PDB Short entry for 5COY HEADER CYTOKINE 20-JUL-15 5COY TITLE CRYSTAL STRUCTURE OF CC CHEMOKINE 5 (CCL5) COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-C MOTIF CHEMOKINE 5; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: EOCP,EOSINOPHIL CHEMOTACTIC CYTOKINE,SIS-DELTA,SMALL- COMPND 5 INDUCIBLE CYTOKINE A5,T CELL-SPECIFIC PROTEIN P228,TCP228,T-CELL- COMPND 6 SPECIFIC PROTEIN RANTES; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CCL5, D17S136E, SCYA5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CC CHEMOKINE, CCL5, DIMER, SIGNALING PROTEIN, CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR W.G.LIANG,W.TANG REVDAT 6 29-JUL-20 5COY 1 COMPND REMARK HET HETNAM REVDAT 6 2 1 FORMUL LINK SITE ATOM REVDAT 5 15-JAN-20 5COY 1 JRNL REMARK REVDAT 4 18-MAY-16 5COY 1 JRNL REVDAT 3 04-MAY-16 5COY 1 JRNL REVDAT 2 20-APR-16 5COY 1 JRNL REVDAT 1 13-APR-16 5COY 0 JRNL AUTH W.G.LIANG,C.G.TRIANDAFILLOU,T.Y.HUANG,M.M.ZULUETA, JRNL AUTH 2 S.BANERJEE,A.R.DINNER,S.C.HUNG,W.J.TANG JRNL TITL STRUCTURAL BASIS FOR OLIGOMERIZATION AND GLYCOSAMINOGLYCAN JRNL TITL 2 BINDING OF CCL5 AND CCL3. JRNL REF PROC.NATL.ACAD.SCI.USA V. 113 5000 2016 JRNL REFN ESSN 1091-6490 JRNL PMID 27091995 JRNL DOI 10.1073/PNAS.1523981113 REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 74.9 REMARK 3 NUMBER OF REFLECTIONS : 22966 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.650 REMARK 3 FREE R VALUE TEST SET COUNT : 1919 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 36.1019 - 3.9151 0.92 1822 177 0.1614 0.1803 REMARK 3 2 3.9151 - 3.1080 0.94 1884 174 0.1438 0.1640 REMARK 3 3 3.1080 - 2.7153 0.96 1917 175 0.1647 0.2182 REMARK 3 4 2.7153 - 2.4671 0.97 1924 189 0.1673 0.1870 REMARK 3 5 2.4671 - 2.2903 0.98 1920 186 0.1595 0.1703 REMARK 3 6 2.2903 - 2.1553 0.99 1946 186 0.1395 0.2058 REMARK 3 7 2.1553 - 2.0474 0.99 2009 190 0.1460 0.1982 REMARK 3 8 2.0474 - 1.9583 0.98 1903 178 0.1428 0.1817 REMARK 3 9 1.9583 - 1.8829 0.92 1866 179 0.1463 0.1915 REMARK 3 10 1.8829 - 1.8179 0.83 1634 148 0.1450 0.2230 REMARK 3 11 1.8179 - 1.7611 0.71 1445 138 0.1490 0.1950 REMARK 3 12 1.7611 - 1.7107 0.62 1200 111 0.1602 0.2054 REMARK 3 13 1.7107 - 1.6657 0.58 1159 108 0.1550 0.1993 REMARK 3 14 1.6657 - 1.6250 0.55 1109 106 0.1587 0.2106 REMARK 3 15 1.6250 - 1.5881 0.53 1035 99 0.1626 0.2432 REMARK 3 16 1.5881 - 1.5543 0.53 1053 100 0.1688 0.2390 REMARK 3 17 1.5543 - 1.5232 0.52 1039 100 0.1748 0.2296 REMARK 3 18 1.5232 - 1.4945 0.52 1033 98 0.1793 0.2332 REMARK 3 19 1.4945 - 1.4678 0.51 1012 97 0.1768 0.2529 REMARK 3 20 1.4678 - 1.4430 0.44 895 85 0.1779 0.2286 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 1128 REMARK 3 ANGLE : 1.337 1523 REMARK 3 CHIRALITY : 0.059 165 REMARK 3 PLANARITY : 0.007 188 REMARK 3 DIHEDRAL : 12.899 415 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5COY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211984. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.021 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23175 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : 0.03500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.41400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1B3A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM PHOSPHATE MONOBASIC, REMARK 280 20% W/V POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 11.80050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.08400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.09800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.08400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 11.80050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.09800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER B 4 N CB OG REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 Z9N C 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DNF RELATED DB: PDB REMARK 900 RELATED ID: 5CMD RELATED DB: PDB DBREF 5COY A 4 68 UNP P13501 CCL5_HUMAN 27 91 DBREF 5COY B 4 68 UNP P13501 CCL5_HUMAN 27 91 SEQRES 1 A 65 SER SER ASP THR THR PRO CYS CYS PHE ALA TYR ILE ALA SEQRES 2 A 65 ARG PRO LEU PRO ARG ALA HIS ILE LYS GLU TYR PHE TYR SEQRES 3 A 65 THR SER GLY LYS CYS SER ASN PRO ALA VAL VAL PHE VAL SEQRES 4 A 65 THR ARG LYS ASN ARG GLN VAL CYS ALA ASN PRO GLU LYS SEQRES 5 A 65 LYS TRP VAL ARG GLU TYR ILE ASN SER LEU GLU MET SER SEQRES 1 B 65 SER SER ASP THR THR PRO CYS CYS PHE ALA TYR ILE ALA SEQRES 2 B 65 ARG PRO LEU PRO ARG ALA HIS ILE LYS GLU TYR PHE TYR SEQRES 3 B 65 THR SER GLY LYS CYS SER ASN PRO ALA VAL VAL PHE VAL SEQRES 4 B 65 THR ARG LYS ASN ARG GLN VAL CYS ALA ASN PRO GLU LYS SEQRES 5 B 65 LYS TRP VAL ARG GLU TYR ILE ASN SER LEU GLU MET SER HET GLC C 1 11 HET Z9N C 2 12 HET PO4 A 101 5 HET PO4 B 101 5 HET PEG B 102 7 HET PEG B 103 7 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM Z9N ALPHA-D-FRUCTOFURANOSE HETNAM PO4 PHOSPHATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 3 GLC C6 H12 O6 FORMUL 3 Z9N C6 H12 O6 FORMUL 4 PO4 2(O4 P 3-) FORMUL 6 PEG 2(C4 H10 O3) FORMUL 8 HOH *140(H2 O) HELIX 1 AA1 PRO A 20 ALA A 22 5 3 HELIX 2 AA2 LYS A 55 GLU A 66 1 12 HELIX 3 AA3 PRO B 20 ALA B 22 5 3 HELIX 4 AA4 LYS B 55 MET B 67 1 13 SHEET 1 AA1 2 THR A 8 CYS A 10 0 SHEET 2 AA1 2 THR B 8 CYS B 10 -1 O THR B 8 N CYS A 10 SHEET 1 AA2 3 ILE A 24 TYR A 29 0 SHEET 2 AA2 3 VAL A 39 THR A 43 -1 O VAL A 40 N PHE A 28 SHEET 3 AA2 3 GLN A 48 ALA A 51 -1 O VAL A 49 N PHE A 41 SHEET 1 AA3 3 ILE B 24 TYR B 29 0 SHEET 2 AA3 3 VAL B 39 THR B 43 -1 O VAL B 40 N PHE B 28 SHEET 3 AA3 3 GLN B 48 ALA B 51 -1 O VAL B 49 N PHE B 41 SSBOND 1 CYS A 10 CYS A 34 1555 1555 2.04 SSBOND 2 CYS A 11 CYS A 50 1555 1555 2.05 SSBOND 3 CYS B 10 CYS B 34 1555 1555 2.06 SSBOND 4 CYS B 11 CYS B 50 1555 1555 2.06 LINK C1 GLC C 1 O2 Z9N C 2 1555 1555 1.40 CRYST1 23.601 56.196 94.168 90.00 90.00 90.00 P 21 21 21 8 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 0.042371 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017795 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010619 0.00000