HEADER IMMUNE SYSTEM 29-AUG-13 4MHE TITLE CRYSTAL STRUCTURE OF CC-CHEMOKINE 18 COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-C MOTIF CHEMOKINE 18; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 21-89; COMPND 5 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: CCL18, AMAC1, DCCK1, MIP4, PARC, SCYA18; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GREEK KEY SHAPE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR W.G.LIANG,W.-J.TANG REVDAT 3 20-SEP-23 4MHE 1 REMARK SEQADV REVDAT 2 13-MAY-15 4MHE 1 JRNL REVDAT 1 03-SEP-14 4MHE 0 JRNL AUTH W.G.LIANG,M.REN,F.ZHAO,W.J.TANG JRNL TITL STRUCTURES OF HUMAN CCL18, CCL3, AND CCL4 REVEAL MOLECULAR JRNL TITL 2 DETERMINANTS FOR QUATERNARY STRUCTURES AND SENSITIVITY TO JRNL TITL 3 INSULIN-DEGRADING ENZYME. JRNL REF J.MOL.BIOL. V. 427 1345 2015 JRNL REFN ISSN 0022-2836 JRNL PMID 25636406 JRNL DOI 10.1016/J.JMB.2015.01.012 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 17436 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1744 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 35.0383 - 4.7933 1.00 1485 165 0.1737 0.1922 REMARK 3 2 4.7933 - 3.8061 1.00 1451 162 0.1387 0.1758 REMARK 3 3 3.8061 - 3.3254 1.00 1448 161 0.1515 0.1872 REMARK 3 4 3.3254 - 3.0215 1.00 1422 157 0.1876 0.2322 REMARK 3 5 3.0215 - 2.8050 1.00 1449 162 0.1994 0.2463 REMARK 3 6 2.8050 - 2.6397 1.00 1424 157 0.2042 0.2706 REMARK 3 7 2.6397 - 2.5076 1.00 1418 158 0.2072 0.2742 REMARK 3 8 2.5076 - 2.3984 1.00 1436 160 0.2030 0.2596 REMARK 3 9 2.3984 - 2.3061 0.98 1406 156 0.1975 0.2336 REMARK 3 10 2.3061 - 2.2266 0.86 1228 137 0.1860 0.2577 REMARK 3 11 2.2266 - 2.1569 0.65 932 103 0.1966 0.2784 REMARK 3 12 2.1569 - 2.1000 0.42 593 66 0.2050 0.2863 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.650 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 : 0.007 2146 REMARK 3 ANGLE : 1.061 2896 REMARK 3 CHIRALITY : 0.070 325 REMARK 3 PLANARITY : 0.005 358 REMARK 3 DIHEDRAL : 13.750 823 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 53.5360 13.3432 18.0152 REMARK 3 T TENSOR REMARK 3 T11: 0.0554 T22: 0.0549 REMARK 3 T33: 0.0438 T12: 0.0052 REMARK 3 T13: 0.0062 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.2584 L22: 0.2242 REMARK 3 L33: 0.2285 L12: -0.1305 REMARK 3 L13: 0.0633 L23: -0.1284 REMARK 3 S TENSOR REMARK 3 S11: 0.0370 S12: 0.0232 S13: 0.0246 REMARK 3 S21: 0.0227 S22: -0.0613 S23: 0.0198 REMARK 3 S31: 0.0157 S32: 0.0461 S33: -0.0008 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 4MHE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000081913. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19065 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 35.033 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2X69 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM REMARK 280 CITRATE TRIBASIC DIHYDRATE, PH 5.6, 30% W/V POLYETHYLENE GLYCOL REMARK 280 4,000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 27.58400 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 350 REMARK 350 BIOMOLECULE: 2 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: 1110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ALA A 70 REMARK 465 ALA B 70 REMARK 465 SER C 1 REMARK 465 ALA C 2 REMARK 465 GLN C 3 REMARK 465 VAL C 4 REMARK 465 GLY C 5 REMARK 465 THR C 6 REMARK 465 ASN C 7 REMARK 465 ASN C 69 REMARK 465 ALA C 70 REMARK 465 SER D 1 REMARK 465 ALA D 2 REMARK 465 GLN D 3 REMARK 465 VAL D 4 REMARK 465 GLY D 5 REMARK 465 THR D 6 REMARK 465 ASN D 7 REMARK 465 LYS D 8 REMARK 465 ASN D 69 REMARK 465 ALA D 70 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 101 DBREF 4MHE A 2 70 UNP P55774 CCL18_HUMAN 21 89 DBREF 4MHE B 2 70 UNP P55774 CCL18_HUMAN 21 89 DBREF 4MHE C 2 70 UNP P55774 CCL18_HUMAN 21 89 DBREF 4MHE D 2 70 UNP P55774 CCL18_HUMAN 21 89 SEQADV 4MHE SER A 1 UNP P55774 EXPRESSION TAG SEQADV 4MHE SER B 1 UNP P55774 EXPRESSION TAG SEQADV 4MHE SER C 1 UNP P55774 EXPRESSION TAG SEQADV 4MHE SER D 1 UNP P55774 EXPRESSION TAG SEQRES 1 A 70 SER ALA GLN VAL GLY THR ASN LYS GLU LEU CYS CYS LEU SEQRES 2 A 70 VAL TYR THR SER TRP GLN ILE PRO GLN LYS PHE ILE VAL SEQRES 3 A 70 ASP TYR SER GLU THR SER PRO GLN CYS PRO LYS PRO GLY SEQRES 4 A 70 VAL ILE LEU LEU THR LYS ARG GLY ARG GLN ILE CYS ALA SEQRES 5 A 70 ASP PRO ASN LYS LYS TRP VAL GLN LYS TYR ILE SER ASP SEQRES 6 A 70 LEU LYS LEU ASN ALA SEQRES 1 B 70 SER ALA GLN VAL GLY THR ASN LYS GLU LEU CYS CYS LEU SEQRES 2 B 70 VAL TYR THR SER TRP GLN ILE PRO GLN LYS PHE ILE VAL SEQRES 3 B 70 ASP TYR SER GLU THR SER PRO GLN CYS PRO LYS PRO GLY SEQRES 4 B 70 VAL ILE LEU LEU THR LYS ARG GLY ARG GLN ILE CYS ALA SEQRES 5 B 70 ASP PRO ASN LYS LYS TRP VAL GLN LYS TYR ILE SER ASP SEQRES 6 B 70 LEU LYS LEU ASN ALA SEQRES 1 C 70 SER ALA GLN VAL GLY THR ASN LYS GLU LEU CYS CYS LEU SEQRES 2 C 70 VAL TYR THR SER TRP GLN ILE PRO GLN LYS PHE ILE VAL SEQRES 3 C 70 ASP TYR SER GLU THR SER PRO GLN CYS PRO LYS PRO GLY SEQRES 4 C 70 VAL ILE LEU LEU THR LYS ARG GLY ARG GLN ILE CYS ALA SEQRES 5 C 70 ASP PRO ASN LYS LYS TRP VAL GLN LYS TYR ILE SER ASP SEQRES 6 C 70 LEU LYS LEU ASN ALA SEQRES 1 D 70 SER ALA GLN VAL GLY THR ASN LYS GLU LEU CYS CYS LEU SEQRES 2 D 70 VAL TYR THR SER TRP GLN ILE PRO GLN LYS PHE ILE VAL SEQRES 3 D 70 ASP TYR SER GLU THR SER PRO GLN CYS PRO LYS PRO GLY SEQRES 4 D 70 VAL ILE LEU LEU THR LYS ARG GLY ARG GLN ILE CYS ALA SEQRES 5 D 70 ASP PRO ASN LYS LYS TRP VAL GLN LYS TYR ILE SER ASP SEQRES 6 D 70 LEU LYS LEU ASN ALA HET ACT B 101 7 HETNAM ACT ACETATE ION FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 HOH *190(H2 O) HELIX 1 1 THR A 6 CYS A 11 1 6 HELIX 2 2 PRO A 21 LYS A 23 5 3 HELIX 3 3 LYS A 56 LEU A 68 1 13 HELIX 4 4 THR B 6 CYS B 11 1 6 HELIX 5 5 PRO B 21 LYS B 23 5 3 HELIX 6 6 LYS B 56 ASN B 69 1 14 HELIX 7 7 PRO C 21 LYS C 23 5 3 HELIX 8 8 LYS C 56 LEU C 66 1 11 HELIX 9 9 PRO D 21 LYS D 23 5 3 HELIX 10 10 LYS D 56 LYS D 67 1 12 SHEET 1 A 4 GLN A 3 VAL A 4 0 SHEET 2 A 4 GLN D 49 ALA D 52 1 O GLN D 49 N VAL A 4 SHEET 3 A 4 VAL D 40 THR D 44 -1 N LEU D 42 O ILE D 50 SHEET 4 A 4 ILE D 25 GLU D 30 -1 N SER D 29 O ILE D 41 SHEET 1 B 3 ILE A 25 GLU A 30 0 SHEET 2 B 3 VAL A 40 THR A 44 -1 O LEU A 43 N ASP A 27 SHEET 3 B 3 GLN A 49 ALA A 52 -1 O ILE A 50 N LEU A 42 SHEET 1 C 4 GLN B 3 VAL B 4 0 SHEET 2 C 4 GLN C 49 ALA C 52 1 O GLN C 49 N VAL B 4 SHEET 3 C 4 VAL C 40 THR C 44 -1 N LEU C 42 O ILE C 50 SHEET 4 C 4 ILE C 25 GLU C 30 -1 N ASP C 27 O LEU C 43 SHEET 1 D 3 ILE B 25 GLU B 30 0 SHEET 2 D 3 VAL B 40 THR B 44 -1 O LEU B 43 N VAL B 26 SHEET 3 D 3 GLN B 49 ALA B 52 -1 O ILE B 50 N LEU B 42 SSBOND 1 CYS A 11 CYS A 35 1555 1555 2.03 SSBOND 2 CYS A 12 CYS A 51 1555 1555 2.06 SSBOND 3 CYS B 11 CYS B 35 1555 1555 2.03 SSBOND 4 CYS B 12 CYS B 51 1555 1555 2.06 SSBOND 5 CYS C 11 CYS C 35 1555 1555 2.05 SSBOND 6 CYS C 12 CYS C 51 1555 1555 2.07 SSBOND 7 CYS D 11 CYS D 35 1555 1555 2.05 SSBOND 8 CYS D 12 CYS D 51 1555 1555 2.07 SITE 1 AC1 6 SER A 32 PRO A 33 GLN A 34 SER B 32 SITE 2 AC1 6 PRO B 33 GLN B 34 CRYST1 52.075 55.168 60.377 90.00 109.25 90.00 P 1 21 1 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 0.019203 0.000000 0.006706 0.00000 SCALE2 0.000000 0.018126 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017543 0.00000