HEADER IMMUNE SYSTEM 10-SEP-19 6STK TITLE CRYSTAL STRUCTURE OF THE CC-CHEMOKINE 5 (CCL5) E66S MUTATION 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; COMPND 8 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: CCL5, D17S136E, SCYA5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CC-CHEMOKINE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.RAMIREZ-ESCUDERO,B.J.C.JANSSEN REVDAT 3 24-JAN-24 6STK 1 REMARK REVDAT 2 28-OCT-20 6STK 1 JRNL REVDAT 1 02-SEP-20 6STK 0 JRNL AUTH S.S.DENISOV,M.RAMIREZ-ESCUDERO,A.C.A.HEINZMANN,J.H.IPPEL, JRNL AUTH 2 P.E.DAWSON,R.R.KOENEN,T.M.HACKENG,B.J.C.JANSSEN,I.DIJKGRAAF JRNL TITL STRUCTURAL CHARACTERIZATION OF ANTI-CCL5 ACTIVITY OF THE JRNL TITL 2 TICK SALIVARY PROTEIN EVASIN-4. JRNL REF J.BIOL.CHEM. V. 295 14367 2020 JRNL REFN ESSN 1083-351X JRNL PMID 32817341 JRNL DOI 10.1074/JBC.RA120.013891 REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20346 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1026 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 36.0700 - 2.9072 1.00 2934 159 0.1697 0.1860 REMARK 3 2 2.9072 - 2.3077 1.00 2789 153 0.1877 0.1961 REMARK 3 3 2.3077 - 2.0160 1.00 2743 145 0.1697 0.2051 REMARK 3 4 2.0160 - 1.8317 1.00 2733 135 0.1767 0.2239 REMARK 3 5 1.8317 - 1.7004 1.00 2703 151 0.1880 0.2196 REMARK 3 6 1.7004 - 1.6001 1.00 2690 147 0.2277 0.2778 REMARK 3 7 1.6001 - 1.5200 1.00 2728 136 0.2545 0.2969 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.97 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 3:104) REMARK 3 ORIGIN FOR THE GROUP (A): 0.8914 -15.3750 -21.8316 REMARK 3 T TENSOR REMARK 3 T11: 0.1825 T22: 0.1508 REMARK 3 T33: 0.1487 T12: 0.0076 REMARK 3 T13: 0.0026 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 1.2162 L22: 4.8652 REMARK 3 L33: 2.2925 L12: 0.3845 REMARK 3 L13: 0.4712 L23: 2.0639 REMARK 3 S TENSOR REMARK 3 S11: 0.0373 S12: 0.0270 S13: -0.0365 REMARK 3 S21: -0.2279 S22: -0.0597 S23: 0.0728 REMARK 3 S31: -0.0227 S32: 0.0483 S33: 0.0138 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESSEQ 3:101) REMARK 3 ORIGIN FOR THE GROUP (A): 10.3921 -4.4193 -1.1522 REMARK 3 T TENSOR REMARK 3 T11: 0.1677 T22: 0.1407 REMARK 3 T33: 0.1721 T12: -0.0025 REMARK 3 T13: -0.0023 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 1.9462 L22: 1.7140 REMARK 3 L33: 7.4178 L12: 0.3726 REMARK 3 L13: 0.8552 L23: -0.0974 REMARK 3 S TENSOR REMARK 3 S11: -0.0541 S12: -0.0274 S13: 0.0121 REMARK 3 S21: 0.1545 S22: -0.0625 S23: -0.1095 REMARK 3 S31: -0.1131 S32: 0.2036 S33: 0.0872 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 26 THROUGH 89 OR REMARK 3 RESID 124)) REMARK 3 SELECTION : (CHAIN B AND (RESID 26 THROUGH 89 OR REMARK 3 RESID 201)) REMARK 3 ATOM PAIRS NUMBER : 627 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6STK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1292104283. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-18 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 : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9787 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20411 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 48.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.14300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5COY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% GLYCEROL, 25.5% PEG 4000, 85MM REMARK 280 ACETATE BUFFER PH 4.6, 0.17 M AMMONIUM ACETATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K 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 11.95800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.00050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.16200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.00050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 11.95800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.16200 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: 1950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 1 REMARK 465 PRO A 2 REMARK 465 SER A 68 REMARK 465 SER B 1 REMARK 465 PRO B 2 REMARK 465 MET B 67 REMARK 465 SER B 68 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5COY RELATED DB: PDB DBREF 6STK A 1 68 UNP P13501 CCL5_HUMAN 24 91 DBREF 6STK B 1 68 UNP P13501 CCL5_HUMAN 24 91 SEQADV 6STK SER A 66 UNP P13501 GLU 89 ENGINEERED MUTATION SEQADV 6STK SER B 66 UNP P13501 GLU 89 ENGINEERED MUTATION SEQRES 1 A 68 SER PRO TYR SER SER ASP THR THR PRO CYS CYS PHE ALA SEQRES 2 A 68 TYR ILE ALA ARG PRO LEU PRO ARG ALA HIS ILE LYS GLU SEQRES 3 A 68 TYR PHE TYR THR SER GLY LYS CYS SER ASN PRO ALA VAL SEQRES 4 A 68 VAL PHE VAL THR ARG LYS ASN ARG GLN VAL CYS ALA ASN SEQRES 5 A 68 PRO GLU LYS LYS TRP VAL ARG GLU TYR ILE ASN SER LEU SEQRES 6 A 68 SER MET SER SEQRES 1 B 68 SER PRO TYR SER SER ASP THR THR PRO CYS CYS PHE ALA SEQRES 2 B 68 TYR ILE ALA ARG PRO LEU PRO ARG ALA HIS ILE LYS GLU SEQRES 3 B 68 TYR PHE TYR THR SER GLY LYS CYS SER ASN PRO ALA VAL SEQRES 4 B 68 VAL PHE VAL THR ARG LYS ASN ARG GLN VAL CYS ALA ASN SEQRES 5 B 68 PRO GLU LYS LYS TRP VAL ARG GLU TYR ILE ASN SER LEU SEQRES 6 B 68 SER MET SER HET ACT A 101 4 HET GOL B 101 6 HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *136(H2 O) HELIX 1 AA1 PRO A 20 ALA A 22 5 3 HELIX 2 AA2 LYS A 55 SER A 66 1 12 HELIX 3 AA3 PRO B 20 ALA B 22 5 3 HELIX 4 AA4 LYS B 55 SER B 66 1 12 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 ALA B 51 N VAL B 39 SSBOND 1 CYS A 10 CYS A 34 1555 1555 2.04 SSBOND 2 CYS A 11 CYS A 50 1555 1555 2.04 SSBOND 3 CYS B 10 CYS B 34 1555 1555 2.03 SSBOND 4 CYS B 11 CYS B 50 1555 1555 2.05 SITE 1 AC1 7 SER A 64 MET A 67 LYS B 33 SER B 35 SITE 2 AC1 7 HOH B 216 HOH B 234 HOH B 247 SITE 1 AC2 4 ARG A 47 GLN A 48 ASP B 6 THR B 7 CRYST1 23.916 56.324 94.001 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 0.041813 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017754 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010638 0.00000