HEADER IMMUNE SYSTEM 07-OCT-25 9YKM TITLE CRYSTAL STRUCTURE OF APO-HUMAN MINCLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-TYPE LECTIN DOMAIN FAMILY 4 MEMBER E; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: C-TYPE LECTIN SUPERFAMILY MEMBER 9,MACROPHAGE-INDUCIBLE C- COMPND 5 TYPE LECTIN,MINCLE; COMPND 6 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: CLEC4E, CLECSF9, MINCLE, UNQ218/PRO244; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CLR, C-TYPE LECTIN RECEPTOR, CARBOHYDRATE RECOGNITION DOMAIN, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.M.S.RIEL,C.K.YATES-HANSEN,L.J.MCCLELLAND REVDAT 1 21-OCT-26 9YKM 0 JRNL AUTH A.M.S.RIEL,C.K.YATES-HANSEN,L.J.MCCLELLAND JRNL TITL CRYSTAL STRUCTURE OF APO-HUMAN MINCLE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 15202 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 756 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 30.4900 - 2.7500 0.99 2909 120 0.1370 0.1563 REMARK 3 2 2.7400 - 2.1800 1.00 2918 152 0.1525 0.1608 REMARK 3 3 2.1800 - 1.9000 1.00 2943 142 0.1502 0.1978 REMARK 3 4 1.9000 - 1.7300 1.00 2938 124 0.1714 0.2281 REMARK 3 5 1.7300 - 1.6100 0.96 2738 218 0.2177 0.2745 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.154 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.259 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.22 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 : 0.008 1102 REMARK 3 ANGLE : 0.951 1496 REMARK 3 CHIRALITY : 0.054 155 REMARK 3 PLANARITY : 0.009 193 REMARK 3 DIHEDRAL : 14.578 391 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 9YKM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1000299082. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-25 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 : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15301 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 30.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.16400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.22300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 10% W/V PEG REMARK 280 6000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.55667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.11333 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: 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. (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 MET A 73 REMARK 465 GLY A 74 REMARK 465 SER A 75 REMARK 465 VAL A 76 REMARK 465 LYS A 77 REMARK 465 ILE A 210 REMARK 465 ASN A 211 REMARK 465 PRO A 212 REMARK 465 LEU A 213 REMARK 465 ASN A 214 REMARK 465 LYS A 215 REMARK 465 GLY A 216 REMARK 465 LYS A 217 REMARK 465 SER A 218 REMARK 465 LEU A 219 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 GLN A 88 65.05 38.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 117 O REMARK 620 2 ASN A 119 OD1 77.8 REMARK 620 3 GLU A 123 OE1 80.4 78.3 REMARK 620 4 GLU A 123 OE2 84.8 126.2 48.6 REMARK 620 5 GLU A 206 OE1 78.8 136.1 132.8 87.6 REMARK 620 6 GLU A 206 OE2 126.6 149.7 119.7 78.2 50.6 REMARK 620 7 HOH A 479 O 103.4 76.8 153.3 156.9 73.3 79.6 REMARK 620 8 HOH A 489 O 150.5 82.3 74.4 89.7 130.0 80.0 92.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 169 OE1 REMARK 620 2 ASN A 171 OD1 83.1 REMARK 620 3 ASN A 193 OD1 68.5 144.3 REMARK 620 4 ASP A 194 O 123.1 133.9 81.1 REMARK 620 5 ASP A 194 OD1 70.7 85.8 103.6 71.6 REMARK 620 6 HOH A 445 O 91.3 83.8 76.1 127.1 160.2 REMARK 620 7 HOH A 477 O 163.2 80.4 125.3 71.8 111.0 83.8 REMARK 620 N 1 2 3 4 5 6 DBREF 9YKM A 74 219 UNP Q9ULY5 CLC4E_HUMAN 74 219 SEQADV 9YKM MET A 73 UNP Q9ULY5 INITIATING METHIONINE SEQADV 9YKM LYS A 99 UNP Q9ULY5 ILE 99 CONFLICT SEQRES 1 A 147 MET GLY SER VAL LYS ASN CYS CYS PRO LEU ASN TRP GLU SEQRES 2 A 147 TYR PHE GLN SER SER CYS TYR PHE PHE SER THR ASP THR SEQRES 3 A 147 LYS SER TRP ALA LEU SER LEU LYS ASN CYS SER ALA MET SEQRES 4 A 147 GLY ALA HIS LEU VAL VAL ILE ASN SER GLN GLU GLU GLN SEQRES 5 A 147 GLU PHE LEU SER TYR LYS LYS PRO LYS MET ARG GLU PHE SEQRES 6 A 147 PHE ILE GLY LEU SER ASP GLN VAL VAL GLU GLY GLN TRP SEQRES 7 A 147 GLN TRP VAL ASP GLY THR PRO LEU THR LYS SER LEU SER SEQRES 8 A 147 PHE TRP ASP VAL GLY GLU PRO ASN ASN ILE ALA THR LEU SEQRES 9 A 147 GLU ASP CYS ALA THR MET ARG ASP SER SER ASN PRO ARG SEQRES 10 A 147 GLN ASN TRP ASN ASP VAL THR CYS PHE LEU ASN TYR PHE SEQRES 11 A 147 ARG ILE CYS GLU MET VAL GLY ILE ASN PRO LEU ASN LYS SEQRES 12 A 147 GLY LYS SER LEU HET CA A 301 1 HET CA A 302 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) FORMUL 4 HOH *151(H2 O) HELIX 1 AA1 SER A 100 MET A 111 1 12 HELIX 2 AA2 SER A 120 LYS A 131 1 12 HELIX 3 AA3 THR A 159 SER A 163 5 5 SHEET 1 AA1 5 GLU A 85 PHE A 87 0 SHEET 2 AA1 5 SER A 90 PHE A 94 -1 O TYR A 92 N GLU A 85 SHEET 3 AA1 5 PHE A 202 VAL A 208 -1 O MET A 207 N CYS A 91 SHEET 4 AA1 5 PHE A 137 ASP A 143 1 N PHE A 138 O PHE A 202 SHEET 5 AA1 5 TRP A 150 TRP A 152 -1 O GLN A 151 N SER A 142 SHEET 1 AA2 5 HIS A 114 LEU A 115 0 SHEET 2 AA2 5 PHE A 202 VAL A 208 -1 O GLU A 206 N HIS A 114 SHEET 3 AA2 5 PHE A 137 ASP A 143 1 N PHE A 138 O PHE A 202 SHEET 4 AA2 5 ASP A 178 MET A 182 -1 O ASP A 178 N ASP A 143 SHEET 5 AA2 5 TRP A 192 THR A 196 -1 O ASN A 193 N THR A 181 SSBOND 1 CYS A 80 CYS A 91 1555 1555 2.05 SSBOND 2 CYS A 108 CYS A 205 1555 1555 2.08 SSBOND 3 CYS A 179 CYS A 197 1555 1555 2.01 LINK O VAL A 117 CA CA A 301 1555 1555 2.30 LINK OD1 ASN A 119 CA CA A 301 1555 1555 2.29 LINK OE1 GLU A 123 CA CA A 301 1555 1555 2.82 LINK OE2 GLU A 123 CA CA A 301 1555 1555 2.41 LINK OE1 GLU A 169 CA CA A 302 1555 1555 2.40 LINK OD1 ASN A 171 CA CA A 302 1555 1555 2.33 LINK OD1 ASN A 193 CA CA A 302 1555 1555 2.35 LINK O ASP A 194 CA CA A 302 1555 1555 2.39 LINK OD1 ASP A 194 CA CA A 302 1555 1555 2.50 LINK OE1 GLU A 206 CA CA A 301 1555 1555 2.69 LINK OE2 GLU A 206 CA CA A 301 1555 1555 2.42 LINK CA CA A 301 O HOH A 479 1555 1555 2.47 LINK CA CA A 301 O HOH A 489 1555 1555 2.29 LINK CA CA A 302 O HOH A 445 1555 1555 2.50 LINK CA CA A 302 O HOH A 477 1555 1555 2.64 CISPEP 1 GLU A 169 PRO A 170 0 -1.96 CRYST1 49.166 49.166 43.670 90.00 90.00 120.00 P 31 3 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 0.020339 0.011743 0.000000 0.00000 SCALE2 0.000000 0.023486 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022899 0.00000 CONECT 30 206 CONECT 206 30 CONECT 480 2007 CONECT 595 2068 CONECT 633 2068 CONECT 691 2068 CONECT 692 2068 CONECT 1444 2069 CONECT 1472 2069 CONECT 1588 1860 CONECT 1805 2069 CONECT 1816 2069 CONECT 1819 2069 CONECT 1860 1588 CONECT 2007 480 CONECT 2019 2068 CONECT 2020 2068 CONECT 2068 595 633 691 692 CONECT 2068 2019 2020 2148 2158 CONECT 2069 1444 1472 1805 1816 CONECT 2069 1819 2114 2146 CONECT 2114 2069 CONECT 2146 2069 CONECT 2148 2068 CONECT 2158 2068 MASTER 256 0 2 3 10 0 0 6 1225 1 25 12 END