HEADER CYTOKINE 20-JUN-06 2HDM TITLE SOLUTION STRUCTURE OF V21C/V59C LYMPHOTACTIN/XCL1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYMPHOTACTIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: XCL1, CYTOKINE SCM-1, ATAC, LYMPHOTAXIN, SCM-1-ALPHA, SMALL COMPND 5 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_STRAIN: SG13009[PREP4]; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE308HT KEYWDS LYMPHOTACTIN, XCL1, CHEMOKINE, CONFORMATIONAL RESTRICTION, CYTOKINE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.F.VOLKMAN,R.L.TUINSTRA,F.C.PETERSON,E.S.ELGIN REVDAT 3 20-OCT-21 2HDM 1 REMARK SEQADV REVDAT 2 24-FEB-09 2HDM 1 VERSN REVDAT 1 01-MAY-07 2HDM 0 JRNL AUTH R.L.TUINSTRA,F.C.PETERSON,E.S.ELGIN,A.J.PELZEK,B.F.VOLKMAN JRNL TITL AN ENGINEERED SECOND DISULFIDE BOND RESTRICTS JRNL TITL 2 LYMPHOTACTIN/XCL1 TO A CHEMOKINE-LIKE CONFORMATION WITH XCR1 JRNL TITL 3 AGONIST ACTIVITY JRNL REF BIOCHEMISTRY V. 46 2564 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17302442 JRNL DOI 10.1021/BI602365D REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, XPLOR-NIH 2.9.3 REMARK 3 AUTHORS : SCHWIETERS, C.D., KUSZEWSKI, J.J, TJANDRA, N., REMARK 3 CLORE, G.M. (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 STRUCTURES ARE BASED ON A TOTAL OF 1234 NOE CONSTRAINTS ( 418 REMARK 3 INTRA, 333 SEQUENTIAL, 153 MEDIUM AND 330 LONG RANGE CONSTRAINTS) REMARK 3 AND 82 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. REMARK 4 REMARK 4 2HDM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000038229. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 10 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM CC3 HLTN, U-15N, 13C; 20 MM REMARK 210 PHOSPATE BUFFER, 90% H2O, 10% 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 : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2004, XEASY 1.3, GARANT REMARK 210 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. 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: ALL TRIPLE-RESONANCE AND NOESY SPECTRA WERE ACQUIRED USING REMARK 210 A CRYOGENIC PROBE 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 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 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 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 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 6 -52.04 -168.88 REMARK 500 1 ASP A 7 -178.46 66.24 REMARK 500 1 LYS A 8 -88.86 64.45 REMARK 500 1 ASN A 71 95.78 -173.49 REMARK 500 2 LYS A 8 170.90 80.08 REMARK 500 2 LEU A 34 103.03 64.20 REMARK 500 2 ASN A 71 78.77 58.24 REMARK 500 2 ASN A 72 99.90 169.46 REMARK 500 3 GLU A 4 -73.62 -142.90 REMARK 500 3 LYS A 8 -155.52 70.30 REMARK 500 3 THR A 10 138.37 76.09 REMARK 500 3 SER A 13 175.20 79.11 REMARK 500 3 LYS A 25 -61.91 -102.69 REMARK 500 3 ARG A 70 -50.25 71.66 REMARK 500 3 ASN A 71 96.33 60.68 REMARK 500 4 SER A 6 -176.49 60.59 REMARK 500 4 ASP A 7 -156.72 -145.46 REMARK 500 4 LYS A 25 -62.19 -105.37 REMARK 500 4 THR A 69 85.75 -159.41 REMARK 500 5 GLU A 4 -65.98 -104.11 REMARK 500 5 VAL A 5 75.09 52.27 REMARK 500 6 SER A 3 -63.23 -132.42 REMARK 500 6 ASP A 7 143.48 73.97 REMARK 500 6 ASN A 68 -154.53 -110.61 REMARK 500 7 LYS A 8 -75.34 -75.70 REMARK 500 7 LEU A 14 -167.26 -126.11 REMARK 500 7 LEU A 34 131.62 178.85 REMARK 500 7 ILE A 74 88.54 60.91 REMARK 500 8 LYS A 8 -162.44 -103.40 REMARK 500 8 ARG A 9 74.64 -109.95 REMARK 500 8 SER A 33 -44.73 72.84 REMARK 500 8 THR A 69 93.51 -176.18 REMARK 500 9 ARG A 9 73.99 47.42 REMARK 500 9 SER A 33 126.63 74.69 REMARK 500 9 LEU A 34 84.10 61.13 REMARK 500 9 ASN A 71 -58.73 -168.49 REMARK 500 10 GLU A 4 -46.99 -142.31 REMARK 500 10 VAL A 5 96.30 65.72 REMARK 500 11 ARG A 9 73.95 60.28 REMARK 500 11 SER A 67 86.17 64.84 REMARK 500 11 ASN A 71 -159.10 63.90 REMARK 500 12 THR A 10 -40.81 77.06 REMARK 500 12 SER A 13 -165.19 -128.05 REMARK 500 12 LYS A 25 -63.32 -99.26 REMARK 500 12 SER A 67 -146.23 -152.10 REMARK 500 12 ASN A 68 104.87 -167.06 REMARK 500 12 ASN A 72 -78.70 53.91 REMARK 500 13 LYS A 8 -49.42 -168.55 REMARK 500 13 THR A 10 -31.81 75.86 REMARK 500 14 VAL A 5 75.97 55.71 REMARK 500 REMARK 500 THIS ENTRY HAS 83 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 18 ARG A 9 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2HDM A 2 93 UNP P47992 XCL1_HUMAN 23 114 SEQADV 2HDM CYS A 21 UNP P47992 VAL 42 ENGINEERED MUTATION SEQADV 2HDM CYS A 59 UNP P47992 VAL 80 ENGINEERED MUTATION SEQRES 1 A 92 GLY SER GLU VAL SER ASP LYS ARG THR CYS VAL SER LEU SEQRES 2 A 92 THR THR GLN ARG LEU PRO CYS SER ARG ILE LYS THR TYR SEQRES 3 A 92 THR ILE THR GLU GLY SER LEU ARG ALA VAL ILE PHE ILE SEQRES 4 A 92 THR LYS ARG GLY LEU LYS VAL CYS ALA ASP PRO GLN ALA SEQRES 5 A 92 THR TRP VAL ARG ASP CYS VAL ARG SER MET ASP ARG LYS SEQRES 6 A 92 SER ASN THR ARG ASN ASN MET ILE GLN THR LYS PRO THR SEQRES 7 A 92 GLY THR GLN GLN SER THR ASN THR ALA VAL THR LEU THR SEQRES 8 A 92 GLY HELIX 1 1 PRO A 20 SER A 22 5 3 HELIX 2 2 ALA A 53 SER A 67 1 15 SHEET 1 A 3 ILE A 24 THR A 30 0 SHEET 2 A 3 ALA A 36 THR A 41 -1 O ILE A 38 N THR A 28 SHEET 3 A 3 LYS A 46 ALA A 49 -1 O ALA A 49 N VAL A 37 SSBOND 1 CYS A 11 CYS A 48 1555 1555 2.01 SSBOND 2 CYS A 21 CYS A 59 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 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20