10 20 30 40 50 60 70 80 2HDM - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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- COMPND 5 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_STRAIN: SG13009[PREP4]; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE308HT
KEYWDS LYMPHOTACTIN, XCL1, CHEMOKINE, NMR, CONFORMATIONAL KEYWDS 2 RESTRICTION, CYTOKINE
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR B.F.VOLKMAN,R.L.TUINSTRA,F.C.PETERSON,E.S.ELGIN
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, JRNL AUTH 2 B.F.VOLKMAN JRNL TITL AN ENGINEERED SECOND DISULFIDE BOND RESTRICTS JRNL TITL 2 LYMPHOTACTIN/XCL1 TO A CHEMOKINE-LIKE CONFORMATION JRNL TITL 3 WITH XCR1 AGONIST ACTIVITY JRNL REF BIOCHEMISTRY V. 46 2564 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17302442 JRNL DOI 10.1021/BI602365D
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.9.3 REMARK 3 AUTHORS : SCHWIETERS, C.D., KUSZEWSKI, J.J, TJANDRA, N., REMARK 3 CLORE, G.M. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 1234 NOE CONSTRAINTS (418 INTRA, 333 SEQUENTIAL, 153 MEDIUM REMARK 3 AND 330 LONG RANGE CONSTRAINTS) AND 82 PHI AND PSI DIHEDRAL REMARK 3 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 23-JUN-06. REMARK 100 THE RCSB ID CODE IS RCSB038229.
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 REMARK 210 MM PHOSPATE BUFFER, 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-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 : XWINNMR 3.5, NMRPIPE 2004, REMARK 210 XEASY 1.3, GARANT 2.1, CYANA REMARK 210 2.1 REMARK 210 METHOD USED : AUTOMATED METHODS WERE USED REMARK 210 FOR 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 REMARK 210 USING 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 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: 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 14 LYS A 8 -65.19 -151.78 REMARK 500 14 ARG A 9 -69.53 67.19 REMARK 500 14 CYS A 21 -36.54 68.51 REMARK 500 14 LEU A 34 91.89 56.67 REMARK 500 14 ASN A 68 -54.69 -172.46 REMARK 500 15 SER A 33 -54.79 -176.86 REMARK 500 16 SER A 6 89.74 -153.58 REMARK 500 16 SER A 33 -60.20 72.41 REMARK 500 16 ASN A 68 90.68 62.17 REMARK 500 17 ASP A 7 106.83 -49.05 REMARK 500 17 ARG A 9 76.88 82.30 REMARK 500 17 LYS A 25 -65.17 -108.68 REMARK 500 17 SER A 33 -49.05 73.71 REMARK 500 18 SER A 3 102.81 66.72 REMARK 500 18 GLU A 4 175.63 72.35 REMARK 500 18 VAL A 5 -68.39 -94.51 REMARK 500 18 ASP A 7 116.07 68.41 REMARK 500 18 ARG A 9 -167.95 -61.25 REMARK 500 18 THR A 10 -38.86 172.12 REMARK 500 18 SER A 13 -168.29 -114.00 REMARK 500 18 ILE A 74 91.11 73.81 REMARK 500 19 VAL A 5 77.39 60.79 REMARK 500 19 ASP A 7 115.17 -164.12 REMARK 500 19 THR A 16 -41.13 69.96 REMARK 500 19 SER A 33 -47.91 75.71 REMARK 500 19 THR A 69 -72.81 -71.57 REMARK 500 19 MET A 73 113.50 -160.64 REMARK 500 20 ASP A 7 -73.37 65.56 REMARK 500 20 ARG A 9 27.61 49.82 REMARK 500 20 ARG A 70 -169.54 52.00 REMARK 500 20 ASN A 71 -35.52 -147.26 REMARK 500 20 ASN A 72 107.39 73.13 REMARK 500 20 MET A 73 124.80 78.20 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 SEQADV 2HDM CYS A 59 UNP P47992 VAL 80 ENGINEERED
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