REMARK 500 4 ARG A 7 -33.83 -165.34 REMARK 500 4 HIS A 10 127.04 -172.59 REMARK 500 4 GLN A 13 -39.11 174.51 REMARK 500 REMARK 500 THIS ENTRY HAS 275 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: ET24 RELATED DB: TARGETDB DBREF 2B3W A 1 160 UNP P30176 YBIA_ECOLI 1 160 SEQADV 2B3W LEU A 161 UNP P30176 CLONING ARTIFACT SEQADV 2B3W GLU A 162 UNP P30176 CLONING ARTIFACT SEQADV 2B3W HIS A 163 UNP P30176 EXPRESSION TAG SEQADV 2B3W HIS A 164 UNP P30176 EXPRESSION TAG SEQADV 2B3W HIS A 165 UNP P30176 EXPRESSION TAG SEQADV 2B3W HIS A 166 UNP P30176 EXPRESSION TAG SEQADV 2B3W HIS A 167 UNP P30176 EXPRESSION TAG SEQADV 2B3W HIS A 168 UNP P30176 EXPRESSION TAG SEQRES 1 A 168 MET PRO VAL ARG ALA GLN ARG ILE GLN HIS VAL MET GLN SEQRES 2 A 168 ASP THR ILE ILE ASN PHE TYR SER THR SER ASP ASP TYR SEQRES 3 A 168 GLY ASP PHE SER ASN PHE ALA ALA TRP PRO ILE LYS VAL SEQRES 4 A 168 ASP GLY LYS THR TRP PRO THR SER GLU HIS TYR PHE GLN SEQRES 5 A 168 ALA GLN LYS PHE LEU ASP GLU LYS TYR ARG GLU GLU ILE SEQRES 6 A 168 ARG ARG VAL SER SER PRO MET VAL ALA ALA ARG MET GLY SEQRES 7 A 168 ARG ASP ARG SER LYS PRO LEU ARG LYS ASN TRP GLU SER SEQRES 8 A 168 VAL LYS GLU GLN VAL MET ARG LYS ALA LEU ARG ALA LYS SEQRES 9 A 168 PHE GLU GLN HIS ALA GLU LEU ARG ALA LEU LEU LEU ALA SEQRES 10 A 168 THR ALA PRO ALA LYS LEU VAL GLU HIS THR GLU ASN ASP SEQRES 11 A 168 ALA TYR TRP GLY ASP GLY GLY HIS GLY LYS GLY LYS ASN SEQRES 12 A 168 ARG LEU GLY TYR LEU LEU MET GLU LEU ARG GLU GLN LEU SEQRES 13 A 168 ALA ILE GLU LYS LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 1 ASP A 24 ASP A 28 5 5 HELIX 2 2 THR A 46 PHE A 56 1 11 HELIX 3 3 ASP A 58 VAL A 68 1 11 HELIX 4 4 SER A 70 ARG A 79 1 10 HELIX 5 5 ASN A 88 GLN A 107 1 20 HELIX 6 6 HIS A 108 THR A 118 1 11 HELIX 7 7 ASN A 143 LEU A 161 1 19 SHEET 1 A 2 THR A 15 PHE A 19 0 SHEET 2 A 2 ALA A 121 GLU A 125 1 O LYS A 122 N ILE A 17 SHEET 1 B 2 ILE A 37 VAL A 39 0 SHEET 2 B 2 LYS A 42 TRP A 44 -1 O TRP A 44 N ILE A 37 CISPEP 1 ALA A 119 PRO A 120 1 -0.75 CISPEP 2 ALA A 119 PRO A 120 2 -1.01 CISPEP 3 ALA A 119 PRO A 120 3 -1.33 CISPEP 4 ALA A 119 PRO A 120 4 -2.32 CISPEP 5 ALA A 119 PRO A 120 5 -1.76 CISPEP 6 ALA A 119 PRO A 120 6 1.08 CISPEP 7 ALA A 119 PRO A 120 7 -5.09 CISPEP 8 ALA A 119 PRO A 120 8 -2.42 CISPEP 9 ALA A 119 PRO A 120 9 -0.51 CISPEP 10 ALA A 119 PRO A 120 10 -3.54 CISPEP 11 ALA A 119 PRO A 120 11 1.40 CISPEP 12 ALA A 119 PRO A 120 12 0.23 CISPEP 13 ALA A 119 PRO A 120 13 -1.20 CISPEP 14 ALA A 119 PRO A 120 14 -0.66 CISPEP 15 ALA A 119 PRO A 120 15 1.07 CISPEP 16 ALA A 119 PRO A 120 16 -1.22 CISPEP 17 ALA A 119 PRO A 120 17 -0.20 CISPEP 18 ALA A 119 PRO A 120 18 0.13 CISPEP 19 ALA A 119 PRO A 120 19 -0.11 CISPEP 20 ALA A 119 PRO A 120 20 1.78 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