10 20 30 40 50 60 70 80 2HEP - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 21-JUN-06 2HEP
TITLE SOLUTION NMR STRUCTURE OF THE UPF0291 PROTEIN YNZC FROM TITLE 2 BACILLUS SUBTILIS. NORTHEAST STRUCTURAL GENOMICS TARGET TITLE 3 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, NMR STRUCTURE, AUTOSTRUCTURE, NORTHEAST STRUCTURAL KEYWDS 2 GENOMICS CONSORTIUM, PSI-1, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 NESG, STRUCTURAL GENOMICS, UNKNOWN FUNCTION
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR J.M.ARAMINI,G.V.T.SWAPNA,C.K.HO,K.SHETTY,K.CUNNINGHAM,L.- AUTHOR 2 C.MA,R.XIAO,J.LIU,M.BARAN,T.B.ACTON,B.ROST,G.T.MONTELIONE, AUTHOR 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG)
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, JRNL AUTH 2 K.SHETTY,K.CUNNINGHAM,L.C.MA,L.ZHAO,L.A.OWENS, JRNL AUTH 3 M.JIANG,R.XIAO,J.LIU,M.C.BARAN,T.B.ACTON,B.ROST, JRNL AUTH 4 G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF THE SOS RESPONSE PROTEIN JRNL TITL 2 YNZC FROM BACILLUS SUBTILIS JRNL REF PROTEINS V. 72 526 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 18431750 JRNL DOI 10.1002/PROT.22064
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AUTOSTRUCTURE 2.1.1, XPLOR-NIH 2.11.2 REMARK 3 AUTHORS : HUANG & MONTELIONE (AUTOSTRUCTURE), CLORE ET AL REMARK 3 (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 403 CONFORMATIONALLY RESTRICTING NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS, 67 DIHEDRAL ANGLE CONSTRAINTS, 42 HYDROGEN BOND REMARK 3 CONSTRAINTS, AND 29 J(HN-HALPHA) COUPLING CONSTANTS (12.5 REMARK 3 CONSTRAINTS PER RESIDUE; 1.1 LONG RANGE CONSTRAINTS PER REMARK 3 RESIDUE; COMPUTED FOR RESIDUES 1 TO 42 BY PSVS 1.2). STRUCTURE REMARK 3 DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE REMARK 3 (XPLOR-NIH). A FINAL XPLOR CALCULATION USING THE FINAL REMARK 3 CONSTRAINTS DERIVED FROM AUTOSTRUCTURE WAS PERFORMED TO YIELD REMARK 3 THE FINAL STRUCTURES. THE UNSTRUCTURED C-TERMINAL HALF OF THE REMARK 3 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 REMARK 3 IN THE C-TERMINAL HALF OF THE PROTEIN (RESIDUES 43 TO C- REMARK 3 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 26-JUN-06. REMARK 100 THE RCSB ID CODE IS RCSB038262.
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, REMARK 210 5% D2O/95% H2O; 1.12MM 5%-13C, REMARK 210 U-15N SR384, 20MM MES, 100MM REMARK 210 NACL, 5 MM CACL2, 10MM DTT, REMARK 210 0.02% NAN3, PH 6.5, 5% D2O/95% REMARK 210 H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-SEPARATED_NOESY, HNHA, 3D REMARK 210 GFT-CBCACACONHN, GFT- REMARK 210 HNNCACBCA, GFT-HABCABCONHN, 3D REMARK 210 HCCH-TOCSY, CCCONH TOCSY, HCCH REMARK 210 -COSY, HIGH RESOLUTION 2D CH- REMARK 210 HQSC (FOR STEREOSPECIFIC REMARK 210 ASSIGNMENT OF VAL/LEU METHYLS) REMARK 210 , 3D HNCO, HNCACO, 2D 15N1H- REMARK 210 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 : VNMR 6.1C, XWINNMR 3.5PL6, REMARK 210 AUTOASSIGN 2.2.1, SPARKY REMARK 210 3.110, AGNUS 2.0, PDBSTAT REMARK 210 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: 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 REMARK 210 USING HYPER. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C- REMARK 210 TERMINAL LEHHHHHH TAG): BACKBONE: 91.9%; SIDE CHAIN: 78.3%; REMARK 210 AROMATICS, 100%: STEREOSPECIFIC METHYL, 87.5%. FINAL STRUCTURE REMARK 210 QUALITY FACTORS (FOR RESIDUES 1 TO 42 ONLY; PSVS 1.2), WHERE REMARK 210 ORDERED RESIDUES [S(PHI)+ S(PSI) > 1.8] COMPRISE 5-20 AND 23- REMARK 210 40: (A) RMSD (ORDERED RESIDUES): BB, 0.9; HEAVY ATOM, 1.5. (B) REMARK 210 RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, REMARK 210 96.4%, ADDITIONALLY ALLOWED, 3.6%, GENEROUSLY ALLOWED, 0.0%, REMARK 210 DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES REMARK 210 (RAW/Z-): PHI-PSI, 0.11/0.75; ALL, -0.12/-0.71. (D) MOLPROBITY REMARK 210 CLASH SCORE (RAW/Z-): 14.69/-1.00. (E) RPF SCORES FOR GOODNESS REMARK 210 OF FIT TO NOESY DATA (ALL RESIDUES): RECALL, 0.952, PRECISION, REMARK 210 0.839, F-MEASURE, 0.892, 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 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: 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 12 VAL A 21 87.88 -165.13 REMARK 500 12 PHE A 41 65.52 21.91 REMARK 500 13 ILE A 2 -131.69 -98.84 REMARK 500 13 SER A 3 3.56 59.70 REMARK 500 13 ASN A 4 -166.14 -76.96 REMARK 500 13 ARG A 9 -75.49 -61.14 REMARK 500 13 VAL A 21 88.92 -175.04 REMARK 500 13 PHE A 41 74.91 -165.78 REMARK 500 14 SER A 3 -34.66 75.03 REMARK 500 14 ASN A 4 -27.70 73.88 REMARK 500 14 ARG A 9 -76.15 -60.98 REMARK 500 14 ALA A 19 -75.26 -74.61 REMARK 500 14 VAL A 21 97.21 162.20 REMARK 500 14 ILE A 22 -170.28 -58.52 REMARK 500 14 PHE A 41 91.92 -167.25 REMARK 500 15 SER A 3 73.06 -158.74 REMARK 500 15 ASN A 4 -146.93 -150.74 REMARK 500 15 ALA A 14 -70.94 -56.06 REMARK 500 15 VAL A 21 100.03 -172.56 REMARK 500 15 PHE A 41 79.18 -174.56 REMARK 500 16 VAL A 21 -44.29 176.97 REMARK 500 16 ILE A 22 165.57 118.86 REMARK 500 16 PHE A 41 95.44 -173.93 REMARK 500 17 ILE A 2 -50.19 -125.83 REMARK 500 17 SER A 3 21.64 47.79 REMARK 500 17 ASN A 4 18.01 53.86 REMARK 500 17 ARG A 9 -75.05 -60.47 REMARK 500 17 VAL A 21 100.15 -174.12 REMARK 500 17 PHE A 41 60.68 20.56 REMARK 500 18 SER A 3 58.35 -108.39 REMARK 500 18 ASN A 4 -93.75 -146.40 REMARK 500 18 ARG A 9 -75.22 -62.34 REMARK 500 18 VAL A 21 100.49 176.74 REMARK 500 18 PHE A 41 74.62 -65.86 REMARK 500 19 ASN A 4 -153.36 -152.09 REMARK 500 19 LYS A 6 -72.90 -68.97 REMARK 500 19 VAL A 21 91.75 -161.34 REMARK 500 20 ILE A 2 -37.78 -144.34 REMARK 500 20 SER A 3 2.05 59.59 REMARK 500 20 ARG A 9 -74.11 -61.86 REMARK 500 20 VAL A 21 90.20 -164.52 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