HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 21-JUN-06 2HEP TITLE SOLUTION NMR STRUCTURE OF THE UPF0291 PROTEIN YNZC FROM BACILLUS TITLE 2 SUBTILIS. NORTHEAST STRUCTURAL GENOMICS TARGET SR384. COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPF0291 PROTEIN YNZC; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: YNZC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)MGK; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21, SR384-21.4 KEYWDS SR384, AUTOSTRUCTURE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, PSI- KEYWDS 2 1, PROTEIN STRUCTURE INITIATIVE, NESG, STRUCTURAL GENOMICS, UNKNOWN KEYWDS 3 FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.M.ARAMINI,G.V.T.SWAPNA,C.K.HO,K.SHETTY,K.CUNNINGHAM,L.-C.MA,R.XIAO, AUTHOR 2 J.LIU,M.BARAN,T.B.ACTON,B.ROST,G.T.MONTELIONE,NORTHEAST STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (NESG) REVDAT 4 09-MAR-22 2HEP 1 REMARK SEQADV REVDAT 3 24-FEB-09 2HEP 1 VERSN REVDAT 2 10-JUN-08 2HEP 1 JRNL REVDAT 1 15-AUG-06 2HEP 0 JRNL AUTH J.M.ARAMINI,S.SHARMA,Y.J.HUANG,G.V.SWAPNA,C.K.HO,K.SHETTY, JRNL AUTH 2 K.CUNNINGHAM,L.C.MA,L.ZHAO,L.A.OWENS,M.JIANG,R.XIAO,J.LIU, JRNL AUTH 3 M.C.BARAN,T.B.ACTON,B.ROST,G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF THE SOS RESPONSE PROTEIN YNZC FROM JRNL TITL 2 BACILLUS SUBTILIS JRNL REF PROTEINS V. 72 526 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 18431750 JRNL DOI 10.1002/PROT.22064 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, AUTOSTRUCTURE 2.1.1, XPLOR-NIH 2.11.2 REMARK 3 AUTHORS : VARIAN (VNMR), HUANG & MONTELIONE (AUTOSTRUCTURE), REMARK 3 CLORE ET AL (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 403 CONFORMATIONALLY REMARK 3 RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 67 DIHEDRAL ANGLE REMARK 3 CONSTRAINTS, 42 HYDROGEN BOND CONSTRAINTS, AND 29 J(HN-HALPHA) REMARK 3 COUPLING CONSTANTS (12.5 CONSTRAINTS PER RESIDUE; 1.1 LONG RANGE REMARK 3 CONSTRAINTS PER RESIDUE; COMPUTED FOR RESIDUES 1 TO 42 BY PSVS 1.2) REMARK 3 . REMARK 3 STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING REMARK 3 AUTOSTRUCTURE (XPLOR-NIH). A FINAL XPLOR CALCULATION USING THE REMARK 3 FINAL CONSTRAINTS DERIVED FROM AUTOSTRUCTURE WAS PERFORMED TO REMARK 3 YIELD THE FINAL STRUCTURES. THE UNSTRUCTURED C-TERMINAL HALF OF REMARK 3 THE MOLECULE WAS INCLUDED IN ALL STRUCTURAL CALCULATIONS BUT HAS REMARK 3 BEEN OMITTED FROM THIS DEPOSITION. HETERONUCLEAR 15N,1H NOE REMARK 3 EXPERIMENTS CORROBORATE THE PRESENCE OF SIGNIFICANT DISORDER IN REMARK 3 THE C-TERMINAL HALF OF THE PROTEIN (RESIDUES 43 TO C-TERMINUS). REMARK 4 REMARK 4 2HEP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000038262. 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 SR384, 20MM REMARK 210 MES, 100MM NACL, 5 MM CACL2, REMARK 210 10MM DTT, 0.02% NAN3, PH 6.5, 5% REMARK 210 D2O/95% H2O; 1.12MM 5%-13C,U-15N REMARK 210 SR384, 20MM MES, 100MM NACL, 5 REMARK 210 MM CACL2, 10MM DTT, 0.02% NAN3, REMARK 210 PH 6.5, 5% D2O/95% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; HNHA; 3D GFT- REMARK 210 CBCACACONHN, GFT-HNNCACBCA, GFT- REMARK 210 HABCABCONHN; 3D HCCH-TOCSY, REMARK 210 CCCONH TOCSY, HCCH-COSY; HIGH REMARK 210 RESOLUTION 2D CH-HQSC (FOR REMARK 210 STEREOSPECIFIC ASSIGNMENT OF VAL/ REMARK 210 LEU METHYLS); 3D HNCO, HNCACO; REMARK 210 2D 15N1H-HETERONUCLEAR NOE REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5PL6, AUTOASSIGN REMARK 210 2.2.1, SPARKY 3.110, AGNUS 2.0, 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 LOWEST REMARK 210 CONFORMATIONAL 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. AUTOASSIGN WAS USED TO OBTAIN AUTOMATIC BACKBONE REMARK 210 ASSIGNMENTS FROM GFT PEAK LISTS. SIDE CHAIN ASSIGNMENTS WERE REMARK 210 COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENT, AS WELL AS REMARK 210 DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING REMARK 210 AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE DETERMINED USING REMARK 210 HYPER. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL REMARK 210 LEHHHHHH TAG): REMARK 210 BACKBONE: 91.9%; SIDE CHAIN: 78.3%; AROMATICS, 100%: REMARK 210 STEREOSPECIFIC METHYL, 87.5%. REMARK 210 FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 42 ONLY; PSVS REMARK 210 1.2), WHERE ORDERED RESIDUES [S(PHI)+ S(PSI) > 1.8] COMPRISE 5-20 REMARK 210 AND 23-40: REMARK 210 (A) RMSD (ORDERED RESIDUES): BB, 0.9; HEAVY ATOM, 1.5. (B) REMARK 210 RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 96.4%, REMARK 210 ADDITIONALLY ALLOWED, 3.6%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, REMARK 210 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, REMARK 210 0.11/0.75; ALL, -0.12/-0.71. (D) MOLPROBITY CLASH SCORE (RAW/Z-): REMARK 210 14.69/-1.00. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA REMARK 210 (ALL RESIDUES): RECALL, 0.952, PRECISION, 0.839, F-MEASURE, 0.892, REMARK 210 DP-SCORE, 0.628 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 SER A 43 REMARK 465 SER A 44 REMARK 465 MET A 45 REMARK 465 LYS A 46 REMARK 465 ASN A 47 REMARK 465 THR A 48 REMARK 465 LEU A 49 REMARK 465 LYS A 50 REMARK 465 SER A 51 REMARK 465 VAL A 52 REMARK 465 LYS A 53 REMARK 465 ILE A 54 REMARK 465 ILE A 55 REMARK 465 ASP A 56 REMARK 465 PRO A 57 REMARK 465 GLU A 58 REMARK 465 GLY A 59 REMARK 465 ASN A 60 REMARK 465 ASP A 61 REMARK 465 VAL A 62 REMARK 465 THR A 63 REMARK 465 PRO A 64 REMARK 465 GLU A 65 REMARK 465 LYS A 66 REMARK 465 LEU A 67 REMARK 465 LYS A 68 REMARK 465 ARG A 69 REMARK 465 GLU A 70 REMARK 465 GLN A 71 REMARK 465 ARG A 72 REMARK 465 ASN A 73 REMARK 465 ASN A 74 REMARK 465 LYS A 75 REMARK 465 LEU A 76 REMARK 465 HIS A 77 REMARK 465 LEU A 78 REMARK 465 GLU A 79 REMARK 465 HIS A 80 REMARK 465 HIS A 81 REMARK 465 HIS A 82 REMARK 465 HIS A 83 REMARK 465 HIS A 84 REMARK 465 HIS A 85 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 37 H PHE A 41 1.55 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 3 19.85 -170.27 REMARK 500 1 ASN A 4 -156.70 -77.92 REMARK 500 1 VAL A 21 -38.78 -156.37 REMARK 500 1 ILE A 22 132.21 69.80 REMARK 500 1 PHE A 41 -106.85 19.89 REMARK 500 2 ILE A 2 -70.38 -108.71 REMARK 500 2 SER A 3 -113.97 44.74 REMARK 500 2 ASN A 4 -159.56 43.12 REMARK 500 2 VAL A 21 -63.89 -152.11 REMARK 500 2 ILE A 22 146.36 69.05 REMARK 500 3 ASN A 4 -68.42 -142.45 REMARK 500 3 ARG A 9 -75.91 -60.10 REMARK 500 3 VAL A 21 99.17 67.05 REMARK 500 3 PHE A 41 -77.02 -66.42 REMARK 500 4 SER A 3 -45.13 73.40 REMARK 500 4 VAL A 21 -36.79 -156.61 REMARK 500 4 ILE A 22 97.45 41.41 REMARK 500 4 PHE A 41 93.87 -172.63 REMARK 500 5 SER A 3 14.51 -156.80 REMARK 500 5 ARG A 9 -74.30 -60.17 REMARK 500 5 VAL A 21 94.59 67.41 REMARK 500 6 SER A 3 -138.36 59.77 REMARK 500 6 ASN A 4 -104.42 57.06 REMARK 500 6 VAL A 21 100.67 -177.20 REMARK 500 6 PHE A 41 -87.70 -64.20 REMARK 500 7 SER A 3 89.10 47.02 REMARK 500 7 ASN A 4 -155.26 -165.78 REMARK 500 7 VAL A 21 -45.75 -159.67 REMARK 500 7 ILE A 22 122.63 67.99 REMARK 500 8 ILE A 2 -13.63 -162.02 REMARK 500 8 ASN A 4 -79.01 -153.04 REMARK 500 8 VAL A 21 -65.07 74.61 REMARK 500 8 ILE A 22 138.59 129.34 REMARK 500 9 SER A 3 65.68 -173.19 REMARK 500 9 ASN A 4 -113.80 -171.85 REMARK 500 9 ARG A 9 -73.81 -61.13 REMARK 500 9 ASN A 11 -70.08 -59.01 REMARK 500 9 VAL A 21 99.45 74.39 REMARK 500 9 PHE A 41 98.88 -64.32 REMARK 500 10 SER A 3 80.06 41.05 REMARK 500 10 ASN A 4 -142.81 -154.91 REMARK 500 10 VAL A 21 76.26 49.32 REMARK 500 10 ILE A 22 -130.46 -87.85 REMARK 500 10 GLU A 29 -70.37 -59.42 REMARK 500 10 PHE A 41 98.17 -172.93 REMARK 500 11 ILE A 2 94.39 55.48 REMARK 500 11 ASN A 4 -154.34 -138.32 REMARK 500 11 VAL A 21 99.65 -172.75 REMARK 500 11 PHE A 41 -161.01 90.23 REMARK 500 12 ASN A 4 -118.91 -173.55 REMARK 500 REMARK 500 THIS ENTRY HAS 91 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SR384 RELATED DB: TARGETDB DBREF 2HEP A 1 77 UNP O31818 YNZC_BACSU 1 77 SEQADV 2HEP LEU A 78 UNP O31818 CLONING ARTIFACT SEQADV 2HEP GLU A 79 UNP O31818 CLONING ARTIFACT SEQADV 2HEP HIS A 80 UNP O31818 EXPRESSION TAG SEQADV 2HEP HIS A 81 UNP O31818 EXPRESSION TAG SEQADV 2HEP HIS A 82 UNP O31818 EXPRESSION TAG SEQADV 2HEP HIS A 83 UNP O31818 EXPRESSION TAG SEQADV 2HEP HIS A 84 UNP O31818 EXPRESSION TAG SEQADV 2HEP HIS A 85 UNP O31818 EXPRESSION TAG SEQRES 1 A 85 MET ILE SER ASN ALA LYS ILE ALA ARG ILE ASN GLU LEU SEQRES 2 A 85 ALA ALA LYS ALA LYS ALA GLY VAL ILE THR GLU GLU GLU SEQRES 3 A 85 LYS ALA GLU GLN GLN LYS LEU ARG GLN GLU TYR LEU LYS SEQRES 4 A 85 GLY PHE ARG SER SER MET LYS ASN THR LEU LYS SER VAL SEQRES 5 A 85 LYS ILE ILE ASP PRO GLU GLY ASN ASP VAL THR PRO GLU SEQRES 6 A 85 LYS LEU LYS ARG GLU GLN ARG ASN ASN LYS LEU HIS LEU SEQRES 7 A 85 GLU HIS HIS HIS HIS HIS HIS HELIX 1 1 ASN A 4 VAL A 21 1 18 HELIX 2 2 THR A 23 PHE A 41 1 19 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