HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 20-SEP-04 1XHS TITLE SOLUTION NMR STRUCTURE OF PROTEIN YTFP FROM ESCHERICHIA COLI. TITLE 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER111. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL UPF0131 PROTEIN YTFP; 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: YTFP; 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_VECTOR: PET21; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: ER111-21 KEYWDS ER111, AUTOSTRUCTURE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, PSI, STRUCTURAL GENOMICS, UNKNOWN KEYWDS 3 FUNCTION EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.M.ARAMINI,Y.J.HUANG,G.V.T.SWAPNA,R.K.PARANJI,R.XIAO,R.SHASTRY, AUTHOR 2 T.B.ACTON,J.R.CORT,M.A.KENNEDY,G.T.MONTELIONE,NORTHEAST STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (NESG) REVDAT 4 02-MAR-22 1XHS 1 REMARK SEQADV REVDAT 3 24-FEB-09 1XHS 1 VERSN REVDAT 2 30-OCT-07 1XHS 1 JRNL REVDAT 1 04-JAN-05 1XHS 0 JRNL AUTH J.M.ARAMINI,Y.J.HUANG,G.V.SWAPNA,J.R.CORT,P.K.RAJAN,R.XIAO, JRNL AUTH 2 R.SHASTRY,T.B.ACTON,J.LIU,B.ROST,M.A.KENNEDY,G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF ESCHERICHIA COLI YTFP EXPANDS THE JRNL TITL 2 STRUCTURAL COVERAGE OF THE UPF0131 PROTEIN DOMAIN FAMILY. JRNL REF PROTEINS V. 68 789 2007 JRNL REFN ISSN 0887-3585 JRNL PMID 17523190 JRNL DOI 10.1002/PROT.21450 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 2.0.6 REMARK 3 AUTHORS : HUANG, MONTELIONE (AUTOSTRUCTURE), SCHWIETERS, REMARK 3 CLORE (XPLOR-NIH), BRUNGER (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 1717 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS, 211 DIHEDRAL ANGLE CONSTRAINTS, AND 68 HYDROGEN REMARK 3 BOND CONSTRAINTS (17.2 CONSTRAINTS PER RESIDUE; 6.9 LONG-RANGE REMARK 3 CONSTRAINTS PER RESIDUE). STRUCTURE DETERMINATION WAS PERFORMED REMARK 3 ITERATIVELY USING AUTOSTRUCTURE (XPLOR). THE 10 LOWEST ENERGY REMARK 3 STRUCTURES WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ REMARK 3 ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). REMARK 4 REMARK 4 1XHS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030377. 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 : 100 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.3 MM ER111 U-13C,15N 20MM REMARK 210 NH4OAC, 5MM CACL2, 10MM DTT, REMARK 210 0.02% NAN3, 5% D2O, 95% H2O; 1.3 REMARK 210 MM ER111 U-13C,15N 20MM NH4OAC, REMARK 210 5MM CACL2, 10MM DTT, 0.02% NAN3, REMARK 210 100% D2O; 1.1 MM ER111 U-15N,5% REMARK 210 13C 20MM NH4OAC, 5MM CACL2, 10MM REMARK 210 DTT, 0.02% NAN3, 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; BACKBONE TR REMARK 210 EXPTS; TOCSYS; HCCH COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ; 800 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1C, PSVS 1.0, NMRPIPE REMARK 210 2.3, SPARKY 3.91, AUTOASSIGN REMARK 210 1.14, HYPER 3.2, PDBSTAT 3.27 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 56 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: REMARK 210 THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. AUTOMATIC BACKBONE ASSIGNMENTS WERE MADE USING REMARK 210 AUTOASSIGN. MANUAL SIDE CHAIN ASSIGNMENTS. AUTOMATIC NOESY REMARK 210 ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE REMARK 210 DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE REMARK 210 DETERMINED USING HYPER AND TALOS.COMPLETENESS OF NMR ASSIGNMENTS: REMARK 210 BACKBONE, 97%; SIDE CHAIN, 91%; STEREOSPECIFIC METHYL, 100%. FINAL REMARK 210 STRUCTURE QUALITY FACTORS FOR THE ENSEMBLE, WHERE ORDERED RESIDUES REMARK 210 [S(PHI) + S(PSI) > 1.8] COMPRISE 1-5,9-10,17-18,23-38,41-70,76-85, REMARK 210 88-93,101-104,106-108: REMARK 210 (A) RMSD FOR ORDERED RESIDUES: BB, 0.7; HEAVY ATOM, 1.2. REMARK 210 (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED: REMARK 210 89.9%; REMARK 210 ADDITIONALLY ALLOWED: 10.1%; GENEROUSLY ALLOWED, 0.0%; DISALLOWED, REMARK 210 0.0% REMARK 210 (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): BB, -0.53/- REMARK 210 1.77; ALL, REMARK 210 -0.49/-2.90. REMARK 210 (D) MAGE MOLPROBITY CLASH SCORE (RAW/Z-): 28.47/-3.36. REMARK 210 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA: F-MEASURE, REMARK 210 0.916; REMARK 210 RECALL, 0.962; PRECISION, 0.874; DP-SCORE, 0.791. 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 1-10 REMARK 465 RES C SSSEQI REMARK 465 LEU A 114 REMARK 465 GLU A 115 REMARK 465 HIS A 116 REMARK 465 HIS A 117 REMARK 465 HIS A 118 REMARK 465 HIS A 119 REMARK 465 HIS A 120 REMARK 465 HIS A 121 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 GLY A 7 HG SER A 8 1.56 REMARK 500 H3 MET A 1 O ILE A 58 1.57 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 SER A 8 152.01 61.68 REMARK 500 1 HIS A 11 -157.92 44.54 REMARK 500 1 SER A 16 -51.16 -178.55 REMARK 500 1 THR A 20 -66.47 -96.88 REMARK 500 1 HIS A 40 -82.99 -104.67 REMARK 500 1 PRO A 96 128.99 -28.35 REMARK 500 1 LEU A 109 -74.20 -99.29 REMARK 500 1 ASP A 110 -48.25 66.51 REMARK 500 2 SER A 8 89.92 -69.61 REMARK 500 2 ASN A 21 17.95 51.54 REMARK 500 2 THR A 71 -19.16 98.14 REMARK 500 2 ARG A 72 -83.64 62.19 REMARK 500 2 ARG A 95 167.91 72.62 REMARK 500 2 ASP A 98 16.18 -64.93 REMARK 500 2 ASP A 110 2.57 57.02 REMARK 500 3 TYR A 6 -43.68 -135.58 REMARK 500 3 SER A 8 96.57 50.46 REMARK 500 3 HIS A 11 -84.60 59.25 REMARK 500 3 LYS A 12 115.68 174.42 REMARK 500 3 GLN A 13 -156.05 -126.73 REMARK 500 3 ASN A 15 -35.30 -136.92 REMARK 500 3 PHE A 28 86.37 -151.82 REMARK 500 3 ASN A 32 33.38 71.01 REMARK 500 3 LEU A 38 16.75 -140.98 REMARK 500 3 TYR A 41 110.88 -167.65 REMARK 500 3 THR A 71 -67.59 -106.61 REMARK 500 3 ARG A 95 -37.46 -162.13 REMARK 500 3 ASP A 98 24.15 -64.48 REMARK 500 3 LEU A 100 -170.00 61.89 REMARK 500 4 SER A 8 103.30 51.36 REMARK 500 4 LEU A 9 17.09 -66.54 REMARK 500 4 HIS A 11 106.17 46.50 REMARK 500 4 ASN A 15 173.02 72.65 REMARK 500 4 THR A 20 46.74 -85.93 REMARK 500 4 ASN A 21 -19.40 163.57 REMARK 500 4 ALA A 22 105.47 -50.00 REMARK 500 4 ASN A 32 36.33 77.03 REMARK 500 4 ARG A 95 169.38 70.91 REMARK 500 4 ASP A 110 -107.54 55.96 REMARK 500 5 GLN A 13 -166.74 -173.27 REMARK 500 5 ASN A 15 -69.82 -136.20 REMARK 500 5 SER A 16 -43.55 -164.41 REMARK 500 5 PHE A 28 87.05 -156.71 REMARK 500 5 THR A 71 124.54 98.40 REMARK 500 5 PRO A 96 121.78 -39.25 REMARK 500 5 ASP A 98 96.64 -60.56 REMARK 500 5 ASP A 110 -79.62 59.68 REMARK 500 5 ASP A 112 96.69 57.57 REMARK 500 6 HIS A 11 75.92 41.11 REMARK 500 6 LYS A 12 -95.41 67.48 REMARK 500 REMARK 500 THIS ENTRY HAS 104 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: ER111 RELATED DB: TARGETDB DBREF 1XHS A 1 113 UNP P39323 YTFP_ECOLI 1 113 SEQADV 1XHS LEU A 114 UNP P39323 EXPRESSION TAG SEQADV 1XHS GLU A 115 UNP P39323 EXPRESSION TAG SEQADV 1XHS HIS A 116 UNP P39323 EXPRESSION TAG SEQADV 1XHS HIS A 117 UNP P39323 EXPRESSION TAG SEQADV 1XHS HIS A 118 UNP P39323 EXPRESSION TAG SEQADV 1XHS HIS A 119 UNP P39323 EXPRESSION TAG SEQADV 1XHS HIS A 120 UNP P39323 EXPRESSION TAG SEQADV 1XHS HIS A 121 UNP P39323 EXPRESSION TAG SEQRES 1 A 121 MET ARG ILE PHE VAL TYR GLY SER LEU ARG HIS LYS GLN SEQRES 2 A 121 GLY ASN SER HIS TRP MET THR ASN ALA GLN LEU LEU GLY SEQRES 3 A 121 ASP PHE SER ILE ASP ASN TYR GLN LEU TYR SER LEU GLY SEQRES 4 A 121 HIS TYR PRO GLY ALA VAL PRO GLY ASN GLY THR VAL HIS SEQRES 5 A 121 GLY GLU VAL TYR ARG ILE ASP ASN ALA THR LEU ALA GLU SEQRES 6 A 121 LEU ASP ALA LEU ARG THR ARG GLY GLY GLU TYR ALA ARG SEQRES 7 A 121 GLN LEU ILE GLN THR PRO TYR GLY SER ALA TRP MET TYR SEQRES 8 A 121 VAL TYR GLN ARG PRO VAL ASP GLY LEU LYS LEU ILE GLU SEQRES 9 A 121 SER GLY ASP TRP LEU ASP ARG ASP LYS LEU GLU HIS HIS SEQRES 10 A 121 HIS HIS HIS HIS HELIX 1 1 SER A 16 ASN A 21 1 6 HELIX 2 2 ASP A 59 THR A 71 1 13 SHEET 1 A 3 ARG A 2 VAL A 5 0 SHEET 2 A 3 VAL A 51 ARG A 57 -1 O GLU A 54 N VAL A 5 SHEET 3 A 3 GLN A 23 ILE A 30 -1 N ILE A 30 O VAL A 51 SHEET 1 B 3 PRO A 42 PRO A 46 0 SHEET 2 B 3 TYR A 33 SER A 37 -1 N TYR A 36 O GLY A 43 SHEET 3 B 3 LYS A 101 ILE A 103 -1 O ILE A 103 N LEU A 35 SHEET 1 C 2 TYR A 76 THR A 83 0 SHEET 2 C 2 GLY A 86 TYR A 93 -1 O MET A 90 N GLN A 79 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