PDB Short entry for 1DGQ HEADER IMMUNE SYSTEM 24-NOV-99 1DGQ TITLE NMR SOLUTION STRUCTURE OF THE INSERTED DOMAIN OF HUMAN LEUKOCYTE TITLE 2 FUNCTION ASSOCIATED ANTIGEN-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUKOCYTE FUNCTION ASSOCIATED ANTIGEN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: INSERTED DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS ROSSMANN FOLD, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 22 AUTHOR G.B.LEGGE,R.W.KRIWACKI,J.CHUNG,U.HOMMEL,P.RAMAGE,D.A.CASE,H.J.DYSON, AUTHOR 2 P.E.WRIGHT REVDAT 4 16-FEB-22 1DGQ 1 REMARK SEQADV REVDAT 3 12-NOV-14 1DGQ 1 KEYWDS REVDAT 2 24-FEB-09 1DGQ 1 VERSN REVDAT 1 03-FEB-00 1DGQ 0 JRNL AUTH G.B.LEGGE,R.W.KRIWACKI,J.CHUNG,U.HOMMEL,P.RAMAGE,D.A.CASE, JRNL AUTH 2 H.J.DYSON,P.E.WRIGHT JRNL TITL NMR SOLUTION STRUCTURE OF THE INSERTED DOMAIN OF HUMAN JRNL TITL 2 LEUKOCYTE FUNCTION ASSOCIATED ANTIGEN-1. JRNL REF J.MOL.BIOL. V. 295 1251 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10653701 JRNL DOI 10.1006/JMBI.1999.3409 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SANE 1.0, AMBER 5.1 REMARK 3 AUTHORS : DUGGAN (SANE), CASE (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 MODEL-BASED APPROACH USED TO ASSIGN NOESY SPECTRA USING EXISTING X- REMARK 3 RAY REMARK 3 STRUCTURES AS A MODEL. THE STRUCTURES ARE BASED ON A TOTAL OF 5656 REMARK 3 RESTRAINTS, REMARK 3 2289 ARE UNIQUE NOE-DERIVED DISTANCE CONSTRAINTS, 3082 AMBIGOUS REMARK 3 NOE-DERIVED REMARK 3 RESTRAINTS, AND 285 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1DGQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1000010073. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295; 295 REMARK 210 PH : 7.2; 7.3 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2 MM NMR SAMPLE OF PURIFIED REMARK 210 AND UNIFORMLY 15N/13C REMARK 210 ISOTOPICALLY LABELED LFA-1 I- REMARK 210 DOMAIN; 1.2 MM 15N UNIFORMLY REMARK 210 LABELED SAMPLE WAS ALSO PREPARED REMARK 210 IN THE FOLLOWING CONDITIONS THAT REMARK 210 WERE LESS AFFECTED BY LINE REMARK 210 BROADENING REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 3D 15N HSQC- REMARK 210 NOESY-HSQC 140 MS MIXING TIME REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX; DRX; AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA 1.5, AMBER 5.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 22 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY, STRUCTURES REMARK 210 WITH FAVORABLE NON- BOND ENERGY, REMARK 210 STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: REMARK 210 NOESY MIXING TIMES OF 60 AND 100 MS FOR THE 3D 1H-15N AND 3D 1H- REMARK 210 13C NOESY-HSQC REMARK 210 SPECTRA. NOESY MIXING TIME OF 140 MS FOR THE 15N HSQC-NOESY-HSQC REMARK 210 SPECTRA. 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: 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 LEU A 161 41.01 -104.34 REMARK 500 1 SER A 174 -130.07 -153.99 REMARK 500 1 THR A 179 107.75 -57.68 REMARK 500 1 LEU A 204 -143.42 -121.97 REMARK 500 1 LEU A 205 -145.53 -82.54 REMARK 500 1 THR A 206 77.14 -150.59 REMARK 500 1 ILE A 248 24.24 -143.20 REMARK 500 1 ARG A 256 87.39 -69.18 REMARK 500 1 LYS A 263 -67.76 -100.67 REMARK 500 2 SER A 126 -70.52 61.57 REMARK 500 2 ASN A 129 168.49 62.09 REMARK 500 2 SER A 162 -99.45 56.14 REMARK 500 2 ASN A 163 -67.24 -108.63 REMARK 500 2 THR A 164 -90.26 46.65 REMARK 500 2 SER A 165 37.43 -149.49 REMARK 500 2 SER A 174 -134.52 -143.48 REMARK 500 2 LEU A 204 -138.54 -113.21 REMARK 500 2 LEU A 205 -164.12 -79.90 REMARK 500 2 ILE A 248 22.88 -143.41 REMARK 500 2 PHE A 265 25.91 -77.31 REMARK 500 3 LYS A 127 77.36 -170.61 REMARK 500 3 LEU A 161 42.43 -104.55 REMARK 500 3 SER A 174 -129.22 -149.64 REMARK 500 3 THR A 179 107.83 -59.38 REMARK 500 3 LYS A 190 -3.64 60.81 REMARK 500 3 LEU A 204 -133.26 -126.02 REMARK 500 3 LEU A 205 -154.63 -85.64 REMARK 500 3 ILE A 248 25.17 -142.28 REMARK 500 3 LYS A 263 -68.85 -93.30 REMARK 500 3 ASP A 290 -67.58 -11.09 REMARK 500 4 SER A 165 -29.65 -146.77 REMARK 500 4 SER A 174 -126.28 -149.27 REMARK 500 4 LYS A 190 14.56 55.49 REMARK 500 4 VAL A 199 94.02 -68.28 REMARK 500 4 LEU A 204 -135.32 -124.94 REMARK 500 4 LEU A 205 -153.47 -84.86 REMARK 500 4 ALA A 242 97.30 -68.42 REMARK 500 4 ILE A 248 25.53 -141.42 REMARK 500 4 LYS A 263 -71.90 -112.80 REMARK 500 4 ASP A 290 -65.63 -5.29 REMARK 500 4 GLU A 310 -65.05 -143.60 REMARK 500 5 ALA A 125 -140.66 52.02 REMARK 500 5 SER A 162 85.73 -67.14 REMARK 500 5 SER A 165 -46.23 -148.60 REMARK 500 5 SER A 174 -131.83 -152.04 REMARK 500 5 VAL A 199 88.26 -69.78 REMARK 500 5 LEU A 204 -143.06 -117.50 REMARK 500 5 LEU A 205 -145.43 -82.68 REMARK 500 5 ILE A 248 23.25 -143.74 REMARK 500 5 PHE A 265 16.61 -69.58 REMARK 500 REMARK 500 THIS ENTRY HAS 216 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 TYR A 166 0.10 SIDE CHAIN REMARK 500 1 TYR A 186 0.09 SIDE CHAIN REMARK 500 1 TYR A 257 0.12 SIDE CHAIN REMARK 500 1 PHE A 285 0.09 SIDE CHAIN REMARK 500 1 TYR A 307 0.16 SIDE CHAIN REMARK 500 2 TYR A 166 0.09 SIDE CHAIN REMARK 500 2 TYR A 186 0.14 SIDE CHAIN REMARK 500 2 PHE A 209 0.08 SIDE CHAIN REMARK 500 2 TYR A 214 0.07 SIDE CHAIN REMARK 500 2 ARG A 221 0.12 SIDE CHAIN REMARK 500 2 TYR A 257 0.12 SIDE CHAIN REMARK 500 2 PHE A 299 0.11 SIDE CHAIN REMARK 500 3 TYR A 186 0.11 SIDE CHAIN REMARK 500 3 TYR A 257 0.16 SIDE CHAIN REMARK 500 3 PHE A 277 0.09 SIDE CHAIN REMARK 500 3 PHE A 299 0.13 SIDE CHAIN REMARK 500 3 TYR A 307 0.17 SIDE CHAIN REMARK 500 4 PHE A 153 0.09 SIDE CHAIN REMARK 500 4 TYR A 166 0.12 SIDE CHAIN REMARK 500 4 TYR A 257 0.16 SIDE CHAIN REMARK 500 4 PHE A 277 0.10 SIDE CHAIN REMARK 500 4 TYR A 307 0.17 SIDE CHAIN REMARK 500 5 TYR A 166 0.18 SIDE CHAIN REMARK 500 5 TYR A 186 0.10 SIDE CHAIN REMARK 500 5 PHE A 209 0.09 SIDE CHAIN REMARK 500 5 TYR A 257 0.16 SIDE CHAIN REMARK 500 5 PHE A 285 0.08 SIDE CHAIN REMARK 500 5 TYR A 307 0.20 SIDE CHAIN REMARK 500 6 PHE A 136 0.09 SIDE CHAIN REMARK 500 6 TYR A 186 0.09 SIDE CHAIN REMARK 500 6 PHE A 209 0.08 SIDE CHAIN REMARK 500 6 TYR A 257 0.12 SIDE CHAIN REMARK 500 6 PHE A 285 0.09 SIDE CHAIN REMARK 500 6 PHE A 299 0.11 SIDE CHAIN REMARK 500 6 TYR A 307 0.18 SIDE CHAIN REMARK 500 7 TYR A 166 0.21 SIDE CHAIN REMARK 500 7 TYR A 186 0.11 SIDE CHAIN REMARK 500 7 PHE A 209 0.09 SIDE CHAIN REMARK 500 7 TYR A 257 0.11 SIDE CHAIN REMARK 500 7 PHE A 285 0.08 SIDE CHAIN REMARK 500 7 PHE A 299 0.08 SIDE CHAIN REMARK 500 8 TYR A 166 0.16 SIDE CHAIN REMARK 500 8 PHE A 209 0.10 SIDE CHAIN REMARK 500 8 TYR A 214 0.09 SIDE CHAIN REMARK 500 8 TYR A 257 0.15 SIDE CHAIN REMARK 500 8 TYR A 307 0.16 SIDE CHAIN REMARK 500 9 TYR A 166 0.08 SIDE CHAIN REMARK 500 9 PHE A 168 0.08 SIDE CHAIN REMARK 500 9 TYR A 186 0.13 SIDE CHAIN REMARK 500 9 TYR A 214 0.11 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 121 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZON RELATED DB: PDB REMARK 900 I-DOMAIN FRAGMENT OF LFA-1 WITH BOUND MG2+ X-RAY DIFFRACTION, REMARK 900 SINGLE CRYSTAL RESOLUTION: 2.00 A REMARK 900 RELATED ID: 1ZOO RELATED DB: PDB REMARK 900 I-DOMAIN FRAGMENT OF LFA-1 IN THE ABSENCE OF DIVALENT CATION X-RAY REMARK 900 DIFFRACTION RESOLUTION: 3.00 A REMARK 900 RELATED ID: 1ZOP RELATED DB: PDB REMARK 900 I-DOMAIN FRAGMENT OF LFA-1 WITH BOUND MN2+ X-RAY DIFFRACTION REMARK 900 RELATED ID: 1LFA RELATED DB: PDB REMARK 900 I-DOMAIN FRAGMENT OF LFA-1 WITH BOUND MN2+ X-RAY DIFFRACTION REMARK 900 RESOLUTION: 1.8 A DBREF 1DGQ A 124 311 UNP P20701 ITAL_HUMAN 149 336 SEQADV 1DGQ MET A 124 UNP P20701 GLU 149 CONFLICT SEQADV 1DGQ ALA A 125 UNP P20701 CYS 150 CONFLICT SEQADV 1DGQ SER A 126 UNP P20701 ILE 151 CONFLICT SEQADV 1DGQ TRP A 189 UNP P20701 ARG 214 CONFLICT SEQRES 1 A 188 MET ALA SER LYS GLY ASN VAL ASP LEU VAL PHE LEU PHE SEQRES 2 A 188 ASP GLY SER MET SER LEU GLN PRO ASP GLU PHE GLN LYS SEQRES 3 A 188 ILE LEU ASP PHE MET LYS ASP VAL MET LYS LYS LEU SER SEQRES 4 A 188 ASN THR SER TYR GLN PHE ALA ALA VAL GLN PHE SER THR SEQRES 5 A 188 SER TYR LYS THR GLU PHE ASP PHE SER ASP TYR VAL LYS SEQRES 6 A 188 TRP LYS ASP PRO ASP ALA LEU LEU LYS HIS VAL LYS HIS SEQRES 7 A 188 MET LEU LEU LEU THR ASN THR PHE GLY ALA ILE ASN TYR SEQRES 8 A 188 VAL ALA THR GLU VAL PHE ARG GLU GLU LEU GLY ALA ARG SEQRES 9 A 188 PRO ASP ALA THR LYS VAL LEU ILE ILE ILE THR ASP GLY SEQRES 10 A 188 GLU ALA THR ASP SER GLY ASN ILE ASP ALA ALA LYS ASP SEQRES 11 A 188 ILE ILE ARG TYR ILE ILE GLY ILE GLY LYS HIS PHE GLN SEQRES 12 A 188 THR LYS GLU SER GLN GLU THR LEU HIS LYS PHE ALA SER SEQRES 13 A 188 LYS PRO ALA SER GLU PHE VAL LYS ILE LEU ASP THR PHE SEQRES 14 A 188 GLU LYS LEU LYS ASP LEU PHE THR GLU LEU GLN LYS LYS SEQRES 15 A 188 ILE TYR VAL ILE GLU GLY HELIX 1 1 GLN A 143 LEU A 161 1 19 HELIX 2 2 ASP A 182 LYS A 190 1 9 HELIX 3 3 ASP A 191 LEU A 196 1 6 HELIX 4 4 LYS A 197 VAL A 199 5 3 HELIX 5 5 ASN A 207 GLU A 218 1 12 HELIX 6 6 ARG A 221 GLY A 225 5 5 HELIX 7 7 ILE A 248 LYS A 252 5 5 HELIX 8 8 THR A 267 ALA A 278 1 12 HELIX 9 9 PRO A 281 PHE A 285 1 5 HELIX 10 10 THR A 291 GLU A 293 5 3 HELIX 11 11 LYS A 294 GLY A 311 1 18 SHEET 1 A 6 TYR A 177 PHE A 181 0 SHEET 2 A 6 TYR A 166 PHE A 173 -1 N ALA A 170 O PHE A 181 SHEET 3 A 6 VAL A 130 ASP A 137 1 O VAL A 130 N GLN A 167 SHEET 4 A 6 THR A 231 THR A 238 1 O THR A 231 N ASP A 131 SHEET 5 A 6 ILE A 255 ILE A 261 1 N ILE A 255 O LYS A 232 SHEET 6 A 6 VAL A 286 LEU A 289 1 N LYS A 287 O ILE A 258 CISPEP 1 LYS A 280 PRO A 281 1 2.59 CISPEP 2 LYS A 280 PRO A 281 2 0.57 CISPEP 3 LYS A 280 PRO A 281 3 1.81 CISPEP 4 LYS A 280 PRO A 281 4 -0.94 CISPEP 5 LYS A 280 PRO A 281 5 2.93 CISPEP 6 LYS A 280 PRO A 281 6 0.78 CISPEP 7 LYS A 280 PRO A 281 7 3.23 CISPEP 8 LYS A 280 PRO A 281 8 2.18 CISPEP 9 LYS A 280 PRO A 281 9 -1.88 CISPEP 10 LYS A 280 PRO A 281 10 -0.74 CISPEP 11 LYS A 280 PRO A 281 11 1.83 CISPEP 12 LYS A 280 PRO A 281 12 2.01 CISPEP 13 LYS A 280 PRO A 281 13 1.42 CISPEP 14 LYS A 280 PRO A 281 14 3.74 CISPEP 15 LYS A 280 PRO A 281 15 -0.50 CISPEP 16 LYS A 280 PRO A 281 16 3.45 CISPEP 17 LYS A 280 PRO A 281 17 1.78 CISPEP 18 LYS A 280 PRO A 281 18 1.79 CISPEP 19 LYS A 280 PRO A 281 19 3.17 CISPEP 20 LYS A 280 PRO A 281 20 4.20 CISPEP 21 LYS A 280 PRO A 281 21 1.67 CISPEP 22 LYS A 280 PRO A 281 22 0.89 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