HEADER SUGAR BINDING PROTEIN 24-SEP-00 1FWV
TITLE CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF MANNOSE RECEPTOR
TITLE 2 COMPLEXED WITH 3-SO4-LEWIS(A)
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(A)
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 3 29-JUL-20 1FWV 1 COMPND REMARK HETNAM LINK
REVDAT 3 2 1 SITE ATOM
REVDAT 2 24-FEB-09 1FWV 1 VERSN
REVDAT 1 17-JAN-01 1FWV 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. 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 : 7965
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) : 0.208
REMARK 3 FREE R VALUE : 0.230
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.300
REMARK 3 FREE R VALUE TEST SET COUNT : 505
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 : 127
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 32.70
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) : 0.007
REMARK 3 BOND ANGLES (DEGREES) : 1.270
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 1FWV 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_1000011968.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 21-FEB-00
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 : 8538
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 (%) : 96.5
REMARK 200 DATA REDUNDANCY : 7.600
REMARK 200 R MERGE (I) : 0.03400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.0000
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 (%) : 89.1
REMARK 200 DATA REDUNDANCY IN SHELL : 2.90
REMARK 200 R MERGE FOR SHELL (I) : 0.08100
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: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 53.21
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63
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 19.80400
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.82300
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.57900
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.82300
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.80400
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.57900
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 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 CB CG
REMARK 480 ASP A 86 CB CG OD1 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 O HOH A 2018 O HOH A 2087 2.10
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 -145.43 -119.03
REMARK 500 SER A 43 -178.13 -171.50
REMARK 500 THR A 68 -152.54 -129.50
REMARK 500 LYS A 84 -139.42 -91.96
REMARK 500 GLU A 95 42.28 -97.21
REMARK 500 GLN A 104 25.85 49.92
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 1FWV 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 SGA B 2 15
HET FUC B 3 10
HETNAM MAG METHYL 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSIDE
HETNAM SGA 3-O-SULFO-BETA-D-GALACTOPYRANOSE
HETNAM FUC ALPHA-L-FUCOPYRANOSE
FORMUL 2 MAG C9 H17 N O6
FORMUL 2 SGA C6 H12 O9 S
FORMUL 2 FUC C6 H12 O5
FORMUL 3 HOH *127(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 N LYS A 109 O 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 SGA B 2 1555 1555 1.44
LINK O4 MAG B 1 C1 FUC B 3 1555 1555 1.44
CRYST1 39.608 41.158 99.646 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 0.025247 0.000000 0.000000 0.00000
SCALE2 0.000000 0.024297 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010036 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
