HEADER SUGAR BINDING PROTEIN 10-SEP-10 2XR6 TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF THE CARBOHYDRATE RECOGNITION TITLE 2 DOMAIN OF HUMAN DC-SIGN WITH PSEUDO TRIMANNOSIDE MIMIC. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD209 ANTIGEN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CARBOHYDRATE RECOGNITION DOMAIN, RESIDUES 250-404; COMPND 5 SYNONYM: DC-SIGN, DENDRITIC CELL-SPECIFIC ICAM-3-GRABBING NON- COMPND 6 INTEGRIN 1, DC-SIGN1, C-TYPE LECTIN DOMAIN FAMILY 4 MEMBER L, CD209; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PASK-IBA7PLUS KEYWDS SUGAR BINDING PROTEIN, CARBOHYDRATE BINDING, MANNOSE EXPDTA X-RAY DIFFRACTION AUTHOR M.THEPAUT,I.SUITKEVICIUTE,S.SATTIN,J.REINA,A.BERNARDI,F.FIESCHI REVDAT 7 20-DEC-23 2XR6 1 HETSYN LINK REVDAT 6 29-JUL-20 2XR6 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE REVDAT 5 06-MAR-19 2XR6 1 REMARK LINK REVDAT 4 30-JAN-19 2XR6 1 REMARK REVDAT 3 27-AUG-14 2XR6 1 JRNL REVDAT 2 30-JUL-14 2XR6 1 JRNL REMARK REVDAT 1 19-OCT-11 2XR6 0 JRNL AUTH I.SUTKEVICIUTE,M.THEPAUT,S.SATTIN,A.BERZI,J.MCGEAGH, JRNL AUTH 2 S.GRUDININ,J.WEISER,A.LE ROY,J.J.REINA,J.ROJO,M.CLERICI, JRNL AUTH 3 A.BERNARDI,C.EBEL,F.FIESCHI JRNL TITL UNIQUE DC-SIGN CLUSTERING ACTIVITY OF A SMALL GLYCOMIMETIC: JRNL TITL 2 A LESSON FOR LIGAND DESIGN. JRNL REF ACS CHEM.BIOL. V. 9 1377 2014 JRNL REFN ISSN 1554-8929 JRNL PMID 24749535 JRNL DOI 10.1021/CB500054H REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 28812 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1536 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2103 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1860 REMARK 3 BIN FREE R VALUE SET COUNT : 109 REMARK 3 BIN FREE R VALUE : 0.2040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1051 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 166 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.09000 REMARK 3 B22 (A**2) : 0.09000 REMARK 3 B33 (A**2) : -0.17000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.050 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.051 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1306 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1815 ; 1.791 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 177 ; 7.196 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 71 ;38.033 ;25.493 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 214 ;13.901 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;25.292 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 185 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1038 ; 0.017 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 682 ; 0.255 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 844 ; 0.321 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 140 ; 0.178 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 8 ; 0.117 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 50 ; 0.228 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.176 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 735 ; 1.555 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1206 ; 2.644 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 571 ; 3.569 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 585 ; 4.879 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3 ; 7.085 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY. REMARK 4 REMARK 4 2XR6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1290043684. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9797 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30348 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.340 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.1300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.820 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: PDB ENTRY 2IT6 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, HANGING DROP, 293K. REMARK 280 35% PEG 3350, 200MM NACL, 100MM CACODYLATE PH 6.5, CRYOPROTECTED REMARK 280 IN PARATONE-N REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.33300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.66500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.66500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.49950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.66500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.66500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 13.16650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.66500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.66500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 39.49950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.66500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.66500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 13.16650 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 26.33300 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2011 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2084 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 253 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 384 TO SER 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 235 REMARK 465 ALA A 236 REMARK 465 SER A 237 REMARK 465 TRP A 238 REMARK 465 SER A 239 REMARK 465 HIS A 240 REMARK 465 PRO A 241 REMARK 465 GLN A 242 REMARK 465 PHE A 243 REMARK 465 GLU A 244 REMARK 465 LYS A 245 REMARK 465 ILE A 246 REMARK 465 GLU A 247 REMARK 465 GLY A 248 REMARK 465 ARG A 249 REMARK 465 GLU A 250 REMARK 465 ARG A 251 REMARK 465 LEU A 252 REMARK 465 SER A 253 REMARK 465 HIS A 254 REMARK 465 SER A 385 REMARK 465 ARG A 386 REMARK 465 ASP A 387 REMARK 465 GLU A 388 REMARK 465 GLU A 389 REMARK 465 GLN A 390 REMARK 465 PHE A 391 REMARK 465 LEU A 392 REMARK 465 SER A 393 REMARK 465 PRO A 394 REMARK 465 ALA A 395 REMARK 465 PRO A 396 REMARK 465 ALA A 397 REMARK 465 THR A 398 REMARK 465 PRO A 399 REMARK 465 ASN A 400 REMARK 465 PRO A 401 REMARK 465 PRO A 402 REMARK 465 PRO A 403 REMARK 465 ALA A 404 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 ARG A 275 CB CG CD REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH2 ARG A 312 O HOH A 2070 2.05 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 259 10.88 87.88 REMARK 500 GLU A 259 13.92 88.16 REMARK 500 GLU A 353 121.12 57.98 REMARK 500 GLU A 353 78.15 97.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE PSEUDO TRIMANNOSIDE MIMIC COMPOSED OF RESIDUES A1385-A1388 REMARK 600 IS DIMETHYL (1S,2S,4S,5S)-4-(1-ALPHA-D-MANNOPYRANOSYL)-5-[6-[1- REMARK 600 (2-AZIDOETHYL)-ALPHA-D-MANNOPYRANOSYL]]-CYCLOHEXANE-1,2-DICARBOXYLAT 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 A1390 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 320 OD1 REMARK 620 2 ASP A 320 OD2 50.9 REMARK 620 3 GLU A 324 OE2 120.5 72.2 REMARK 620 4 GLU A 324 OE1 99.3 82.3 52.5 REMARK 620 5 ASN A 350 OD1 160.7 147.6 75.9 82.7 REMARK 620 6 GLU A 354 O 90.3 128.0 145.0 144.6 77.9 REMARK 620 7 ASP A 355 OD1 75.5 116.0 124.5 73.5 86.8 76.1 REMARK 620 8 HOH A2166 O 107.3 84.1 79.2 131.6 84.7 75.8 151.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1389 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 324 OE1 REMARK 620 2 GLU A 353 OE2 86.7 REMARK 620 3 GLU A 353 OE1 95.1 12.4 REMARK 620 4 ASP A 355 OD1 72.6 94.6 88.6 REMARK 620 5 ASP A 355 OD2 117.7 117.5 105.4 50.5 REMARK 620 6 HOH A2077 O 87.1 161.1 170.9 100.5 81.2 REMARK 620 7 HOH A2148 O 165.2 88.4 82.4 121.8 76.9 93.1 REMARK 620 8 HOH A2149 O 89.7 78.1 87.1 161.3 147.9 84.0 75.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1391 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 347 OE1 REMARK 620 2 ASN A 349 OD1 73.6 REMARK 620 3 GLU A 354 OE1 142.9 73.3 REMARK 620 4 ASN A 365 OD1 69.1 141.3 145.3 REMARK 620 5 ASP A 366 O 128.0 140.2 72.8 74.4 REMARK 620 6 ASP A 366 OD1 71.2 85.0 89.7 92.1 74.6 REMARK 620 7 MAN A1385 O3 134.5 118.7 77.3 82.7 72.8 147.2 REMARK 620 8 MAN A1385 O4 73.8 80.5 116.2 80.0 133.9 144.6 66.4 REMARK 620 N 1 2 3 4 5 6 7 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2B6B RELATED DB: PDB REMARK 900 CRYO EM STRUCTURE OF DENGUE COMPLEXED WITH CRD OF DC -SIGN REMARK 900 RELATED ID: 1SL4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DC-SIGN CARBOHYDRATE RECOGNITIONDOMAIN REMARK 900 COMPLEXED WITH MAN4 REMARK 900 RELATED ID: 1K9I RELATED DB: PDB REMARK 900 COMPLEX OF DC-SIGN AND GLCNAC2MAN3 REMARK 900 RELATED ID: 1SL5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DC-SIGN CARBOHYDRATE RECOGNITIONDOMAIN REMARK 900 COMPLEXED WITH LNFP III (DEXTRA L504). REMARK 900 RELATED ID: 2XR5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF THE CARBOHYDRATE RECOGNITION REMARK 900 DOMAIN OF HUMAN DC-SIGN WITH PSEUDO DIMANNOSIDE MIMIC. REMARK 999 REMARK 999 SEQUENCE REMARK 999 C235S, C384S, RESIDUES MASWSHPQFEKIEGR COMING FROM EXPRESSION PLASMI REMARK 999 COMING FROM EXPRESSION PLASMID WERE INSERTED AT THE N-TERMINUS DBREF 2XR6 A 250 404 UNP Q9NNX6 CD209_HUMAN 250 404 SEQADV 2XR6 MET A 235 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR6 ALA A 236 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR6 SER A 237 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR6 TRP A 238 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR6 SER A 239 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR6 HIS A 240 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR6 PRO A 241 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR6 GLN A 242 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR6 PHE A 243 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR6 GLU A 244 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR6 LYS A 245 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR6 ILE A 246 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR6 GLU A 247 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR6 GLY A 248 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR6 ARG A 249 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR6 SER A 253 UNP Q9NNX6 CYS 253 ENGINEERED MUTATION SEQADV 2XR6 SER A 384 UNP Q9NNX6 CYS 384 ENGINEERED MUTATION SEQRES 1 A 170 MET ALA SER TRP SER HIS PRO GLN PHE GLU LYS ILE GLU SEQRES 2 A 170 GLY ARG GLU ARG LEU SER HIS PRO CYS PRO TRP GLU TRP SEQRES 3 A 170 THR PHE PHE GLN GLY ASN CYS TYR PHE MET SER ASN SER SEQRES 4 A 170 GLN ARG ASN TRP HIS ASP SER ILE THR ALA CYS LYS GLU SEQRES 5 A 170 VAL GLY ALA GLN LEU VAL VAL ILE LYS SER ALA GLU GLU SEQRES 6 A 170 GLN ASN PHE LEU GLN LEU GLN SER SER ARG SER ASN ARG SEQRES 7 A 170 PHE THR TRP MET GLY LEU SER ASP LEU ASN GLN GLU GLY SEQRES 8 A 170 THR TRP GLN TRP VAL ASP GLY SER PRO LEU LEU PRO SER SEQRES 9 A 170 PHE LYS GLN TYR TRP ASN ARG GLY GLU PRO ASN ASN VAL SEQRES 10 A 170 GLY GLU GLU ASP CYS ALA GLU PHE SER GLY ASN GLY TRP SEQRES 11 A 170 ASN ASP ASP LYS CYS ASN LEU ALA LYS PHE TRP ILE CYS SEQRES 12 A 170 LYS LYS SER ALA ALA SER SER SER ARG ASP GLU GLU GLN SEQRES 13 A 170 PHE LEU SER PRO ALA PRO ALA THR PRO ASN PRO PRO PRO SEQRES 14 A 170 ALA HET MAN A1385 12 HET 07B A1386 14 HET MAN A1387 11 HET AE9 A1388 6 HET CA A1389 1 HET CA A1390 1 HET CA A1391 1 HET CL A1392 1 HET CL A1393 1 HET CL A1394 1 HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM 07B DIMETHYL (1S,2S,4S,5S)-4,5-DIHYDROXYCYCLOHEXANE-1,2- HETNAM 2 07B DICARBOXYLATE HETNAM AE9 2-AZIDOETHANOL HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 MAN 2(C6 H12 O6) FORMUL 3 07B C10 H16 O6 FORMUL 5 AE9 C2 H5 N3 O FORMUL 6 CA 3(CA 2+) FORMUL 9 CL 3(CL 1-) FORMUL 12 HOH *166(H2 O) HELIX 1 1 ASN A 276 VAL A 287 1 12 HELIX 2 2 SER A 296 ASN A 311 1 16 HELIX 3 3 LEU A 336 TYR A 342 5 7 SHEET 1 AA 5 THR A 261 PHE A 263 0 SHEET 2 AA 5 ASN A 266 MET A 270 -1 O ASN A 266 N PHE A 263 SHEET 3 AA 5 PHE A 374 SER A 380 -1 O CYS A 377 N PHE A 269 SHEET 4 AA 5 THR A 314 GLN A 323 1 O TRP A 315 N ILE A 376 SHEET 5 AA 5 THR A 326 TRP A 329 1 O THR A 326 N GLN A 323 SHEET 1 AB 4 THR A 261 PHE A 263 0 SHEET 2 AB 4 ASN A 266 MET A 270 -1 O ASN A 266 N PHE A 263 SHEET 3 AB 4 PHE A 374 SER A 380 -1 O CYS A 377 N PHE A 269 SHEET 4 AB 4 GLN A 290 LEU A 291 -1 O GLN A 290 N LYS A 378 SHEET 1 AC 2 THR A 326 TRP A 329 0 SHEET 2 AC 2 THR A 314 GLN A 323 1 O SER A 319 N GLN A 328 SHEET 1 AD 6 THR A 261 PHE A 263 0 SHEET 2 AD 6 ASN A 266 MET A 270 -1 O ASN A 266 N PHE A 263 SHEET 3 AD 6 PHE A 374 SER A 380 -1 O CYS A 377 N PHE A 269 SHEET 4 AD 6 THR A 314 GLN A 323 1 O TRP A 315 N ILE A 376 SHEET 5 AD 6 CYS A 356 SER A 360 -1 O ALA A 357 N MET A 316 SHEET 6 AD 6 GLY A 363 ASP A 367 -1 O GLY A 363 N SER A 360 SSBOND 1 CYS A 256 CYS A 267 1555 1555 2.08 SSBOND 2 CYS A 284 CYS A 377 1555 1555 2.04 SSBOND 3 CYS A 356 CYS A 369 1555 1555 2.00 LINK O1 MAN A1385 CBK 07B A1386 1555 1555 1.46 LINK CBJ 07B A1386 O6 MAN A1387 1555 1555 1.46 LINK C1 MAN A1387 O1 AE9 A1388 1555 1555 1.43 LINK OD1 ASP A 320 CA CA A1390 1555 1555 2.54 LINK OD2 ASP A 320 CA CA A1390 1555 1555 2.53 LINK OE1 GLU A 324 CA CA A1389 1555 1555 2.33 LINK OE2 GLU A 324 CA CA A1390 1555 1555 2.49 LINK OE1 GLU A 324 CA CA A1390 1555 1555 2.47 LINK OE1 GLU A 347 CA CA A1391 1555 1555 2.53 LINK OD1 ASN A 349 CA CA A1391 1555 1555 2.43 LINK OD1 ASN A 350 CA CA A1390 1555 1555 2.46 LINK OE2AGLU A 353 CA CA A1389 1555 1555 2.44 LINK OE1BGLU A 353 CA CA A1389 1555 1555 2.13 LINK O GLU A 354 CA CA A1390 1555 1555 2.43 LINK OE1 GLU A 354 CA CA A1391 1555 1555 2.45 LINK OD1 ASP A 355 CA CA A1389 1555 1555 2.57 LINK OD2 ASP A 355 CA CA A1389 1555 1555 2.50 LINK OD1 ASP A 355 CA CA A1390 1555 1555 2.38 LINK OD1 ASN A 365 CA CA A1391 1555 1555 2.41 LINK O ASP A 366 CA CA A1391 1555 1555 2.52 LINK OD1 ASP A 366 CA CA A1391 1555 1555 2.40 LINK O3 MAN A1385 CA CA A1391 1555 1555 2.50 LINK O4 MAN A1385 CA CA A1391 1555 1555 2.54 LINK CA CA A1389 O HOH A2077 1555 1555 2.37 LINK CA CA A1389 O HOH A2148 1555 1555 2.35 LINK CA CA A1389 O HOH A2149 1555 1555 2.43 LINK CA CA A1390 O HOH A2166 1555 1555 2.35 CISPEP 1 GLU A 347 PRO A 348 0 -8.37 CRYST1 71.330 71.330 52.666 90.00 90.00 90.00 P 43 21 2 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 0.014019 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014019 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018988 0.00000