HEADER CYTOKINE 07-JUL-15 2N54 TITLE SOLUTION STRUCTURE OF A DISULFIDE STABILIZED XCL1 DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYMPHOTACTIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ATAC, C MOTIF CHEMOKINE 1, CYTOKINE SCM-1, LYMPHOTAXIN, SCM- COMPND 5 1-ALPHA, SMALL-INDUCIBLE CYTOKINE C1, XC CHEMOKINE LIGAND 1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: XCL1, LTN, SCYC1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS XCL1, DIMER, CHEMOKINE, METAMORPHIC, GAG-BINDING, HIV-1 INHIBITION, KEYWDS 2 LYMPHOTACTIN, ATAC, CYTOKINE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.C.TYLER,R.L.TUINSTRA,F.F.PETERSON,B.F.VOLKMAN REVDAT 4 14-JUN-23 2N54 1 REMARK REVDAT 3 02-DEC-15 2N54 1 JRNL REVDAT 2 14-OCT-15 2N54 1 JRNL REVDAT 1 07-OCT-15 2N54 0 JRNL AUTH J.C.FOX,R.C.TYLER,C.GUZZO,R.L.TUINSTRA,F.C.PETERSON,P.LUSSO, JRNL AUTH 2 B.F.VOLKMAN JRNL TITL ENGINEERING METAMORPHIC CHEMOKINE LYMPHOTACTIN/XCL1 INTO THE JRNL TITL 2 GAG-BINDING, HIV-INHIBITORY DIMER CONFORMATION. JRNL REF ACS CHEM.BIOL. V. 10 2580 2015 JRNL REFN ISSN 1554-8929 JRNL PMID 26302421 JRNL DOI 10.1021/ACSCHEMBIO.5B00542 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, CYANA, X-PLOR NIH REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), GUNTERT, MUMENTHALER AND REMARK 3 WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N54 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000104433. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.02 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 13C; U-99% 15N] REMARK 210 XCL1, 20 MM POTASSIUM PHOSPHATE, REMARK 210 0.02 % [U-100% 15N] SODIUM AZIDE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D F1-13C/F3-13C REMARK 210 EDITED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, XEASY, GARANT, TALOS, REMARK 210 CYANA, X-PLOR NIH REMARK 210 METHOD USED : MOLECULAR DYNAMICS 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 67 REMARK 465 ASN A 68 REMARK 465 THR A 69 REMARK 465 ARG A 70 REMARK 465 ASN A 71 REMARK 465 ASN A 72 REMARK 465 MET A 73 REMARK 465 ILE A 74 REMARK 465 GLN A 75 REMARK 465 THR A 76 REMARK 465 LYS A 77 REMARK 465 PRO A 78 REMARK 465 THR A 79 REMARK 465 GLY A 80 REMARK 465 THR A 81 REMARK 465 GLN A 82 REMARK 465 GLN A 83 REMARK 465 SER A 84 REMARK 465 THR A 85 REMARK 465 ASN A 86 REMARK 465 THR A 87 REMARK 465 ALA A 88 REMARK 465 VAL A 89 REMARK 465 THR A 90 REMARK 465 LEU A 91 REMARK 465 THR A 92 REMARK 465 GLY A 93 REMARK 465 SER B 267 REMARK 465 ASN B 268 REMARK 465 THR B 269 REMARK 465 ARG B 270 REMARK 465 ASN B 271 REMARK 465 ASN B 272 REMARK 465 MET B 273 REMARK 465 ILE B 274 REMARK 465 GLN B 275 REMARK 465 THR B 276 REMARK 465 LYS B 277 REMARK 465 PRO B 278 REMARK 465 THR B 279 REMARK 465 GLY B 280 REMARK 465 THR B 281 REMARK 465 GLN B 282 REMARK 465 GLN B 283 REMARK 465 SER B 284 REMARK 465 THR B 285 REMARK 465 ASN B 286 REMARK 465 THR B 287 REMARK 465 ALA B 288 REMARK 465 VAL B 289 REMARK 465 THR B 290 REMARK 465 LEU B 291 REMARK 465 THR B 292 REMARK 465 GLY B 293 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 ARG B 235 H ASP B 250 1.59 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 VAL A 5 89.68 -166.61 REMARK 500 1 GLN A 17 176.08 66.75 REMARK 500 1 ARG A 18 14.32 -149.98 REMARK 500 1 ARG A 43 17.29 -142.46 REMARK 500 1 PRO A 51 29.96 -79.89 REMARK 500 1 GLN A 52 75.22 70.75 REMARK 500 1 ALA A 53 -35.34 -146.29 REMARK 500 1 ASP A 58 -171.63 -173.82 REMARK 500 1 VAL A 59 -65.37 74.18 REMARK 500 1 VAL A 60 83.82 55.27 REMARK 500 1 MET A 63 109.70 -51.06 REMARK 500 1 SER B 206 -72.56 -141.85 REMARK 500 1 LYS B 208 -82.54 -95.00 REMARK 500 1 GLN B 217 -177.59 64.48 REMARK 500 1 ARG B 218 19.13 -148.12 REMARK 500 1 PRO B 251 36.21 -83.13 REMARK 500 1 VAL B 259 -43.43 72.31 REMARK 500 1 VAL B 260 95.38 72.22 REMARK 500 2 GLN A 17 -80.81 -62.66 REMARK 500 2 ARG A 43 7.36 111.11 REMARK 500 2 GLN A 52 77.85 58.48 REMARK 500 2 TRP A 55 -27.93 176.25 REMARK 500 2 ASP A 58 -166.24 66.19 REMARK 500 2 ARG B 209 98.41 -68.95 REMARK 500 2 ARG B 218 105.51 -51.37 REMARK 500 2 SER B 233 69.14 66.64 REMARK 500 2 ARG B 243 -25.88 -160.30 REMARK 500 2 TRP B 255 17.74 -179.12 REMARK 500 2 ASP B 258 -153.56 -136.74 REMARK 500 2 VAL B 259 61.73 71.20 REMARK 500 3 LYS A 8 -72.24 -102.95 REMARK 500 3 GLN A 17 -171.62 58.70 REMARK 500 3 ARG A 18 74.79 -154.73 REMARK 500 3 PRO A 51 2.21 -63.91 REMARK 500 3 GLN A 52 27.06 49.94 REMARK 500 3 VAL A 56 122.64 61.61 REMARK 500 3 VAL A 59 -37.14 -144.84 REMARK 500 3 ARG A 65 99.55 71.02 REMARK 500 3 SER B 203 81.53 57.75 REMARK 500 3 GLN B 217 178.64 64.50 REMARK 500 3 ARG B 218 13.59 -146.83 REMARK 500 3 GLN B 252 1.80 52.86 REMARK 500 3 VAL B 256 119.10 78.42 REMARK 500 3 ARG B 265 136.20 75.76 REMARK 500 4 VAL A 5 -45.27 -172.87 REMARK 500 4 GLN A 17 -179.98 69.14 REMARK 500 4 ARG A 18 21.83 -153.90 REMARK 500 4 ARG A 23 161.23 61.03 REMARK 500 4 SER A 33 20.00 -148.08 REMARK 500 4 PRO A 51 20.85 -77.77 REMARK 500 REMARK 500 THIS ENTRY HAS 300 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 4 ARG A 9 0.07 SIDE CHAIN REMARK 500 15 ARG B 235 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25693 RELATED DB: BMRB DBREF 2N54 A 1 93 UNP P47992 XCL1_HUMAN 22 114 DBREF 2N54 B 201 293 UNP P47992 XCL1_HUMAN 22 114 SEQADV 2N54 CYS A 36 UNP P47992 ALA 57 ENGINEERED MUTATION SEQADV 2N54 CYS A 49 UNP P47992 ALA 70 ENGINEERED MUTATION SEQADV 2N54 CYS B 236 UNP P47992 ALA 57 ENGINEERED MUTATION SEQADV 2N54 CYS B 249 UNP P47992 ALA 70 ENGINEERED MUTATION SEQRES 1 A 93 VAL GLY SER GLU VAL SER ASP LYS ARG THR CYS VAL SER SEQRES 2 A 93 LEU THR THR GLN ARG LEU PRO VAL SER ARG ILE LYS THR SEQRES 3 A 93 TYR THR ILE THR GLU GLY SER LEU ARG CYS VAL ILE PHE SEQRES 4 A 93 ILE THR LYS ARG GLY LEU LYS VAL CYS CYS ASP PRO GLN SEQRES 5 A 93 ALA THR TRP VAL ARG ASP VAL VAL ARG SER MET ASP ARG SEQRES 6 A 93 LYS SER ASN THR ARG ASN ASN MET ILE GLN THR LYS PRO SEQRES 7 A 93 THR GLY THR GLN GLN SER THR ASN THR ALA VAL THR LEU SEQRES 8 A 93 THR GLY SEQRES 1 B 93 VAL GLY SER GLU VAL SER ASP LYS ARG THR CYS VAL SER SEQRES 2 B 93 LEU THR THR GLN ARG LEU PRO VAL SER ARG ILE LYS THR SEQRES 3 B 93 TYR THR ILE THR GLU GLY SER LEU ARG CYS VAL ILE PHE SEQRES 4 B 93 ILE THR LYS ARG GLY LEU LYS VAL CYS CYS ASP PRO GLN SEQRES 5 B 93 ALA THR TRP VAL ARG ASP VAL VAL ARG SER MET ASP ARG SEQRES 6 B 93 LYS SER ASN THR ARG ASN ASN MET ILE GLN THR LYS PRO SEQRES 7 B 93 THR GLY THR GLN GLN SER THR ASN THR ALA VAL THR LEU SEQRES 8 B 93 THR GLY SHEET 1 A 4 VAL A 12 LEU A 14 0 SHEET 2 A 4 GLY A 44 ASP A 50 -1 O LEU A 45 N LEU A 14 SHEET 3 A 4 LEU A 34 THR A 41 -1 N ARG A 35 O ASP A 50 SHEET 4 A 4 LYS A 25 GLU A 31 -1 N ILE A 29 O CYS A 36 SHEET 1 B 4 CYS B 211 LEU B 214 0 SHEET 2 B 4 GLY B 244 ASP B 250 -1 O VAL B 247 N VAL B 212 SHEET 3 B 4 LEU B 234 THR B 241 -1 N ARG B 235 O ASP B 250 SHEET 4 B 4 LYS B 225 GLU B 231 -1 N ILE B 229 O CYS B 236 SSBOND 1 CYS A 11 CYS A 48 1555 1555 2.03 SSBOND 2 CYS A 36 CYS A 49 1555 1555 2.04 SSBOND 3 CYS B 211 CYS B 248 1555 1555 2.02 SSBOND 4 CYS B 236 CYS B 249 1555 1555 2.04 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