HEADER IMMUNE SYSTEM 11-NOV-09 2KQN TITLE SOLUTION STRUCTURE OF THE AL-09 H87Y IMMUNOGLOBULIN LIGHT CHAIN TITLE 2 VARIABLE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: IG KAPPA CHAIN V-I REGION AU; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: IMMUNOGLOBULIN KAPPA LIGHT CHAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 GOLD(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET-12A KEYWDS AMYLOIDOSIS, IMMUNOGLOBULIN KAPPA LIGHT CHAIN, HOMODIMER, BENCE-JONES KEYWDS 2 PROTEIN, DISULFIDE BOND, IMMUNOGLOBULIN DOMAIN, IMMUNOGLOBULIN V KEYWDS 3 REGION, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.F.VOLKMAN,F.C.PETERSON,M.RAMIREZ-ALVARADO,E.M.BADEN REVDAT 3 16-MAR-22 2KQN 1 REMARK REVDAT 2 26-MAY-10 2KQN 1 JRNL REVDAT 1 16-MAR-10 2KQN 0 JRNL AUTH F.C.PETERSON,E.M.BADEN,B.A.OWEN,B.F.VOLKMAN, JRNL AUTH 2 M.RAMIREZ-ALVARADO JRNL TITL A SINGLE MUTATION PROMOTES AMYLOIDOGENICITY THROUGH A HIGHLY JRNL TITL 2 PROMISCUOUS DIMER INTERFACE. JRNL REF STRUCTURE V. 18 563 2010 JRNL REFN ISSN 0969-2126 JRNL PMID 20462490 JRNL DOI 10.1016/J.STR.2010.02.012 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.9.3 REMARK 3 AUTHORS : REMARK 3 SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HOMODIMER STRUCTURES ARE BASED ON A REMARK 3 TOTAL OF 2104 NOE CONSTRAINTS (341 INTRA, 394 SEQUENTIAL, 265 REMARK 3 MEDIUM, 1027 INTRAMONOMER LONG RANGE AND 77 INTERMONOMER NOE REMARK 3 CONSTRAINTS) AND 149 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS PER REMARK 3 MONOMER. CONSTRAINTS WERE ASSIGNED AND VALIDATED IN ONE MONOMER REMARK 3 AND THEN DUPLICATED TO GENERATE A SYMMETRY RELATED CONSTRAINTS REMARK 3 IN THE SECOND MONOMER. REMARK 4 REMARK 4 2KQN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000101452. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 8 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-100% 13C; U-100% 15N] REMARK 210 AL-09 H87Y-1, 10 MM [U-2H] MES-2, REMARK 210 0.02 % SODIUM AZIDE-3, 95% H2O, REMARK 210 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY (AROMATIC) REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, NMRPIPE 2007, XEASY REMARK 210 1.3, GARANT 2.1, CYANA 2.1 REMARK 210 METHOD USED : AUTOMATED METHODS WERE USED FOR REMARK 210 BACKBONE CHEMICAL SHIFT REMARK 210 ASSIGNMENT AND ITERATIVE NOE REMARK 210 REFINEMENT. FINAL STRUCTURES REMARK 210 WERE OBTAINED BY MOLECULAR REMARK 210 DYNAMICS IN EXPLICIT SOLVENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 -1 REMARK 465 THR A 0 REMARK 465 SER B 199 REMARK 465 THR B 200 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 SER B 212 HZ3 LYS B 307 1.58 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 ASN A 30 -76.56 64.05 REMARK 500 1 ASN A 31 6.80 -161.27 REMARK 500 1 ALA A 51 14.17 58.95 REMARK 500 1 SER A 52 -45.82 -158.87 REMARK 500 1 ASN B 230 -82.69 61.19 REMARK 500 1 ASN B 231 13.93 -155.16 REMARK 500 1 ALA B 251 -49.25 70.09 REMARK 500 2 ASN A 30 -77.98 64.67 REMARK 500 2 ASN A 31 11.82 -159.13 REMARK 500 2 SER A 52 -48.10 -170.51 REMARK 500 2 ASN B 230 -65.65 65.31 REMARK 500 2 ASN B 231 -19.70 -155.62 REMARK 500 2 ASP B 250 -46.78 70.42 REMARK 500 2 ALA B 251 -46.52 167.28 REMARK 500 2 ALA B 284 -178.26 -171.81 REMARK 500 3 ASN A 30 -66.51 66.35 REMARK 500 3 ASN A 31 -14.35 -160.78 REMARK 500 3 ASP A 50 -53.51 72.72 REMARK 500 3 ALA A 51 -49.48 169.73 REMARK 500 3 ASN B 230 -91.50 61.68 REMARK 500 3 ASN B 231 10.07 -141.29 REMARK 500 3 SER B 252 -41.38 -173.65 REMARK 500 3 ALA B 284 -175.51 -170.99 REMARK 500 3 GLN B 300 4.87 -62.54 REMARK 500 4 ASN A 30 -64.45 65.71 REMARK 500 4 ASN A 31 -18.30 -162.95 REMARK 500 4 ASP A 50 -55.93 71.92 REMARK 500 4 ALA A 51 -38.91 160.67 REMARK 500 4 ALA A 84 -179.85 -174.28 REMARK 500 4 ASN B 230 -73.84 66.63 REMARK 500 4 ASN B 231 13.16 -161.81 REMARK 500 4 PRO B 240 105.97 -51.01 REMARK 500 4 SER B 252 -40.80 -167.39 REMARK 500 5 ASN A 30 -72.01 65.52 REMARK 500 5 ASN A 31 12.14 -165.13 REMARK 500 5 PRO A 40 108.36 -50.48 REMARK 500 5 ALA A 51 -46.50 73.50 REMARK 500 5 ASN B 230 -68.74 66.06 REMARK 500 5 ASN B 231 13.75 -170.02 REMARK 500 5 LEU B 247 -64.50 -102.53 REMARK 500 5 ALA B 251 -34.04 71.99 REMARK 500 6 ASN A 30 -72.32 63.59 REMARK 500 6 ASN A 31 3.92 -155.58 REMARK 500 6 ALA A 51 -27.31 72.13 REMARK 500 6 ASN B 230 -71.85 66.46 REMARK 500 6 ASN B 231 10.60 -165.09 REMARK 500 6 PRO B 240 108.04 -50.83 REMARK 500 6 ALA B 251 -36.32 71.80 REMARK 500 7 ASN A 30 -88.19 61.91 REMARK 500 7 ALA A 51 -51.34 65.74 REMARK 500 REMARK 500 THIS ENTRY HAS 180 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KQM RELATED DB: PDB DBREF 2KQN A -1 108 PDB 2KQN 2KQN -1 108 DBREF 2KQN B 199 308 PDB 2KQN 2KQN 199 308 SEQRES 1 A 110 SER THR ASP ILE GLN MET THR GLN SER PRO SER SER LEU SEQRES 2 A 110 SER ALA SER VAL GLY ASP ARG VAL THR ILE THR CYS GLN SEQRES 3 A 110 ALA SER GLN ASP ILE ASN ASN TYR LEU ILE TRP TYR GLN SEQRES 4 A 110 GLN LYS PRO GLY GLN ALA PRO LYS LEU LEU ILE TYR ASP SEQRES 5 A 110 ALA SER THR LEU GLU THR GLY VAL PRO SER ARG PHE SER SEQRES 6 A 110 GLY SER GLY SER GLY THR GLU PHE THR PHE THR ILE SER SEQRES 7 A 110 SER LEU GLN PRO GLU ASP LEU ALA THR TYR TYR CYS GLN SEQRES 8 A 110 GLN TYR ASP ASN LEU PRO TYR THR PHE GLY GLN GLY THR SEQRES 9 A 110 LYS LEU GLU ILE LYS ARG SEQRES 1 B 110 SER THR ASP ILE GLN MET THR GLN SER PRO SER SER LEU SEQRES 2 B 110 SER ALA SER VAL GLY ASP ARG VAL THR ILE THR CYS GLN SEQRES 3 B 110 ALA SER GLN ASP ILE ASN ASN TYR LEU ILE TRP TYR GLN SEQRES 4 B 110 GLN LYS PRO GLY GLN ALA PRO LYS LEU LEU ILE TYR ASP SEQRES 5 B 110 ALA SER THR LEU GLU THR GLY VAL PRO SER ARG PHE SER SEQRES 6 B 110 GLY SER GLY SER GLY THR GLU PHE THR PHE THR ILE SER SEQRES 7 B 110 SER LEU GLN PRO GLU ASP LEU ALA THR TYR TYR CYS GLN SEQRES 8 B 110 GLN TYR ASP ASN LEU PRO TYR THR PHE GLY GLN GLY THR SEQRES 9 B 110 LYS LEU GLU ILE LYS ARG HELIX 1 1 GLN A 79 LEU A 83 5 5 HELIX 2 2 GLN B 279 LEU B 283 5 5 SHEET 1 A 4 MET A 4 SER A 7 0 SHEET 2 A 4 VAL A 19 ALA A 25 -1 O GLN A 24 N THR A 5 SHEET 3 A 4 GLU A 70 ILE A 75 -1 O PHE A 73 N ILE A 21 SHEET 4 A 4 PHE A 62 SER A 67 -1 N SER A 63 O THR A 74 SHEET 1 B 6 SER A 10 SER A 12 0 SHEET 2 B 6 THR A 102 GLU A 105 1 O LYS A 103 N LEU A 11 SHEET 3 B 6 THR A 85 GLN A 90 -1 N TYR A 86 O THR A 102 SHEET 4 B 6 LEU A 33 GLN A 38 -1 N GLN A 38 O THR A 85 SHEET 5 B 6 LYS A 45 TYR A 49 -1 O ILE A 48 N TRP A 35 SHEET 6 B 6 THR A 53 LEU A 54 -1 O THR A 53 N TYR A 49 SHEET 1 C 4 MET B 204 SER B 207 0 SHEET 2 C 4 VAL B 219 ALA B 225 -1 O GLN B 224 N THR B 205 SHEET 3 C 4 GLU B 270 ILE B 275 -1 O PHE B 273 N ILE B 221 SHEET 4 C 4 PHE B 262 SER B 267 -1 N SER B 265 O THR B 272 SHEET 1 D 6 SER B 210 ALA B 213 0 SHEET 2 D 6 PHE B 298 ILE B 306 1 O GLU B 305 N ALA B 213 SHEET 3 D 6 THR B 285 GLN B 290 -1 N CYS B 288 O GLY B 299 SHEET 4 D 6 LEU B 233 GLN B 238 -1 N TYR B 236 O TYR B 287 SHEET 5 D 6 LYS B 245 TYR B 249 -1 O ILE B 248 N TRP B 235 SHEET 6 D 6 THR B 253 LEU B 254 -1 O THR B 253 N TYR B 249 SSBOND 1 CYS A 23 CYS A 88 1555 1555 2.04 SSBOND 2 CYS B 223 CYS B 288 1555 1555 2.04 CISPEP 1 SER A 7 PRO A 8 1 1.74 CISPEP 2 LEU A 94 PRO A 95 1 -0.17 CISPEP 3 SER B 207 PRO B 208 1 0.92 CISPEP 4 LEU B 294 PRO B 295 1 -2.79 CISPEP 5 SER A 7 PRO A 8 2 -0.23 CISPEP 6 LEU A 94 PRO A 95 2 -1.07 CISPEP 7 SER B 207 PRO B 208 2 0.30 CISPEP 8 LEU B 294 PRO B 295 2 -2.86 CISPEP 9 SER A 7 PRO A 8 3 0.13 CISPEP 10 LEU A 94 PRO A 95 3 -2.59 CISPEP 11 SER B 207 PRO B 208 3 -0.40 CISPEP 12 LEU B 294 PRO B 295 3 -2.06 CISPEP 13 SER A 7 PRO A 8 4 -0.94 CISPEP 14 LEU A 94 PRO A 95 4 -1.89 CISPEP 15 SER B 207 PRO B 208 4 1.48 CISPEP 16 LEU B 294 PRO B 295 4 -2.81 CISPEP 17 SER A 7 PRO A 8 5 0.62 CISPEP 18 LEU A 94 PRO A 95 5 -4.08 CISPEP 19 SER B 207 PRO B 208 5 0.60 CISPEP 20 LEU B 294 PRO B 295 5 -3.16 CISPEP 21 SER A 7 PRO A 8 6 0.60 CISPEP 22 LEU A 94 PRO A 95 6 -2.51 CISPEP 23 SER B 207 PRO B 208 6 0.34 CISPEP 24 LEU B 294 PRO B 295 6 -5.95 CISPEP 25 SER A 7 PRO A 8 7 1.44 CISPEP 26 LEU A 94 PRO A 95 7 -2.91 CISPEP 27 SER B 207 PRO B 208 7 2.14 CISPEP 28 LEU B 294 PRO B 295 7 -2.99 CISPEP 29 SER A 7 PRO A 8 8 0.12 CISPEP 30 LEU A 94 PRO A 95 8 -3.96 CISPEP 31 SER B 207 PRO B 208 8 0.16 CISPEP 32 LEU B 294 PRO B 295 8 -3.75 CISPEP 33 SER A 7 PRO A 8 9 1.97 CISPEP 34 LEU A 94 PRO A 95 9 -4.45 CISPEP 35 SER B 207 PRO B 208 9 1.35 CISPEP 36 LEU B 294 PRO B 295 9 -4.91 CISPEP 37 SER A 7 PRO A 8 10 1.71 CISPEP 38 LEU A 94 PRO A 95 10 -2.15 CISPEP 39 SER B 207 PRO B 208 10 -0.55 CISPEP 40 LEU B 294 PRO B 295 10 -4.59 CISPEP 41 SER A 7 PRO A 8 11 2.17 CISPEP 42 LEU A 94 PRO A 95 11 -3.06 CISPEP 43 SER B 207 PRO B 208 11 0.24 CISPEP 44 LEU B 294 PRO B 295 11 -2.53 CISPEP 45 SER A 7 PRO A 8 12 0.01 CISPEP 46 LEU A 94 PRO A 95 12 -2.88 CISPEP 47 SER B 207 PRO B 208 12 -0.16 CISPEP 48 LEU B 294 PRO B 295 12 -2.50 CISPEP 49 SER A 7 PRO A 8 13 2.91 CISPEP 50 LEU A 94 PRO A 95 13 -4.31 CISPEP 51 SER B 207 PRO B 208 13 -0.94 CISPEP 52 LEU B 294 PRO B 295 13 -4.68 CISPEP 53 SER A 7 PRO A 8 14 -0.70 CISPEP 54 LEU A 94 PRO A 95 14 -0.84 CISPEP 55 SER B 207 PRO B 208 14 -0.47 CISPEP 56 LEU B 294 PRO B 295 14 -2.65 CISPEP 57 SER A 7 PRO A 8 15 -0.35 CISPEP 58 LEU A 94 PRO A 95 15 -3.05 CISPEP 59 SER B 207 PRO B 208 15 0.63 CISPEP 60 LEU B 294 PRO B 295 15 -6.12 CISPEP 61 SER A 7 PRO A 8 16 0.29 CISPEP 62 LEU A 94 PRO A 95 16 -1.60 CISPEP 63 SER B 207 PRO B 208 16 0.01 CISPEP 64 LEU B 294 PRO B 295 16 -3.19 CISPEP 65 SER A 7 PRO A 8 17 0.90 CISPEP 66 LEU A 94 PRO A 95 17 -2.16 CISPEP 67 SER B 207 PRO B 208 17 1.82 CISPEP 68 LEU B 294 PRO B 295 17 -2.09 CISPEP 69 SER A 7 PRO A 8 18 0.28 CISPEP 70 LEU A 94 PRO A 95 18 -2.68 CISPEP 71 SER B 207 PRO B 208 18 2.15 CISPEP 72 LEU B 294 PRO B 295 18 -5.44 CISPEP 73 SER A 7 PRO A 8 19 1.52 CISPEP 74 LEU A 94 PRO A 95 19 -3.48 CISPEP 75 SER B 207 PRO B 208 19 1.98 CISPEP 76 LEU B 294 PRO B 295 19 -1.49 CISPEP 77 SER A 7 PRO A 8 20 0.38 CISPEP 78 LEU A 94 PRO A 95 20 -6.09 CISPEP 79 SER B 207 PRO B 208 20 -0.67 CISPEP 80 LEU B 294 PRO B 295 20 -5.96 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