PDB Short entry for 2VM9 HEADER CELL ADHESION 24-JAN-08 2VM9 TITLE NATIVE STRUCTURE OF THE RECOMBINANT DISCOIDIN II OF TITLE 2 DICTYOSTELIUM DISCOIDEUM AT 1.75 ANGSTROM 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 3 08-JUN-11 2VM9 1 VERSN REVDAT 2 24-FEB-09 2VM9 1 VERSN REVDAT 1 01-JUL-08 2VM9 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 JRNL TITL 3 LECTIN 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. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 32309 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) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1725 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2317 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2020 REMARK 3 BIN FREE R VALUE SET COUNT : 131 REMARK 3 BIN FREE R VALUE : 0.2400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2027 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : -0.18000 REMARK 3 B12 (A**2) : 0.06000 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): 0.088 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.087 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.054 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.628 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2106 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2877 ; 1.492 ; 1.927 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 265 ; 6.956 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 105 ;36.070 ;24.476 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 336 ;12.345 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;16.014 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 314 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1625 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 945 ; 0.208 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1450 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 256 ; 0.131 ; 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): 110 ; 0.215 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 75 ; 0.203 ; 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): 1299 ; 0.814 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2081 ; 1.329 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 889 ; 2.089 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 791 ; 3.184 ; 4.500 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 REMARK 3 RIDING POSITIONS. 1-5 ARE DISORDERED. DISORDERED SIDE CHAIN REMARK 3 WERE MODELED STEREOCHEMICALLY REMARK 4 REMARK 4 2VM9 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JAN-08. REMARK 100 THE PDBE ID CODE IS EBI-33190. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34043 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.75 REMARK 200 RESOLUTION RANGE LOW (A) : 37.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.9 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.50 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11 REMARK 200 R MERGE FOR SHELL (I) : 0.35 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.10 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: MERCURY STRUCTURE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.7 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM AMMONIUM PHOSPHATE REMARK 280 MONOBASIC, 100 MM TRIS PH 8.5, 50 % MPD 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 40.91650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 23.62315 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 85.94100 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 40.91650 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 23.62315 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 85.94100 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 40.91650 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 23.62315 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 85.94100 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 40.91650 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 23.62315 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 85.94100 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 40.91650 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 23.62315 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 85.94100 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 40.91650 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 23.62315 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 85.94100 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 47.24630 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 171.88200 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 47.24630 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 171.88200 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 47.24630 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 171.88200 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 47.24630 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 171.88200 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 47.24630 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 171.88200 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 47.24630 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 171.88200 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: 16130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -249.2 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 P PO4 A 505 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 A2016 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2312 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2347 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 ASP A 39 -150.95 -127.64 REMARK 500 ASP A 42 109.15 -58.51 REMARK 500 SER A 51 160.31 177.15 REMARK 500 VAL A 100 -51.96 -125.23 REMARK 500 ALA A 113 -123.66 -119.56 REMARK 500 ASN A 143 -46.51 71.31 REMARK 500 REMARK 500 REMARK: NULL 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 91.8 REMARK 620 3 ASP A 47 OD1 75.7 113.1 REMARK 620 4 HOH A2088 O 100.4 165.1 78.4 REMARK 620 5 HOH A2070 O 151.4 93.6 126.9 71.6 REMARK 620 6 HOH A2072 O 135.2 72.8 72.7 103.4 73.0 REMARK 620 7 HOH A2091 O 73.9 83.8 145.5 91.5 78.8 141.7 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 511 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VMC RELATED DB: PDB REMARK 900 STRUCTURE OF THE COMPLEX OF DISCOIDIN II FROM REMARK 900 DICTYOSTELIUM DISCOIDEUM WITH N-ACETYL-GALACTOSAMINE REMARK 900 RELATED ID: 2VMD RELATED DB: PDB REMARK 900 STRUCTURE OF THE COMPLEX OF DISCOIDIN II FROM REMARK 900 DICTYOSTELIUM DISCOIDEUM WITH BETA-METHYL-GALACTOSE REMARK 900 RELATED ID: 2VME RELATED DB: PDB REMARK 900 STRUCTURE OF THE WILD-TYPE DISCOIDIN II REMARK 900 FROM DICTYOSTELIUM DISCOIDEUM DBREF 2VM9 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 CA A 500 1 HET MPD A 502 8 HET MPD A 503 8 HET PO4 A 505 5 HET PO4 A 506 5 HET PO4 A 507 5 HET CL A 509 1 HET CL A 510 1 HET CL A 511 1 HETNAM CA CALCIUM ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM PO4 PHOSPHATE ION HETNAM CL CHLORIDE ION FORMUL 2 CA CA 2+ FORMUL 3 MPD 2(C6 H14 O2) FORMUL 4 PO4 3(O4 P 3-) FORMUL 5 CL 3(CL 1-) FORMUL 6 HOH *370(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 O TRP A 87 N ASN A 142 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 -5 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 O VAL A 74 N PHE A 125 SHEET 3 AB 3 SER A 146 ALA A 153 0 O ARG A 148 N GLN A 79 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 CA CA A 500 OD1 ASN A 39 1555 1555 2.57 LINK CA CA A 500 O SER A 40 1555 1555 2.44 LINK CA CA A 500 OD1 ASP A 47 1555 1555 2.47 LINK CA CA A 500 O HOH A2088 1555 1555 2.42 LINK CA CA A 500 O HOH A2070 1555 1555 2.50 LINK CA CA A 500 O HOH A2072 1555 1555 2.78 LINK CA CA A 500 O HOH A2091 1555 1555 2.30 CISPEP 1 ASN A 126 PRO A 127 0 -1.18 SITE 1 AC1 7 ASN A 39 SER A 40 ASP A 47 HOH A2070 SITE 2 AC1 7 HOH A2072 HOH A2088 HOH A2091 SITE 1 AC2 7 TYR A 24 ARG A 81 GLN A 86 HIS A 144 SITE 2 AC2 7 PO4 A 507 HOH A2362 HOH A2363 SITE 1 AC3 8 ASP A 85 GLN A 86 THR A 140 ASN A 143 SITE 2 AC3 8 CL A 511 HOH A2363 HOH A2364 HOH A2365 SITE 1 AC4 3 VAL A 208 MET A 217 TRP A 219 SITE 1 AC5 2 SER A 7 HOH A2366 SITE 1 AC6 8 HIS A 28 PHE A 46 ARG A 81 MPD A 502 SITE 2 AC6 8 HOH A2367 HOH A2368 HOH A2369 HOH A2370 SITE 1 AC7 2 GLY A 239 HOH A2052 SITE 1 AC8 4 ASP A 58 LYS A 59 HOH A2039 HOH A2097 SITE 1 AC9 5 HIS A 84 ASP A 85 ARG A 117 MPD A 503 SITE 2 AC9 5 HOH A2365 CRYST1 81.833 81.833 257.823 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 0.012220 0.007055 0.000000 0.00000 SCALE2 0.000000 0.014110 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003879 0.00000