HEADER CELL ADHESION 25-JAN-08 2VMD TITLE STRUCTURE OF THE COMPLEX OF DISCOIDIN II FROM DICTYOSTELIUM DISCOIDEUM TITLE 2 WITH BETA-METHYL-GALACTOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISCOIDIN-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DISCOIDIN II; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICTYOSTELIUM DISCOIDEUM; SOURCE 3 ORGANISM_COMMON: SLIME MOLD; SOURCE 4 ORGANISM_TAXID: 366501; SOURCE 5 STRAIN: AX2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: ROSETTA2 PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PPROEXHTB KEYWDS DDR, LECTIN, AGGREGATION, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR K.S.ARAGAO,M.SATRE,A.IMBERTY,A.VARROT REVDAT 5 13-DEC-23 2VMD 1 HETSYN REVDAT 4 29-JUL-20 2VMD 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 08-JUN-11 2VMD 1 VERSN REVDAT 2 24-FEB-09 2VMD 1 VERSN REVDAT 1 01-JUL-08 2VMD 0 JRNL AUTH K.S.ARAGAO,M.SATRE,A.IMBERTY,A.VARROT JRNL TITL STRUCTURE DETERMINATION OF DISCOIDIN II FROM DICTYOSTELIUM JRNL TITL 2 DISCOIDEUM AND CARBOHYDRATE BINDING PROPERTIES OF THE LECTIN JRNL TITL 3 DOMAIN. JRNL REF PROTEINS V. 73 43 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 18384150 JRNL DOI 10.1002/PROT.22038 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 24868 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1326 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1745 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE SET COUNT : 94 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1986 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 228 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.58000 REMARK 3 B22 (A**2) : 1.58000 REMARK 3 B33 (A**2) : -2.37000 REMARK 3 B12 (A**2) : 0.79000 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): 0.131 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.133 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.096 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.276 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2075 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2814 ; 1.494 ; 1.925 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 253 ; 7.426 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;36.856 ;24.510 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 327 ;13.827 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;19.319 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 311 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1584 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 841 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1423 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 188 ; 0.137 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 100 ; 0.229 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 36 ; 0.150 ; 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): 1274 ; 0.878 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2040 ; 1.465 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 895 ; 2.361 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 774 ; 3.483 ; 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 : 1.40 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. RESIDUES 1-5 ARE DISORDERED.DISORDERED SIDE CHAINS REMARK 3 WERE MODELED STEREOCHEMICALLY REMARK 4 REMARK 4 2VMD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1290034033. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.99 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26194 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 36.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 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) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.06 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.350 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2VM9 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 % PEG550 MME, PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 40.57000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 23.42310 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 86.42667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 40.57000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 23.42310 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 86.42667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 40.57000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 23.42310 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 86.42667 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 40.57000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 23.42310 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 86.42667 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 40.57000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 23.42310 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 86.42667 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 40.57000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 23.42310 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 86.42667 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 46.84620 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 172.85333 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 46.84620 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 172.85333 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 46.84620 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 172.85333 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 46.84620 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 172.85333 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 46.84620 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 172.85333 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 46.84620 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 172.85333 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.7 KCAL/MOL 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 CL CL A 499 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2006 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2013 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2014 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2015 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2080 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2200 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2216 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 1 REMARK 465 SER A 2 REMARK 465 VAL A 3 REMARK 465 PRO A 4 REMARK 465 ALA A 5 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 ASN A 39 -147.65 -125.78 REMARK 500 SER A 51 160.87 174.78 REMARK 500 ALA A 113 -123.74 -119.09 REMARK 500 ASN A 143 -54.65 77.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 51 TRP A 52 149.50 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 A2006 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A2007 DISTANCE = 6.21 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY) REMARK 600 -ETHANOL (1PG): 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 1PG A 502 REMARK 610 1PG A 503 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 A 500 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 39 OD1 REMARK 620 2 SER A 40 O 95.9 REMARK 620 3 ASP A 47 OD1 76.2 111.3 REMARK 620 4 HOH A2051 O 149.5 85.5 131.6 REMARK 620 5 HOH A2056 O 143.5 76.8 73.6 66.5 REMARK 620 6 HOH A2064 O 97.4 165.6 77.5 80.2 95.6 REMARK 620 7 HOH A2065 O 75.7 89.1 146.6 73.9 138.7 88.7 REMARK 620 N 1 2 3 4 5 6 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VM9 RELATED DB: PDB REMARK 900 NATIVE STRUCTURE OF THE RECOMBINANT DISCOIDIN II OF DICTYOSTELIUM REMARK 900 DISCOIDEUM AT 1.75 ANGSTROM REMARK 900 RELATED ID: 2VMC RELATED DB: PDB REMARK 900 STRUCTURE OF THE COMPLEX OF DISCOIDIN II FROM DICTYOSTELIUM REMARK 900 DISCOIDEUM WITH N-ACETYL-GALACTOSAMINE REMARK 900 RELATED ID: 2VME RELATED DB: PDB REMARK 900 STRUCTURE OF THE WILD-TYPE DISCOIDIN II FROM DICTYOSTELIUM REMARK 900 DISCOIDEUM DBREF 2VMD A 1 257 UNP P42530 DIS2_DICDI 1 257 SEQRES 1 A 257 MET SER VAL PRO ALA GLY SER VAL SER CYS LEU ALA ASN SEQRES 2 A 257 ALA LEU LEU ASN LEU ARG SER SER THR ASP TYR ASN ALA SEQRES 3 A 257 ASP HIS GLY VAL LYS ASN SER ILE LEU ASN PHE SER ASN SEQRES 4 A 257 SER LYS ASP ALA SER ARG PHE ASP GLY SER GLU SER TRP SEQRES 5 A 257 SER SER SER VAL LEU ASP LYS ASN GLN PHE ILE VAL ALA SEQRES 6 A 257 GLY SER ASP SER VAL LYS HIS PHE VAL ALA ILE SER THR SEQRES 7 A 257 GLN GLY ARG GLY ASP HIS ASP GLN TRP VAL THR SER TYR SEQRES 8 A 257 LYS LEU ARG TYR THR LEU ASP ASN VAL ASN TRP VAL GLU SEQRES 9 A 257 TYR ASN ASN GLY GLU ILE ILE ASN ALA ASN LYS ASP ARG SEQRES 10 A 257 ASN SER ILE VAL THR ILE ASN PHE ASN PRO PRO ILE LYS SEQRES 11 A 257 ALA ARG SER ILE ALA ILE HIS PRO GLN THR TYR ASN ASN SEQRES 12 A 257 HIS ILE SER LEU ARG TRP GLU LEU TYR ALA LEU PRO VAL SEQRES 13 A 257 LYS SER TYR SER ASN PRO SER VAL GLN VAL GLY GLU VAL SEQRES 14 A 257 SER ILE GLY ASP ARG SER LEU ASN SER GLY THR GLY SER SEQRES 15 A 257 ARG THR ILE VAL ARG HIS VAL LYS PHE PRO VAL GLU PHE SEQRES 16 A 257 LEU SER VAL PRO ILE VAL SER ILE GLY CYS LYS LYS VAL SEQRES 17 A 257 ASP ALA HIS THR ASP ASN GLY GLN MET ARG TRP GLU GLY SEQRES 18 A 257 LYS SER GLU ASN ILE THR THR LYS GLY PHE ASP LEU THR SEQRES 19 A 257 PHE ILE THR TRP GLY ASN ASN ALA VAL TYR ASP LEU THR SEQRES 20 A 257 PHE ASP TYR VAL ALA VAL GLU PHE ASN ASN HET CL A 499 1 HET CA A 500 1 HET MBG A 501 13 HET 1PG A 502 11 HET 1PG A 503 7 HET EDO A 504 4 HETNAM CL CHLORIDE ION HETNAM CA CALCIUM ION HETNAM MBG METHYL BETA-D-GALACTOPYRANOSIDE HETNAM 1PG 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)- HETNAM 2 1PG ETHANOL HETNAM EDO 1,2-ETHANEDIOL HETSYN MBG METHYL-BETA-GALACTOSE; METHYL BETA-D-GALACTOSIDE; HETSYN 2 MBG METHYL D-GALACTOSIDE; METHYL GALACTOSIDE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 CL CL 1- FORMUL 3 CA CA 2+ FORMUL 4 MBG C7 H14 O6 FORMUL 5 1PG 2(C11 H24 O6) FORMUL 7 EDO C2 H6 O2 FORMUL 8 HOH *228(H2 O) HELIX 1 1 CYS A 10 ALA A 14 1 5 SHEET 1 AA 6 ASN A 17 SER A 20 0 SHEET 2 AA 6 ILE A 63 GLY A 66 -1 O VAL A 64 N ARG A 19 SHEET 3 AA 6 ILE A 129 ASN A 142 -1 O ILE A 134 N ALA A 65 SHEET 4 AA 6 TRP A 87 THR A 96 0 SHEET 5 AA 6 TRP A 102 GLU A 104 -1 O VAL A 103 N TYR A 95 SHEET 6 AA 6 ILE A 111 ASN A 114 -1 O ILE A 111 N TYR A 91 SHEET 1 AB 3 VAL A 121 PHE A 125 0 SHEET 2 AB 3 LYS A 71 GLN A 79 0 SHEET 3 AB 3 SER A 146 ALA A 153 0 SHEET 1 AC 3 SER A 163 SER A 170 0 SHEET 2 AC 3 VAL A 243 GLU A 254 -1 O PHE A 248 N VAL A 169 SHEET 3 AC 3 ILE A 200 ALA A 210 -1 O ILE A 200 N VAL A 253 SHEET 1 AD 3 ARG A 183 LYS A 190 0 SHEET 2 AD 3 GLY A 230 THR A 237 -1 O PHE A 231 N VAL A 189 SHEET 3 AD 3 GLU A 220 GLU A 224 -1 O GLU A 220 N ILE A 236 LINK OD1 ASN A 39 CA CA A 500 1555 1555 2.48 LINK O SER A 40 CA CA A 500 1555 1555 2.30 LINK OD1 ASP A 47 CA CA A 500 1555 1555 2.50 LINK CA CA A 500 O HOH A2051 1555 1555 2.54 LINK CA CA A 500 O HOH A2056 1555 1555 2.71 LINK CA CA A 500 O HOH A2064 1555 1555 2.35 LINK CA CA A 500 O HOH A2065 1555 1555 2.32 CISPEP 1 ASN A 126 PRO A 127 0 -1.34 CRYST1 81.140 81.140 259.280 90.00 90.00 120.00 H 3 2 18 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 0.012324 0.007115 0.000000 0.00000 SCALE2 0.000000 0.014231 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003857 0.00000