HEADER SUGAR BINDING PROTEIN 24-SEP-00 1FWU TITLE CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF MANNOSE RECEPTOR TITLE 2 COMPLEXED WITH 3-SO4-LEWIS(X) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTEINE-RICH DOMAIN OF MANNOSE RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN OF MANNOSE RECEPTOR; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: COMPLEXED WITH 3-SO4-LEWIS(X) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: SUS SCROFA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: PIG; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9823; SOURCE 8 EXPRESSION_SYSTEM_CELL: 293 CELLS KEYWDS BETA TREFOIL, MANNOSE RECEPTOR, SULFATED CARBOHYDRATE, SUGAR BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,Z.MISULOVIN,P.J.BJORKMAN REVDAT 4 16-OCT-24 1FWU 1 REMARK HETSYN REVDAT 3 29-JUL-20 1FWU 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 24-FEB-09 1FWU 1 VERSN REVDAT 1 17-JAN-01 1FWU 0 JRNL AUTH Y.LIU,Z.MISULOVIN,P.J.BJORKMAN JRNL TITL THE MOLECULAR MECHANISM OF SULFATED CARBOHYDRATE RECOGNITION JRNL TITL 2 BY THE CYSTEINE-RICH DOMAIN OF MANNOSE RECEPTOR. JRNL REF J.MOL.BIOL. V. 305 481 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11152606 JRNL DOI 10.1006/JMBI.2000.4326 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 12433 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 SET) : 0.213 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.400 REMARK 3 FREE R VALUE TEST SET COUNT : 793 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1085 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.00 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FWU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1000011967. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-99 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13262 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.12300 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, (NH4)2SO4, PH 6.5 - 7.5, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 19.79500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.20000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.65000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.20000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.79500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.65000 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: MONOMERIC 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ALA A 3 CB REMARK 480 LYS A 14 CE NZ REMARK 480 ARG A 40 CG CD REMARK 480 LYS A 53 NZ REMARK 480 LYS A 75 CD CE NZ REMARK 480 LYS A 84 CE NZ REMARK 480 ASN A 85 CB CG REMARK 480 ASP A 86 CB OD2 REMARK 480 GLU A 95 OE1 OE2 REMARK 480 GLN A 104 CD OE1 NE2 REMARK 480 LYS A 121 CE 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 C ASP A 2 N ARG A 4 0.49 REMARK 500 N ALA A 3 N ARG A 4 1.11 REMARK 500 O ASP A 2 N ARG A 4 1.20 REMARK 500 O ASP A 2 CA ARG A 4 1.51 REMARK 500 OD2 ASP A 2 NH2 ARG A 40 1.54 REMARK 500 O ASP A 2 N GLN A 5 1.56 REMARK 500 C ALA A 3 CA ARG A 4 1.68 REMARK 500 O ASP A 2 C ARG A 4 1.70 REMARK 500 OD1 ASP A 2 CB ARG A 4 1.72 REMARK 500 C ASP A 2 CA ARG A 4 1.86 REMARK 500 O ALA A 3 O HOH A 2065 1.94 REMARK 500 CA ASP A 2 N ARG A 4 1.98 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 GLN A 26 -145.31 -118.76 REMARK 500 SER A 43 -176.35 -172.87 REMARK 500 THR A 68 -149.02 -132.02 REMARK 500 LYS A 84 -153.32 -91.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 MAG B 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DQG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF MANNOSE RECEPTOR DBREF 1FWU A 2 135 PIR A48925 A48925 21 154 SEQRES 1 A 134 ASP ALA ARG GLN PHE LEU ILE TYR ASN GLU ASP HIS LYS SEQRES 2 A 134 ARG CYS VAL ASP ALA LEU SER ALA ILE SER VAL GLN THR SEQRES 3 A 134 ALA THR CYS ASN PRO GLU ALA GLU SER GLN LYS PHE ARG SEQRES 4 A 134 TRP VAL SER ASP SER GLN ILE MET SER VAL ALA PHE LYS SEQRES 5 A 134 LEU CYS LEU GLY VAL PRO SER LYS THR ASP TRP ALA SER SEQRES 6 A 134 VAL THR LEU TYR ALA CYS ASP SER LYS SER GLU TYR GLN SEQRES 7 A 134 LYS TRP GLU CYS LYS ASN ASP THR LEU PHE GLY ILE LYS SEQRES 8 A 134 GLY THR GLU LEU TYR PHE ASN TYR GLY ASN ARG GLN GLU SEQRES 9 A 134 LYS ASN ILE LYS LEU TYR LYS GLY SER GLY LEU TRP SER SEQRES 10 A 134 ARG TRP LYS VAL TYR GLY THR THR ASP ASP LEU CYS SER SEQRES 11 A 134 ARG GLY TYR GLU HET MAG B 1 15 HET FUC B 2 10 HET SGA B 3 15 HETNAM MAG METHYL 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSIDE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM SGA 3-O-SULFO-BETA-D-GALACTOPYRANOSE HETSYN MAG BETA-METHYL-N-ACETYL-D-GLUCOSAMINE; METHYL 2-ACETAMIDO- HETSYN 2 MAG 2-DEOXY-BETA-D-GLUCOSIDE; METHYL 2-ACETAMIDO-2-DEOXY- HETSYN 3 MAG D-GLUCOSIDE; METHYL 2-ACETAMIDO-2-DEOXY-GLUCOSIDE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN SGA O3-SULFONYLGALACTOSE; 3-O-SULFO-BETA-D-GALACTOSE; 3-O- HETSYN 2 SGA SULFO-D-GALACTOSE; 3-O-SULFO-GALACTOSE FORMUL 2 MAG C9 H17 N O6 FORMUL 2 FUC C6 H12 O5 FORMUL 2 SGA C6 H12 O9 S FORMUL 3 HOH *130(H2 O) HELIX 1 1 ALA A 34 GLN A 37 5 4 HELIX 2 2 SER A 76 GLN A 79 5 4 HELIX 3 3 GLY A 101 GLU A 105 5 5 HELIX 4 4 GLY A 115 SER A 118 5 4 HELIX 5 5 LEU A 129 GLY A 133 5 5 SHEET 1 A 4 SER A 24 ALA A 28 0 SHEET 2 A 4 ARG A 15 SER A 21 -1 N CYS A 16 O ALA A 28 SHEET 3 A 4 ILE A 8 ASN A 10 -1 O ILE A 8 N VAL A 17 SHEET 4 A 4 LYS A 121 VAL A 122 -1 O LYS A 121 N TYR A 9 SHEET 1 B 4 PHE A 39 TRP A 41 0 SHEET 2 B 4 ILE A 47 SER A 49 -1 N MET A 48 O ARG A 40 SHEET 3 B 4 LEU A 54 GLY A 57 -1 O LEU A 54 N SER A 49 SHEET 4 B 4 THR A 68 TYR A 70 -1 O THR A 68 N GLY A 57 SHEET 1 C 2 TRP A 81 CYS A 83 0 SHEET 2 C 2 PHE A 89 ILE A 91 -1 O GLY A 90 N GLU A 82 SHEET 1 D 2 TYR A 97 ASN A 99 0 SHEET 2 D 2 LYS A 109 TYR A 111 -1 O LYS A 109 N ASN A 99 SSBOND 1 CYS A 16 CYS A 30 1555 1555 2.03 SSBOND 2 CYS A 55 CYS A 72 1555 1555 2.03 SSBOND 3 CYS A 83 CYS A 130 1555 1555 2.03 LINK O3 MAG B 1 C1 FUC B 2 1555 1555 1.44 LINK O4 MAG B 1 C1 SGA B 3 1555 1555 1.45 CRYST1 39.590 41.300 100.400 90.00 90.00 90.00 P 21 21 21 4 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 0.025259 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024213 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009960 0.00000