HEADER IMMUNE SYSTEM 20-JAN-09 2KDY TITLE NMR STRUCTURE OF LP2086-B01 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FACTOR H BINDING PROTEIN VARIANT B01_001; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 3 ORGANISM_TAXID: 487; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA BARREL, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 17 AUTHOR A.MASCIONI,B.E.BENTLEY,R.CAMARDA,D.A.DILTS,P.FINK,V.GUSAROVA, AUTHOR 2 S.HOISETH,J.JACOB,S.L.LIN,K.MALAKIAN,L.K.MCNEIL,T.MININNI,F.MOY, AUTHOR 3 E.MURPHY,E.NOVIKOVA,S.SIGETHY,Y.WEN,G.W.ZLOTNICK,D.H.H.TSAO REVDAT 3 16-MAR-22 2KDY 1 REMARK SEQADV REVDAT 2 07-APR-09 2KDY 1 JRNL REVDAT 1 17-FEB-09 2KDY 0 JRNL AUTH A.MASCIONI,B.E.BENTLEY,R.CAMARDA,D.A.DILTS,P.FINK, JRNL AUTH 2 V.GUSAROVA,S.K.HOISETH,J.JACOB,S.L.LIN,K.MALAKIAN, JRNL AUTH 3 L.K.MCNEIL,T.MININNI,F.MOY,E.MURPHY,E.NOVIKOVA,S.SIGETHY, JRNL AUTH 4 Y.WEN,G.W.ZLOTNICK,D.H.TSAO JRNL TITL STRUCTURAL BASIS FOR THE IMMUNOGENIC PROPERTIES OF THE JRNL TITL 2 MENINGOCOCCAL VACCINE CANDIDATE LP2086. JRNL REF J.BIOL.CHEM. V. 284 8738 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19103601 JRNL DOI 10.1074/JBC.M808831200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, A.T. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KDY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000101001. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 4.7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-100% 15N] LP2086-1, 90 REMARK 210 MM SODIUM CHLORIDE-2, 30 MM REMARK 210 SODIUM PHOSPHATE-3, 5 % D2O-4, REMARK 210 95% H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 17 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 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 H SER A 227 O GLU A 245 1.33 REMARK 500 O GLU A 127 H MET A 129 1.33 REMARK 500 H ALA A 56 O ALA A 59 1.37 REMARK 500 O ALA A 179 H LYS A 181 1.39 REMARK 500 O THR A 113 H GLY A 138 1.41 REMARK 500 O LYS A 171 H GLU A 188 1.56 REMARK 500 O THR A 20 H ALA A 23 1.56 REMARK 500 H ALA A 162 O GLY A 170 1.56 REMARK 500 O GLU A 120 H VAL A 130 1.57 REMARK 500 H ASP A 122 O GLU A 127 1.58 REMARK 500 H PHE A 163 O GLY A 256 1.58 REMARK 500 H TYR A 105 O LEU A 112 1.59 REMARK 500 H LEU A 115 O ARG A 136 1.59 REMARK 500 H LEU A 40 O LEU A 69 1.59 REMARK 500 H VAL A 240 O ALA A 259 1.59 REMARK 500 O GLN A 238 H GLN A 261 1.59 REMARK 500 O GLY A 242 H LEU A 257 1.60 REMARK 500 O VAL A 240 H ALA A 259 1.60 REMARK 500 O PHE A 163 H GLY A 256 1.60 REMARK 500 O LYS A 171 O GLU A 188 2.15 REMARK 500 O ALA A 111 O ILE A 140 2.18 REMARK 500 O THR A 157 OXT GLN A 261 2.18 REMARK 500 O ALA A 237 OE1 GLN A 261 2.18 REMARK 500 OD2 ASP A 207 O ALA A 212 2.18 REMARK 500 OG1 THR A 51 O GLN A 87 2.18 REMARK 500 O ALA A 180 N GLN A 182 2.19 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 9 54.48 -90.44 REMARK 500 1 THR A 15 -160.98 -116.23 REMARK 500 1 ALA A 16 6.74 -69.40 REMARK 500 1 ASP A 17 47.43 -162.29 REMARK 500 1 ILE A 18 -78.36 -106.29 REMARK 500 1 PRO A 29 -162.12 -72.77 REMARK 500 1 LEU A 30 -167.86 -48.65 REMARK 500 1 ASP A 31 -157.95 -165.34 REMARK 500 1 LYS A 33 21.85 -168.12 REMARK 500 1 LEU A 37 142.59 -29.33 REMARK 500 1 SER A 39 177.33 175.52 REMARK 500 1 ILE A 46 -161.85 -125.81 REMARK 500 1 SER A 47 -25.10 179.13 REMARK 500 1 GLN A 57 43.43 -74.62 REMARK 500 1 LEU A 74 164.73 -35.56 REMARK 500 1 LYS A 75 -158.52 -125.98 REMARK 500 1 GLN A 93 -138.13 -152.41 REMARK 500 1 LEU A 94 158.81 -45.52 REMARK 500 1 ILE A 95 96.54 -169.82 REMARK 500 1 THR A 96 173.73 179.92 REMARK 500 1 GLN A 107 -139.72 -101.75 REMARK 500 1 SER A 110 -154.98 -114.64 REMARK 500 1 GLU A 118 -33.55 -147.41 REMARK 500 1 PRO A 123 48.83 -74.73 REMARK 500 1 HIS A 125 -75.70 -179.57 REMARK 500 1 LYS A 128 36.92 -57.62 REMARK 500 1 LYS A 132 164.77 174.36 REMARK 500 1 ILE A 137 158.64 -49.87 REMARK 500 1 ASP A 139 133.53 -0.41 REMARK 500 1 ILE A 140 -152.45 -58.69 REMARK 500 1 PHE A 147 -18.47 -45.60 REMARK 500 1 LEU A 150 57.30 179.74 REMARK 500 1 LYS A 152 -76.97 -141.28 REMARK 500 1 ASP A 153 42.65 -151.10 REMARK 500 1 PHE A 178 -147.34 -42.43 REMARK 500 1 ALA A 180 52.24 -67.40 REMARK 500 1 LYS A 181 76.22 -17.87 REMARK 500 1 HIS A 184 134.24 179.44 REMARK 500 1 HIS A 189 -64.54 -162.73 REMARK 500 1 SER A 192 -166.68 -48.31 REMARK 500 1 LYS A 205 -73.22 -82.08 REMARK 500 1 ASP A 207 -129.41 -70.97 REMARK 500 1 LYS A 209 -48.47 -152.88 REMARK 500 1 HIS A 210 40.86 -170.13 REMARK 500 1 HIS A 211 -166.58 -126.41 REMARK 500 1 GLN A 222 -60.59 -93.72 REMARK 500 1 ASP A 223 26.56 178.70 REMARK 500 1 LYS A 236 37.48 177.83 REMARK 500 1 ALA A 237 15.05 -170.03 REMARK 500 1 GLN A 238 -97.51 -93.50 REMARK 500 REMARK 500 THIS ENTRY HAS 937 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 81 0.32 SIDE CHAIN REMARK 500 1 ARG A 86 0.31 SIDE CHAIN REMARK 500 1 ARG A 133 0.17 SIDE CHAIN REMARK 500 1 ARG A 134 0.17 SIDE CHAIN REMARK 500 1 ARG A 136 0.31 SIDE CHAIN REMARK 500 1 ARG A 159 0.27 SIDE CHAIN REMARK 500 2 ARG A 81 0.23 SIDE CHAIN REMARK 500 2 ARG A 86 0.16 SIDE CHAIN REMARK 500 2 ARG A 133 0.32 SIDE CHAIN REMARK 500 2 ARG A 134 0.30 SIDE CHAIN REMARK 500 2 ARG A 136 0.30 SIDE CHAIN REMARK 500 2 ARG A 159 0.25 SIDE CHAIN REMARK 500 3 ARG A 81 0.31 SIDE CHAIN REMARK 500 3 ARG A 86 0.32 SIDE CHAIN REMARK 500 3 ARG A 133 0.32 SIDE CHAIN REMARK 500 3 ARG A 134 0.31 SIDE CHAIN REMARK 500 3 ARG A 136 0.32 SIDE CHAIN REMARK 500 3 ARG A 159 0.32 SIDE CHAIN REMARK 500 4 ARG A 81 0.31 SIDE CHAIN REMARK 500 4 ARG A 86 0.30 SIDE CHAIN REMARK 500 4 ARG A 133 0.23 SIDE CHAIN REMARK 500 4 ARG A 134 0.32 SIDE CHAIN REMARK 500 4 ARG A 136 0.32 SIDE CHAIN REMARK 500 4 ARG A 159 0.28 SIDE CHAIN REMARK 500 5 ARG A 81 0.24 SIDE CHAIN REMARK 500 5 ARG A 86 0.31 SIDE CHAIN REMARK 500 5 ARG A 133 0.29 SIDE CHAIN REMARK 500 5 ARG A 134 0.31 SIDE CHAIN REMARK 500 5 ARG A 136 0.32 SIDE CHAIN REMARK 500 5 ARG A 159 0.32 SIDE CHAIN REMARK 500 6 ARG A 81 0.31 SIDE CHAIN REMARK 500 6 ARG A 86 0.32 SIDE CHAIN REMARK 500 6 ARG A 133 0.32 SIDE CHAIN REMARK 500 6 ARG A 134 0.31 SIDE CHAIN REMARK 500 6 ARG A 136 0.29 SIDE CHAIN REMARK 500 6 ARG A 159 0.29 SIDE CHAIN REMARK 500 7 ARG A 81 0.28 SIDE CHAIN REMARK 500 7 ARG A 86 0.17 SIDE CHAIN REMARK 500 7 ARG A 133 0.32 SIDE CHAIN REMARK 500 7 ARG A 134 0.31 SIDE CHAIN REMARK 500 7 ARG A 136 0.28 SIDE CHAIN REMARK 500 7 ARG A 159 0.29 SIDE CHAIN REMARK 500 8 ARG A 81 0.29 SIDE CHAIN REMARK 500 8 ARG A 86 0.27 SIDE CHAIN REMARK 500 8 ARG A 133 0.30 SIDE CHAIN REMARK 500 8 ARG A 134 0.31 SIDE CHAIN REMARK 500 8 ARG A 136 0.29 SIDE CHAIN REMARK 500 8 ARG A 159 0.32 SIDE CHAIN REMARK 500 9 ARG A 81 0.26 SIDE CHAIN REMARK 500 9 ARG A 86 0.30 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 102 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2KDY A 3 261 UNP Q6VRY4 Q6VRY4_NEIME 2 260 SEQADV 2KDY MET A 1 UNP Q6VRY4 EXPRESSION TAG SEQADV 2KDY GLY A 2 UNP Q6VRY4 EXPRESSION TAG SEQRES 1 A 261 MET GLY SER SER GLY GLY GLY GLY SER GLY GLY GLY GLY SEQRES 2 A 261 VAL THR ALA ASP ILE GLY THR GLY LEU ALA ASP ALA LEU SEQRES 3 A 261 THR ALA PRO LEU ASP HIS LYS ASP LYS GLY LEU LYS SER SEQRES 4 A 261 LEU THR LEU GLU ASP SER ILE SER GLN ASN GLY THR LEU SEQRES 5 A 261 THR LEU SER ALA GLN GLY ALA GLU LYS THR TYR GLY ASN SEQRES 6 A 261 GLY ASP SER LEU ASN THR GLY LYS LEU LYS ASN ASP LYS SEQRES 7 A 261 VAL SER ARG PHE ASP PHE ILE ARG GLN ILE GLU VAL ASP SEQRES 8 A 261 GLY GLN LEU ILE THR LEU GLU SER GLY GLU PHE GLN VAL SEQRES 9 A 261 TYR LYS GLN SER HIS SER ALA LEU THR ALA LEU GLN THR SEQRES 10 A 261 GLU GLN GLU GLN ASP PRO GLU HIS SER GLU LYS MET VAL SEQRES 11 A 261 ALA LYS ARG ARG PHE ARG ILE GLY ASP ILE ALA GLY GLU SEQRES 12 A 261 HIS THR SER PHE ASP LYS LEU PRO LYS ASP VAL MET ALA SEQRES 13 A 261 THR TYR ARG GLY THR ALA PHE GLY SER ASP ASP ALA GLY SEQRES 14 A 261 GLY LYS LEU THR TYR THR ILE ASP PHE ALA ALA LYS GLN SEQRES 15 A 261 GLY HIS GLY LYS ILE GLU HIS LEU LYS SER PRO GLU LEU SEQRES 16 A 261 ASN VAL ASP LEU ALA VAL ALA TYR ILE LYS PRO ASP GLU SEQRES 17 A 261 LYS HIS HIS ALA VAL ILE SER GLY SER VAL LEU TYR ASN SEQRES 18 A 261 GLN ASP GLU LYS GLY SER TYR SER LEU GLY ILE PHE GLY SEQRES 19 A 261 GLU LYS ALA GLN GLU VAL ALA GLY SER ALA GLU VAL GLU SEQRES 20 A 261 THR ALA ASN GLY ILE HIS HIS ILE GLY LEU ALA ALA LYS SEQRES 21 A 261 GLN HELIX 1 1 GLY A 19 GLY A 21 5 3 HELIX 2 2 LEU A 22 THR A 27 1 6 HELIX 3 3 SER A 146 LEU A 150 5 5 SHEET 1 A 2 LEU A 40 THR A 41 0 SHEET 2 A 2 SER A 68 LEU A 69 -1 O LEU A 69 N LEU A 40 SHEET 1 B 6 GLU A 60 TYR A 63 0 SHEET 2 B 6 THR A 51 SER A 55 -1 N LEU A 52 O TYR A 63 SHEET 3 B 6 LYS A 78 GLU A 89 -1 O GLN A 87 N THR A 51 SHEET 4 B 6 ILE A 95 LYS A 106 -1 O LYS A 106 N LYS A 78 SHEET 5 B 6 ALA A 111 GLN A 116 -1 O LEU A 112 N TYR A 105 SHEET 6 B 6 PHE A 135 ILE A 137 -1 O ARG A 136 N LEU A 115 SHEET 1 C 2 GLN A 119 GLU A 120 0 SHEET 2 C 2 VAL A 130 ALA A 131 -1 O VAL A 130 N GLU A 120 SHEET 1 D10 TYR A 203 ILE A 204 0 SHEET 2 D10 ALA A 212 GLY A 216 -1 O VAL A 213 N ILE A 204 SHEET 3 D10 LYS A 225 PHE A 233 -1 O TYR A 228 N GLY A 216 SHEET 4 D10 GLU A 239 GLU A 247 -1 O GLU A 245 N SER A 227 SHEET 5 D10 ILE A 252 LYS A 260 -1 O ALA A 259 N VAL A 240 SHEET 6 D10 THR A 157 GLY A 164 -1 N PHE A 163 O GLY A 256 SHEET 7 D10 GLY A 170 THR A 175 -1 O TYR A 174 N TYR A 158 SHEET 8 D10 GLY A 183 GLU A 188 -1 O GLU A 188 N LYS A 171 SHEET 9 D10 ASN A 196 VAL A 201 -1 O VAL A 201 N GLY A 183 SHEET 10 D10 VAL A 218 LEU A 219 -1 O LEU A 219 N ASP A 198 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