PDB Short entry for 1NY8 HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 11-FEB-03 1NY8 TITLE SOLUTION STRUCTURE OF PROTEIN YRBA FROM ESCHERICHIA COLI: NORTHEAST TITLE 2 STRUCTURAL GENOMICS CONSORTIUM TARGET ER115 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN YRBA; 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: YRBA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21MGK; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS ER115, YRBA, AUTOASSIGN, AUTOSTRUCTURE, NESG, STRUCTURAL GENOMICS, KEYWDS 2 PSI, PROTEIN STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS KEYWDS 3 CONSORTIUM, UNKNOWN FUNCTION EXPDTA SOLUTION NMR NUMMDL 16 AUTHOR G.V.T.SWAPNA,J.Y.HUANG,T.B.ACTON,R.SHASTRY,Y.-W.CHIANG, AUTHOR 2 G.T.MONTELIONE,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 4 23-FEB-22 1NY8 1 REMARK SEQADV REVDAT 3 24-FEB-09 1NY8 1 VERSN REVDAT 2 25-JAN-05 1NY8 1 AUTHOR KEYWDS REMARK REVDAT 1 15-JUN-04 1NY8 0 JRNL AUTH G.V.T.SWAPNA,J.Y.HUANG,T.B.ACTON,R.SHASTRY,Y.-W.CHIANG, JRNL AUTH 2 G.T.MONTELIONE JRNL TITL SOLUTION STRUCTURE OF PROTEIN YRBA FROM ESCHERICHIA COLI: JRNL TITL 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER115 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1B, DYANA 1.5 REMARK 3 AUTHORS : VARIAN (VNMR), GUNTERT (DYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 1005 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS. 74 DIHEDRAL ANGLE RESTRIANTS FROM TALOS AND 64 REMARK 3 HYDROGEN-BOND RESTRAINTS. REMARK 4 REMARK 4 1NY8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018343. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 100 MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 13C,15N-ER115 0.8MM IN 20MM REMARK 210 NH4OAC, 100MM NACL, 5MM CACL2, REMARK 210 10MM DTT, 0.02% AZIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, SPARKY 3.106, REMARK 210 AUTOASSIGN 1.9, AUTOSTRUCTURE REMARK 210 1.1.2, HYPER 3.2 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 AUTOMATED RESONANCE ASSIGNMENTS OF BACKBONE RESONANCES USING REMARK 210 AUTOASSIGN. MANUAL SIDECHAIN ASSIGNMENTS. AUTOMATED 3D 13C-NOESY REMARK 210 AND 15N-NOESY ANALYSIS FOR STRUCTURE DETERMINATION USING REMARK 210 AUTOSTRUCTURE 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 ASN A 65 H HIS A 68 1.48 REMARK 500 O SER A 46 H LYS A 50 1.55 REMARK 500 O TRP A 80 H ARG A 84 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 ILE A 2 122.48 -171.65 REMARK 500 1 ASP A 4 108.69 -179.79 REMARK 500 1 MET A 6 95.89 173.43 REMARK 500 1 GLU A 7 -146.86 -60.33 REMARK 500 1 ASN A 8 -0.74 81.23 REMARK 500 1 LEU A 19 112.15 -176.72 REMARK 500 1 SER A 20 -152.16 -75.43 REMARK 500 1 LEU A 21 -49.83 172.74 REMARK 500 1 GLN A 22 -62.81 173.67 REMARK 500 1 ASP A 29 -59.50 -121.73 REMARK 500 1 GLU A 40 -32.40 178.24 REMARK 500 1 PHE A 42 38.37 -84.85 REMARK 500 1 LYS A 50 -76.27 -70.08 REMARK 500 1 GLN A 52 -75.04 -66.01 REMARK 500 1 LEU A 58 39.15 -86.80 REMARK 500 1 ARG A 66 -37.93 -32.17 REMARK 500 1 ILE A 67 -32.83 -37.67 REMARK 500 1 HIS A 68 -147.38 -122.23 REMARK 500 1 TRP A 80 -75.99 -66.16 REMARK 500 1 LEU A 86 -165.02 -73.27 REMARK 500 1 GLU A 91 42.71 -179.84 REMARK 500 1 HIS A 93 77.97 69.32 REMARK 500 1 HIS A 95 120.84 62.60 REMARK 500 2 ILE A 2 87.53 76.32 REMARK 500 2 GLU A 3 115.10 -164.49 REMARK 500 2 ASP A 4 83.74 171.94 REMARK 500 2 MET A 6 -70.12 -164.31 REMARK 500 2 GLU A 7 45.58 166.54 REMARK 500 2 GLU A 10 -74.61 -39.40 REMARK 500 2 LEU A 19 -125.68 -165.03 REMARK 500 2 SER A 20 -161.26 176.61 REMARK 500 2 LEU A 21 -44.75 176.10 REMARK 500 2 GLN A 22 -70.32 154.93 REMARK 500 2 ASP A 29 -65.32 -122.67 REMARK 500 2 GLU A 40 19.08 -159.11 REMARK 500 2 PHE A 42 38.93 -87.74 REMARK 500 2 ARG A 47 -31.75 -37.18 REMARK 500 2 LYS A 50 -76.09 -70.70 REMARK 500 2 GLN A 52 -73.78 -64.87 REMARK 500 2 LEU A 58 38.93 -86.76 REMARK 500 2 ARG A 66 -35.41 -34.04 REMARK 500 2 ILE A 67 -37.80 -39.45 REMARK 500 2 HIS A 68 -146.33 -107.86 REMARK 500 2 ALA A 69 78.23 -150.66 REMARK 500 2 TRP A 80 -75.04 -60.33 REMARK 500 2 LEU A 86 -164.92 -75.08 REMARK 500 2 GLU A 91 -172.75 -178.52 REMARK 500 2 HIS A 92 100.42 -166.93 REMARK 500 2 HIS A 94 -179.76 63.62 REMARK 500 2 HIS A 95 80.40 68.09 REMARK 500 REMARK 500 THIS ENTRY HAS 382 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: ER115 RELATED DB: TARGETDB DBREF 1NY8 A 1 89 UNP P0A9W6 YRBA_ECOLI 1 89 SEQADV 1NY8 LEU A 90 UNP P0A9W6 EXPRESSION TAG SEQADV 1NY8 GLU A 91 UNP P0A9W6 EXPRESSION TAG SEQADV 1NY8 HIS A 92 UNP P0A9W6 EXPRESSION TAG SEQADV 1NY8 HIS A 93 UNP P0A9W6 EXPRESSION TAG SEQADV 1NY8 HIS A 94 UNP P0A9W6 EXPRESSION TAG SEQADV 1NY8 HIS A 95 UNP P0A9W6 EXPRESSION TAG SEQADV 1NY8 HIS A 96 UNP P0A9W6 EXPRESSION TAG SEQADV 1NY8 HIS A 97 UNP P0A9W6 EXPRESSION TAG SEQRES 1 A 97 MET ILE GLU ASP PRO MET GLU ASN ASN GLU ILE GLN SER SEQRES 2 A 97 VAL LEU MET ASN ALA LEU SER LEU GLN GLU VAL HIS VAL SEQRES 3 A 97 SER GLY ASP GLY SER HIS PHE GLN VAL ILE ALA VAL GLY SEQRES 4 A 97 GLU LEU PHE ASP GLY MET SER ARG VAL LYS LYS GLN GLN SEQRES 5 A 97 THR VAL TYR GLY PRO LEU MET GLU TYR ILE ALA ASP ASN SEQRES 6 A 97 ARG ILE HIS ALA VAL SER ILE LYS ALA TYR THR PRO ALA SEQRES 7 A 97 GLU TRP ALA ARG ASP ARG LYS LEU ASN GLY PHE LEU GLU SEQRES 8 A 97 HIS HIS HIS HIS HIS HIS HELIX 1 1 ASN A 8 SER A 20 1 13 HELIX 2 2 SER A 46 GLY A 56 1 11 HELIX 3 3 LEU A 58 ARG A 66 1 9 HELIX 4 4 THR A 76 LEU A 86 1 11 SHEET 1 A 3 GLU A 23 GLY A 28 0 SHEET 2 A 3 HIS A 32 VAL A 38 -1 O ILE A 36 N HIS A 25 SHEET 3 A 3 ALA A 69 ALA A 74 1 O SER A 71 N VAL A 35 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