HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 27-JUN-11 2LF0 TITLE SOLUTION STRUCTURE OF SF3636, A TWO-DOMAIN UNKNOWN FUNCTION PROTEIN TITLE 2 FROM SHIGELLA FLEXNERI 2A, DETERMINED BY JOINT REFINEMENT OF NMR, TITLE 3 RESIDUAL DIPOLAR COUPLINGS AND SMALL-ANGLE X-RAY SCATTERING, NESG TITLE 4 TARGET SFR339/OCSP TARGET SF3636 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN YIBL; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHIGELLA FLEXNERI; SOURCE 3 ORGANISM_TAXID: 623; SOURCE 4 GENE: YIBL, S4132, SF3636; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: P15TV LIC KEYWDS TWO-DOMAIN PROTEIN, STRUCTURAL GENOMICS, PSI-BIOLOGY, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, KEYWDS 3 NESG, ONTARIO CENTRE FOR STRUCTURAL PROTEOMICS, OCSP, UNKNOWN KEYWDS 4 FUNCTION EXPDTA SOLUTION NMR; SOLUTION SCATTERING NUMMDL 20 AUTHOR B.WU,A.LEMAK,A.YEE,H.LEE,A.GUTMANAS,A.SEMESI,M.GARCIA,X.FANG,Y.WANG, AUTHOR 2 J.H.PRESTEGARD,C.H.ARROWSMITH,NORTHEAST STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (NESG),ONTARIO CENTRE FOR STRUCTURAL PROTEOMICS (OCSP) REVDAT 6 15-MAY-24 2LF0 1 REMARK REVDAT 5 14-JUN-23 2LF0 1 REMARK SEQADV REVDAT 4 08-MAY-19 2LF0 1 EXPDTA REMARK REVDAT 3 07-NOV-12 2LF0 1 TITLE JRNL REVDAT 2 22-FEB-12 2LF0 1 KEYWDS REVDAT 1 13-JUL-11 2LF0 0 JRNL AUTH B.WU,A.LEMAK,A.YEE,H.LEE,A.GUTMANAS,A.SEMESI,M.GARCIA, JRNL AUTH 2 X.FANG,Y.WANG,J.H.PRESTEGARD,C.H.ARROWSMITH JRNL TITL SOLUTION STRUCTURE OF SF3636, A TWO-DOMAIN UNKNOWN FUNCTION JRNL TITL 2 PROTEIN FROM SHIGELLA FLEXNERI 2A, DETERMINED BY JOINT JRNL TITL 3 REFINEMENT OF NMR, RESIDUAL DIPOLAR COUPLINGS AND JRNL TITL 4 SMALL-ANGLE X-RAY SCATTERING JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.3, CNS REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE SOLUTION STRUCTURES WERE GENERATED REMARK 3 USING CYANA 3.0 WITH AUTOMATED NOESY ASSIGNMENTS AND RDC REMARK 3 RESTRAINTS AND FURTHER REFINED BY INCORPORATING RDC RESTRAINTS REMARK 3 AND SAXS DATA IN RESTRAINED MOLECULAR DYNAMICS SIMULATION WITH REMARK 3 THE PROGRAM CNS. ALTHOUGH THE CURRENT MODELS FIT WELL WITH BOTH REMARK 3 RDCS AND SAXS, SF3636 MAY SAMPLE A RANGE OF RELATIVE DOMAIN REMARK 3 ORIENTATIONS DEPENDING ON DATA TYPES AND REFINEMENT TOOLS. TO REMARK 3 FURTHER INVESTIGATE SF3636 DOMAIN ORIENTATION AND ITS INTRINSIC REMARK 3 DYNAMIC NATURE, PRESTEGARD LAB IS DEVELOPING A NEW PROTOCOL REMARK 3 USING RCSAS AND RDCS FROM SEVERAL MEDIUMS. THEIR REFINED MODELS REMARK 3 WILL BE DEPOSITED LATER. REMARK 4 REMARK 4 2LF0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1000102311. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 300 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7 MM [U-100% 13C; U-100% 15N] REMARK 210 SF3636, 10 MM [U-100% 2H] TRIS, REMARK 210 300 MM SODIUM CHLORIDE, 10 UM REMARK 210 ZINC SULPHATE, 10 MM [U-100% 2H] REMARK 210 DTT, 0.01 % NAN3-6, 10 MM REMARK 210 BENZAMIDINE, 1 X INHIBITOR REMARK 210 COCKTAIL, 90% H2O/10% D2O; 0.5 REMARK 210 MM [U-100% 13C; U-100% 15N] REMARK 210 SF3636, 10 MM [U-100% 2H] TRIS, REMARK 210 300 MM SODIUM CHLORIDE, 10 UM REMARK 210 ZINC SULPHATE, 10 MM [U-100% 2H] REMARK 210 DTT, 0.01 % NAN3, 10 MM REMARK 210 BENZAMIDINE, 1 X INHIBITOR REMARK 210 COCKTAIL, 100% D2O; 0.5 MM [U-7% REMARK 210 13C; U-100% 15N] SF3636, 10 MM REMARK 210 [U-100% 2H] TRIS, 300 MM SODIUM REMARK 210 CHLORIDE, 10 UM ZINC SULPHATE, REMARK 210 10 MM [U-100% 2H] DTT, 0.01 % REMARK 210 NAN3, 10 MM BENZAMIDINE, 1 X REMARK 210 INHIBITOR COCKTAIL, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCO; 3D CBCA(CO)NH; 3D REMARK 210 HBHA(CO)NH; 3D HNCA; 3D HCCH- REMARK 210 TOCSY; 3D CCH-TOCSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY; 3D 1H- REMARK 210 13C NOESY AROMATIC; 2D 1H-13C REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MDDGUI 1.0, SPARKY 3.95, FMCGUI REMARK 210 2.4, CYANA 3.0, AUTOSTRUCTURE, REMARK 210 PSVS, ABACUS 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 THE LOWEST REMARK 210 ENERGY 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 265 REMARK 265 EXPERIMENTAL DETAILS 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 GLN A -2 REMARK 465 GLY A -1 REMARK 465 HIS A 0 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 LYS A 2 -51.78 74.81 REMARK 500 1 GLU A 3 -27.05 84.12 REMARK 500 1 VAL A 4 -9.31 71.78 REMARK 500 1 ASP A 33 -81.56 -172.40 REMARK 500 1 GLU A 46 -74.45 -57.48 REMARK 500 1 ALA A 47 -46.65 -27.79 REMARK 500 1 SER A 57 -52.64 -130.82 REMARK 500 1 LYS A 59 74.46 -114.38 REMARK 500 1 LYS A 62 -70.52 -60.98 REMARK 500 1 ARG A 74 -173.35 -178.94 REMARK 500 1 ARG A 92 53.49 74.27 REMARK 500 2 ALA A 31 64.93 -150.89 REMARK 500 2 ASP A 33 -83.25 126.37 REMARK 500 2 SER A 57 -55.52 -139.12 REMARK 500 2 LYS A 62 -75.78 -51.93 REMARK 500 2 PRO A 71 -84.36 -72.14 REMARK 500 2 SER A 90 -54.61 -123.50 REMARK 500 2 ARG A 92 95.09 60.68 REMARK 500 3 ALA A 32 45.40 -91.98 REMARK 500 3 ASP A 33 -87.69 -161.16 REMARK 500 3 GLU A 46 -73.64 -59.42 REMARK 500 3 ALA A 47 -47.30 -27.57 REMARK 500 3 HIS A 56 42.26 -93.66 REMARK 500 3 SER A 57 -46.90 -141.73 REMARK 500 3 ARG A 74 -170.57 177.82 REMARK 500 3 SER A 90 -1.40 -57.04 REMARK 500 3 ARG A 92 -1.85 87.82 REMARK 500 4 GLU A 3 10.81 -162.22 REMARK 500 4 GLU A 46 -71.67 -60.94 REMARK 500 4 LYS A 62 -76.05 -61.30 REMARK 500 4 ARG A 74 -169.33 -179.87 REMARK 500 4 ASP A 83 42.18 -140.12 REMARK 500 4 ARG A 92 -75.15 72.83 REMARK 500 4 LEU A 94 131.51 -3.76 REMARK 500 5 LYS A 2 -70.80 67.88 REMARK 500 5 GLU A 46 -74.81 -58.83 REMARK 500 5 ALA A 47 -48.33 -26.58 REMARK 500 5 HIS A 56 41.92 -95.30 REMARK 500 5 SER A 57 -59.07 -139.24 REMARK 500 5 LEU A 60 -71.94 -14.21 REMARK 500 5 LYS A 69 31.70 -97.79 REMARK 500 5 ARG A 74 -169.84 -179.03 REMARK 500 5 ARG A 92 -53.38 80.39 REMARK 500 6 GLU A 3 -101.70 61.84 REMARK 500 6 VAL A 4 -28.90 63.70 REMARK 500 6 LEU A 60 91.76 -64.97 REMARK 500 6 SER A 61 164.74 61.60 REMARK 500 6 LYS A 62 -76.69 -67.73 REMARK 500 6 PRO A 71 -71.80 -75.93 REMARK 500 6 ARG A 74 -166.72 -175.39 REMARK 500 REMARK 500 THIS ENTRY HAS 176 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 54 VAL A 55 4 149.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17735 RELATED DB: BMRB REMARK 900 RELATED ID: SFR339 RELATED DB: TARGETDB DBREF 2LF0 A 1 120 UNP Q83J25 Q83J25_SHIFL 1 120 SEQADV 2LF0 GLN A -2 UNP Q83J25 EXPRESSION TAG SEQADV 2LF0 GLY A -1 UNP Q83J25 EXPRESSION TAG SEQADV 2LF0 HIS A 0 UNP Q83J25 EXPRESSION TAG SEQRES 1 A 123 GLN GLY HIS MET LYS GLU VAL GLU LYS ASN GLU ILE LYS SEQRES 2 A 123 ARG LEU SER ASP ARG LEU ASP ALA ILE ARG HIS GLN GLN SEQRES 3 A 123 ALA ASP LEU SER LEU VAL GLU ALA ALA ASP LYS TYR ALA SEQRES 4 A 123 GLU LEU GLU LYS GLU LYS ALA THR LEU GLU ALA GLU ILE SEQRES 5 A 123 ALA ARG LEU ARG GLU VAL HIS SER GLN LYS LEU SER LYS SEQRES 6 A 123 GLU ALA GLN LYS LEU MET LYS MET PRO PHE GLN ARG ALA SEQRES 7 A 123 ILE THR LYS LYS GLU GLN ALA ASP MET GLY LYS LEU LYS SEQRES 8 A 123 LYS SER VAL ARG GLY LEU VAL VAL VAL HIS PRO MET THR SEQRES 9 A 123 ALA LEU GLY ARG GLU MET GLY LEU GLU GLU MET THR GLY SEQRES 10 A 123 PHE SER LYS THR THR PHE HELIX 1 1 VAL A 4 LEU A 26 1 23 HELIX 2 2 ASP A 33 LYS A 59 1 27 HELIX 3 3 SER A 61 LYS A 69 1 9 HELIX 4 4 THR A 77 ASP A 83 1 7 HELIX 5 5 ASP A 83 VAL A 91 1 9 HELIX 6 6 THR A 101 MET A 107 1 7 SHEET 1 A 3 PHE A 72 ALA A 75 0 SHEET 2 A 3 THR A 113 SER A 116 -1 O GLY A 114 N ARG A 74 SHEET 3 A 3 VAL A 95 VAL A 97 -1 N VAL A 97 O THR A 113 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