HEADER SUGAR BINDING PROTEIN 04-JAN-00 1DQO TITLE CRYSTAL STRUCTURE OF THE CYSTEINE RICH DOMAIN OF MANNOSE RECEPTOR TITLE 2 COMPLEXED WITH ACETYLGALACTOSAMINE-4-SULFATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MANNOSE RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CYSTEINE RICH DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 CELL_LINE: EPITHELIAL CELL; SOURCE 6 CELL: MACROPHAGE; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PIG KEYWDS BETA TREFOIL, MULTILECTIN RECEPTOR, PITUITARY HORMONES, SULFATED KEYWDS 2 CARBOHYDRATE, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,A.J.CHIRINO,Z.MISULOVIN,C.LETEUX,T.FEIZI,M.C.NUSSENZWEIG, AUTHOR 2 P.J.BJORKMAN REVDAT 5 13-NOV-24 1DQO 1 REMARK REVDAT 4 09-AUG-23 1DQO 1 REMARK HETSYN REVDAT 3 29-JUL-20 1DQO 1 COMPND REMARK HETNAM SITE REVDAT 3 2 1 ATOM REVDAT 2 24-FEB-09 1DQO 1 VERSN REVDAT 1 10-MAY-00 1DQO 0 JRNL AUTH Y.LIU,A.J.CHIRINO,Z.MISULOVIN,C.LETEUX,T.FEIZI, JRNL AUTH 2 M.C.NUSSENZWEIG,P.J.BJORKMAN JRNL TITL CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF MANNOSE JRNL TITL 2 RECEPTOR COMPLEXED WITH A SULFATED CARBOHYDRATE LIGAND. JRNL REF J.EXP.MED. V. 191 1105 2000 JRNL REFN ISSN 0022-1007 JRNL PMID 10748229 JRNL DOI 10.1084/JEM.191.7.1105 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 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 : 8639 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 483 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 : 18 REMARK 3 SOLVENT ATOMS : 153 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.10 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.490 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 1DQO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JAN-00. REMARK 100 THE DEPOSITION ID IS D_1000010301. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-98 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 6.5 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 : 8984 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.10500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 1DQG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, AMMONIUM SULFATE, PH 6.5, REMARK 280 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 19.71500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.15000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.74000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.15000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.71500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.74000 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 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 LEU A 1 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 ASP A 2 OD2 REMARK 480 ALA A 3 CB REMARK 480 LYS A 14 CD CE NZ REMARK 480 ASP A 44 OD1 REMARK 480 LYS A 53 NZ REMARK 480 LYS A 75 CD CE NZ REMARK 480 ASN A 85 CG OD1 ND2 REMARK 480 GLU A 95 OE1 OE2 REMARK 480 GLN A 104 CD OE1 NE2 REMARK 480 LYS A 121 CE REMARK 480 GLU A 135 OE1 OE2 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 -147.07 -118.00 REMARK 500 SER A 43 -177.19 -176.60 REMARK 500 THR A 68 -158.48 -131.53 REMARK 500 LYS A 84 -156.20 -98.92 REMARK 500 ASP A 86 62.74 31.43 REMARK 500 GLU A 95 50.41 -94.84 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 ASG A 2001 REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 ASG A 2001 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 1DQO A 1 135 UNP Q61830 MANR1_MOUSE 20 154 SEQRES 1 A 135 LEU ASP ALA ARG GLN PHE LEU ILE TYR ASN GLU ASP HIS SEQRES 2 A 135 LYS ARG CYS VAL ASP ALA LEU SER ALA ILE SER VAL GLN SEQRES 3 A 135 THR ALA THR CYS ASN PRO GLU ALA GLU SER GLN LYS PHE SEQRES 4 A 135 ARG TRP VAL SER ASP SER GLN ILE MET SER VAL ALA PHE SEQRES 5 A 135 LYS LEU CYS LEU GLY VAL PRO SER LYS THR ASP TRP ALA SEQRES 6 A 135 SER VAL THR LEU TYR ALA CYS ASP SER LYS SER GLU TYR SEQRES 7 A 135 GLN LYS TRP GLU CYS LYS ASN ASP THR LEU PHE GLY ILE SEQRES 8 A 135 LYS GLY THR GLU LEU TYR PHE ASN TYR GLY ASN ARG GLN SEQRES 9 A 135 GLU LYS ASN ILE LYS LEU TYR LYS GLY SER GLY LEU TRP SEQRES 10 A 135 SER ARG TRP LYS VAL TYR GLY THR THR ASP ASP LEU CYS SEQRES 11 A 135 SER ARG GLY TYR GLU HET ASG A2001 18 HETNAM ASG 2-ACETAMIDO-2-DEOXY-4-O-SULFO-BETA-D-GALACTOPYRANOSE HETSYN ASG 2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE; N- HETSYN 2 ASG ACETYL-4-O-SULFO-BETA-D-GALACTOSAMINE; 2-ACETAMIDO-2- HETSYN 3 ASG DEOXY-4-O-SULFO-BETA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY- HETSYN 4 ASG 4-O-SULFO-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-4-O-SULFO- HETSYN 5 ASG GALACTOSE FORMUL 2 ASG C8 H15 N O9 S FORMUL 3 HOH *153(H2 O) HELIX 1 1 ALA A 34 GLN A 37 5 4 HELIX 2 2 GLY A 115 SER A 118 5 4 HELIX 3 3 ASP A 128 GLY A 133 5 6 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 CRYST1 39.430 41.480 100.300 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 0.025361 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024108 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009970 0.00000