HEADER SUGAR BINDING PROTEIN 10-SEP-10 2XR5 TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF THE CARBOHYDRATE RECOGNITION TITLE 2 DOMAIN OF HUMAN DC-SIGN WITH PSEUDO DIMANNOSIDE MIMIC. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD209 ANTIGEN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CARBOHYDRATE RECOGNITION DOMAIN, RESIDUES 254-404; 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 MDC-SIGN1A TYPE I; COMPND 8 ENGINEERED: 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 EXPDTA X-RAY DIFFRACTION AUTHOR M.THEPAUT,I.SUITKEVICIUTE,S.SATTIN,J.REINA,A.BERNARDI,F.FIESCHI REVDAT 7 20-DEC-23 2XR5 1 REMARK REVDAT 6 15-NOV-23 2XR5 1 HETSYN LINK ATOM REVDAT 5 29-JUL-20 2XR5 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 06-MAR-19 2XR5 1 REMARK LINK REVDAT 3 30-JAN-19 2XR5 1 REMARK REVDAT 2 25-DEC-13 2XR5 1 JRNL REVDAT 1 19-OCT-11 2XR5 0 JRNL AUTH M.THEPAUT,C.GUZZI,I.SUTKEVICIUTE,S.SATTIN,R.RIBEIRO-VIANA, JRNL AUTH 2 N.VARGA,E.CHABROL,J.ROJO,A.BERNARDI,J.ANGULO,P.M.NIETO, JRNL AUTH 3 F.FIESCHI JRNL TITL STRUCTURE OF A GLYCOMIMETIC LIGAND IN THE CARBOHYDRATE JRNL TITL 2 RECOGNITION DOMAIN OF C-TYPE LECTIN DC-SIGN. STRUCTURAL JRNL TITL 3 REQUIREMENTS FOR SELECTIVITY AND LIGAND DESIGN. JRNL REF J.AM.CHEM.SOC. V. 135 2518 2013 JRNL REFN ISSN 0002-7863 JRNL PMID 23360500 JRNL DOI 10.1021/JA3053305 REMARK 2 REMARK 2 RESOLUTION. 1.42 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 24628 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) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1297 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) : 1.42 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1672 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1750 REMARK 3 BIN FREE R VALUE SET COUNT : 88 REMARK 3 BIN FREE R VALUE : 0.2140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1064 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 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) : 13.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : 0.08000 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): 0.059 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.059 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.033 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.843 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1291 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1779 ; 1.553 ; 1.915 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 176 ; 6.865 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 72 ;38.118 ;25.417 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 208 ;13.676 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;17.542 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 179 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1040 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 621 ; 0.269 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 843 ; 0.317 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 125 ; 0.201 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.048 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 59 ; 0.244 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.231 ; 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): 738 ; 1.497 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1194 ; 2.659 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 553 ; 3.554 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 561 ; 4.978 ; 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): NULL ; NULL ; NULL 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 : 1.20 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 2XR5 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_1290045251. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-08 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 : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9809 REMARK 200 MONOCHROMATOR : CHANNEL-CUT SILICON REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25925 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 42.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 25.40 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.6700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.22 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.560 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 20% PEG 3350, 200 MM NACL, 100 MM CACODYLATE PH 6.5, REMARK 280 CRYOPROTECTED 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 26.33500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.72500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.72500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.50250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.72500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.72500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 13.16750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.72500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.72500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 39.50250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.72500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.72500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 13.16750 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 26.33500 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 A2009 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2070 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2133 LIES ON A SPECIAL POSITION. 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 239 REMARK 465 ALA A 240 REMARK 465 SER A 241 REMARK 465 TRP A 242 REMARK 465 SER A 243 REMARK 465 HIS A 244 REMARK 465 PRO A 245 REMARK 465 GLN A 246 REMARK 465 PHE A 247 REMARK 465 GLU A 248 REMARK 465 LYS A 249 REMARK 465 ILE A 250 REMARK 465 GLU A 251 REMARK 465 GLY A 252 REMARK 465 ARG A 253 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 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 NE2 GLN A 341 O HOH A 2108 1.81 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 -20.82 86.68 REMARK 500 GLU A 353 102.96 79.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2156 DISTANCE = 6.97 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE PSEUDO DIMANNOSIDE MIMIC COMPOSED OF RESIDUES A1384-A1386 REMARK 600 IS DIMETHYL (1S,2S,4S,5S)-4-(1-ALPHA-D-MANNOPYRANOSYL)-5-(2- REMARK 600 AMINO-1-ETHYLOXY)-CYCLOHEXANE-1,2-DICARBOXYLATE 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 A1388 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 320 OD2 REMARK 620 2 ASP A 320 OD1 49.7 REMARK 620 3 GLU A 324 OE1 82.4 100.1 REMARK 620 4 GLU A 324 OE2 71.8 119.6 53.0 REMARK 620 5 ASN A 350 OD1 147.5 162.1 82.1 76.0 REMARK 620 6 GLU A 354 O 127.3 90.5 145.7 144.2 78.5 REMARK 620 7 ASP A 355 OD1 115.4 76.2 74.3 126.1 87.4 76.8 REMARK 620 8 HOH A2147 O 84.2 106.4 130.9 77.9 84.7 75.1 151.8 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 OE1 90.5 REMARK 620 3 ASP A 355 OD1 71.0 95.0 REMARK 620 4 ASP A 355 OD2 116.6 114.5 50.7 REMARK 620 5 HOH A2066 O 87.5 164.6 98.8 79.8 REMARK 620 6 HOH A2131 O 89.7 79.5 160.0 148.8 85.3 REMARK 620 7 HOH A2135 O 167.3 84.8 121.1 76.0 93.9 77.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1387 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 347 OE1 REMARK 620 2 ASN A 349 OD1 72.9 REMARK 620 3 GLU A 354 OE1 144.1 74.1 REMARK 620 4 ASN A 365 OD1 68.8 140.6 145.3 REMARK 620 5 ASP A 366 O 128.8 141.8 73.8 73.7 REMARK 620 6 ASP A 366 OD1 72.5 84.2 90.7 92.9 76.0 REMARK 620 7 MAN A1384 O3 133.0 119.2 76.5 82.4 72.0 147.7 REMARK 620 8 MAN A1384 O4 73.1 79.8 114.1 80.6 132.9 145.0 65.9 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: 2XR6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF THE CARBOHYDRATE RECOGNITION REMARK 900 DOMAIN OF HUMAN DC-SIGN WITH PSEUDO TRIMANNOSIDE MIMIC. 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 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE NUMBERING CORRESPONDS TO ISOFORM 1 (MDC-SIGN1A TYPE I). REMARK 999 THE SIXTEEN RESIDUES INSERTED AT THE N-TERMINUS (MASWSHPQFEKIEGRM) REMARK 999 COME FROM THE EXPRESSION PLASMID. DBREF 2XR5 A 254 404 UNP Q9NNX6 CD209_HUMAN 254 404 SEQADV 2XR5 MET A 239 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR5 ALA A 240 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR5 SER A 241 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR5 TRP A 242 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR5 SER A 243 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR5 HIS A 244 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR5 PRO A 245 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR5 GLN A 246 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR5 PHE A 247 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR5 GLU A 248 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR5 LYS A 249 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR5 ILE A 250 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR5 GLU A 251 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR5 GLY A 252 UNP Q9NNX6 EXPRESSION TAG SEQADV 2XR5 ARG A 253 UNP Q9NNX6 EXPRESSION TAG SEQRES 1 A 166 MET ALA SER TRP SER HIS PRO GLN PHE GLU LYS ILE GLU SEQRES 2 A 166 GLY ARG HIS PRO CYS PRO TRP GLU TRP THR PHE PHE GLN SEQRES 3 A 166 GLY ASN CYS TYR PHE MET SER ASN SER GLN ARG ASN TRP SEQRES 4 A 166 HIS ASP SER ILE THR ALA CYS LYS GLU VAL GLY ALA GLN SEQRES 5 A 166 LEU VAL VAL ILE LYS SER ALA GLU GLU GLN ASN PHE LEU SEQRES 6 A 166 GLN LEU GLN SER SER ARG SER ASN ARG PHE THR TRP MET SEQRES 7 A 166 GLY LEU SER ASP LEU ASN GLN GLU GLY THR TRP GLN TRP SEQRES 8 A 166 VAL ASP GLY SER PRO LEU LEU PRO SER PHE LYS GLN TYR SEQRES 9 A 166 TRP ASN ARG GLY GLU PRO ASN ASN VAL GLY GLU GLU ASP SEQRES 10 A 166 CYS ALA GLU PHE SER GLY ASN GLY TRP ASN ASP ASP LYS SEQRES 11 A 166 CYS ASN LEU ALA LYS PHE TRP ILE CYS LYS LYS SER ALA SEQRES 12 A 166 ALA SER CYS SER ARG ASP GLU GLU GLN PHE LEU SER PRO SEQRES 13 A 166 ALA PRO ALA THR PRO ASN PRO PRO PRO ALA HET MAN A1384 12 HET 07B A1385 14 HET ETA A1386 4 HET CA A1387 1 HET CA A1388 1 HET CA A1389 1 HET CL A1390 1 HET CL A1391 1 HET CL A1392 1 HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM 07B DIMETHYL (1S,2S,4S,5S)-4,5-DIHYDROXYCYCLOHEXANE-1,2- HETNAM 2 07B DICARBOXYLATE HETNAM ETA ETHANOLAMINE HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 MAN C6 H12 O6 FORMUL 3 07B C10 H16 O6 FORMUL 4 ETA C2 H7 N O FORMUL 5 CA 3(CA 2+) FORMUL 8 CL 3(CL 1-) FORMUL 11 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 HELIX 4 4 ALA A 382 CYS A 384 5 3 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 2.10 SSBOND 2 CYS A 284 CYS A 377 1555 1555 2.14 SSBOND 3 CYS A 356 CYS A 369 1555 1555 2.02 LINK O1 MAN A1384 CBJ 07B A1385 1555 1555 1.44 LINK CBK 07B A1385 O ETA A1386 1555 1555 1.43 LINK OD2 ASP A 320 CA CA A1388 1555 1555 2.54 LINK OD1 ASP A 320 CA CA A1388 1555 1555 2.56 LINK OE1 GLU A 324 CA CA A1388 1555 1555 2.41 LINK OE2 GLU A 324 CA CA A1388 1555 1555 2.54 LINK OE1 GLU A 324 CA CA A1389 1555 1555 2.36 LINK OE1 GLU A 347 CA CA A1387 1555 1555 2.52 LINK OD1 ASN A 349 CA CA A1387 1555 1555 2.40 LINK OD1 ASN A 350 CA CA A1388 1555 1555 2.40 LINK OE1 GLU A 353 CA CA A1389 1555 1555 2.36 LINK OE1 GLU A 354 CA CA A1387 1555 1555 2.40 LINK O GLU A 354 CA CA A1388 1555 1555 2.42 LINK OD1 ASP A 355 CA CA A1388 1555 1555 2.34 LINK OD1 ASP A 355 CA CA A1389 1555 1555 2.57 LINK OD2 ASP A 355 CA CA A1389 1555 1555 2.53 LINK OD1 ASN A 365 CA CA A1387 1555 1555 2.39 LINK O ASP A 366 CA CA A1387 1555 1555 2.45 LINK OD1 ASP A 366 CA CA A1387 1555 1555 2.35 LINK O3 MAN A1384 CA CA A1387 1555 1555 2.52 LINK O4 MAN A1384 CA CA A1387 1555 1555 2.43 LINK CA CA A1388 O HOH A2147 1555 1555 2.39 LINK CA CA A1389 O HOH A2066 1555 1555 2.37 LINK CA CA A1389 O HOH A2131 1555 1555 2.41 LINK CA CA A1389 O HOH A2135 1555 1555 2.35 CISPEP 1 GLU A 347 PRO A 348 0 -5.81 CRYST1 71.450 71.450 52.670 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 0.013996 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013996 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018986 0.00000