HEADER CELL ADHESION 21-JAN-09 2W94 TITLE NATIVE STRUCTURE OF THE DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM AT TITLE 2 1.8 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISCOIDIN-1 SUBUNIT A; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: DISCOIDIN I, DISCOIDIN-1 SUBUNIT ALPHA, DISCOIDIN I CHAIN A; 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: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPROEXHTB KEYWDS CELL ADHESION, H TYPE LECTIN EXPDTA X-RAY DIFFRACTION AUTHOR K.SABOIA ARAGAO,A.IMBERTY,A.VARROT REVDAT 5 13-DEC-23 2W94 1 REMARK LINK REVDAT 4 21-JUL-10 2W94 1 JRNL REMARK REVDAT 3 07-JUL-10 2W94 1 JRNL REVDAT 2 26-MAY-10 2W94 1 JRNL FORMUL REVDAT 1 31-MAR-10 2W94 0 JRNL AUTH S.MATHIEU,K.SABOIA ARAGAO,A.IMBERTY,A.VARROT JRNL TITL DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM AND INTERACTIONS JRNL TITL 2 WITH OLIGOSACCHARIDES: SPECIFICITY, AFFINITY, CRYSTAL JRNL TITL 3 STRUCTURES AND COMPARISON WITH DISCOIDIN II. JRNL REF J.MOL.BIOL. V. 400 540 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20580724 JRNL DOI 10.1016/J.JMB.2010.05.042 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 71665 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3802 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4683 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE SET COUNT : 245 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5975 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 981 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.31000 REMARK 3 B22 (A**2) : -2.32000 REMARK 3 B33 (A**2) : 1.01000 REMARK 3 B12 (A**2) : 0.00000 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): 0.123 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.120 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.447 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6158 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 5323 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8406 ; 1.496 ; 1.920 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12323 ; 0.695 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 757 ; 7.365 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 309 ;35.000 ;24.272 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 933 ;11.892 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;20.859 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 945 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6967 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1309 ; 0.000 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 3773 ; 0.839 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6124 ; 1.379 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2385 ; 2.190 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2282 ; 3.171 ; 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. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY REMARK 4 REMARK 4 2W94 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1290038601. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-07 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 : 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 CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29532 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 28.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2VM9 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M LISO4 100 MM HEPES 7.5, PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.96400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.96400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 36.26500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 137.18550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.26500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 137.18550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.96400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.26500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 137.18550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 42.96400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.26500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 137.18550 REMARK 290 SMTRY3 8 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -142.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 HOH B2038 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2039 LIES ON A SPECIAL POSITION. REMARK 375 HOH C2081 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 ALA B 0 REMARK 465 ALA C 0 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 OG SER B 156 O HOH B 2232 2.16 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 ASN A 38 -161.57 -128.12 REMARK 500 ALA A 49 159.40 169.14 REMARK 500 THR A 211 53.34 37.21 REMARK 500 ASN A 236 -141.51 50.99 REMARK 500 ASN B 24 -167.09 -160.74 REMARK 500 ASN B 38 -164.02 -121.60 REMARK 500 ALA B 49 158.81 176.34 REMARK 500 VAL B 98 -58.05 -125.41 REMARK 500 ASP B 164 42.75 70.07 REMARK 500 ASN B 236 -142.49 58.00 REMARK 500 ASN C 38 -163.58 -125.40 REMARK 500 ALA C 49 158.76 169.33 REMARK 500 ASN C 236 -142.73 55.12 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 B2049 DISTANCE = 6.27 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 2-METHYL-2,4-PENTANEDIOL (MPD): CYOPROTECTANT 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 NI A1258 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 16 ND1 REMARK 620 2 HIS B 16 ND1 108.6 REMARK 620 3 HIS C 16 ND1 110.9 112.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1257 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 164 OD1 REMARK 620 2 ASP A 203 OD2 87.4 REMARK 620 3 ASP A 246 OD2 128.3 98.9 REMARK 620 4 ASP A 246 OD1 78.5 92.6 50.2 REMARK 620 5 GLN B 219 OE1 81.2 85.3 150.2 159.6 REMARK 620 6 HOH B2281 O 90.4 176.0 85.1 90.3 91.0 REMARK 620 7 HOH B2282 O 153.5 80.9 77.2 125.4 74.3 99.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C1257 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 219 OE1 REMARK 620 2 HOH A2288 O 91.4 REMARK 620 3 HOH A2289 O 75.1 97.5 REMARK 620 4 ASP C 164 OD1 83.5 92.6 156.4 REMARK 620 5 ASP C 203 OD2 88.8 179.4 82.0 87.9 REMARK 620 6 ASP C 246 OD2 147.3 81.6 74.2 128.5 97.9 REMARK 620 7 ASP C 246 OD1 163.6 91.1 120.6 80.2 88.8 49.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1256 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 164 OD1 REMARK 620 2 ASP B 203 OD2 88.7 REMARK 620 3 ASP B 246 OD2 128.3 97.3 REMARK 620 4 ASP B 246 OD1 78.7 87.9 50.5 REMARK 620 5 GLN C 219 OE1 81.5 88.7 149.5 160.0 REMARK 620 6 HOH C2263 O 94.0 175.7 83.5 95.8 88.5 REMARK 620 7 HOH C2264 O 157.0 82.1 74.1 121.8 77.2 94.2 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 MPD A 1254 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1255 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1256 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1257 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1258 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1254 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1255 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1256 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD C 1254 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD C 1255 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 1256 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 1257 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2W95 RELATED DB: PDB REMARK 900 STRUCTURE OF THE DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM IN REMARK 900 COMPLEX WITH GALNAC AT 1.75 ANGSTROM RESOLUTION REMARK 999 REMARK 999 SEQUENCE REMARK 999 FIRST RESIDUE IS ADDED FOLLOWING THE CLEAVAGE OF THE REMARK 999 N TERMINAL HIS TAG DBREF 2W94 A 0 0 PDB 2W94 2W94 0 0 DBREF 2W94 A 1 253 UNP P02886 DIS1A_DICDI 1 253 DBREF 2W94 B 0 0 PDB 2W94 2W94 0 0 DBREF 2W94 B 1 253 UNP P02886 DIS1A_DICDI 1 253 DBREF 2W94 C 0 0 PDB 2W94 2W94 0 0 DBREF 2W94 C 1 253 UNP P02886 DIS1A_DICDI 1 253 SEQRES 1 A 254 ALA MET SER THR GLN GLY LEU VAL GLN LEU LEU ALA ASN SEQRES 2 A 254 ALA GLN CYS HIS LEU ARG THR SER THR ASN TYR ASN GLY SEQRES 3 A 254 VAL HIS THR GLN PHE ASN SER ALA LEU ASN TYR LYS ASN SEQRES 4 A 254 ASN GLY THR ASN THR ILE ASP GLY SER GLU ALA TRP CYS SEQRES 5 A 254 SER SER ILE VAL ASP THR ASN GLN TYR ILE VAL ALA GLY SEQRES 6 A 254 CYS GLU VAL PRO ARG THR PHE MET CYS VAL ALA LEU GLN SEQRES 7 A 254 GLY ARG GLY ASP ALA ASP GLN TRP VAL THR SER TYR LYS SEQRES 8 A 254 ILE ARG TYR SER LEU ASP ASN VAL SER TRP PHE GLU TYR SEQRES 9 A 254 ARG ASN GLY ALA ALA VAL THR GLY VAL THR ASP ARG ASN SEQRES 10 A 254 THR VAL VAL ASN HIS PHE PHE ASP THR PRO ILE ARG ALA SEQRES 11 A 254 ARG SER ILE ALA ILE HIS PRO LEU THR TRP ASN GLY HIS SEQRES 12 A 254 ILE SER LEU ARG CYS GLU PHE TYR THR GLN PRO VAL GLN SEQRES 13 A 254 SER SER VAL THR GLN VAL GLY ALA ASP ILE TYR THR GLY SEQRES 14 A 254 ASP ASN CYS ALA LEU ASN THR GLY SER GLY LYS ARG GLU SEQRES 15 A 254 VAL VAL VAL PRO VAL LYS PHE GLN PHE GLU PHE ALA THR SEQRES 16 A 254 LEU PRO LYS VAL ALA LEU ASN PHE ASP GLN ILE ASP CYS SEQRES 17 A 254 THR ASP ALA THR ASN GLN THR ARG ILE GLY VAL GLN PRO SEQRES 18 A 254 ARG ASN ILE THR THR LYS GLY PHE ASP CYS VAL PHE TYR SEQRES 19 A 254 THR TRP ASN GLU ASN LYS VAL TYR SER LEU ARG ALA ASP SEQRES 20 A 254 TYR ILE ALA THR ALA LEU GLU SEQRES 1 B 254 ALA MET SER THR GLN GLY LEU VAL GLN LEU LEU ALA ASN SEQRES 2 B 254 ALA GLN CYS HIS LEU ARG THR SER THR ASN TYR ASN GLY SEQRES 3 B 254 VAL HIS THR GLN PHE ASN SER ALA LEU ASN TYR LYS ASN SEQRES 4 B 254 ASN GLY THR ASN THR ILE ASP GLY SER GLU ALA TRP CYS SEQRES 5 B 254 SER SER ILE VAL ASP THR ASN GLN TYR ILE VAL ALA GLY SEQRES 6 B 254 CYS GLU VAL PRO ARG THR PHE MET CYS VAL ALA LEU GLN SEQRES 7 B 254 GLY ARG GLY ASP ALA ASP GLN TRP VAL THR SER TYR LYS SEQRES 8 B 254 ILE ARG TYR SER LEU ASP ASN VAL SER TRP PHE GLU TYR SEQRES 9 B 254 ARG ASN GLY ALA ALA VAL THR GLY VAL THR ASP ARG ASN SEQRES 10 B 254 THR VAL VAL ASN HIS PHE PHE ASP THR PRO ILE ARG ALA SEQRES 11 B 254 ARG SER ILE ALA ILE HIS PRO LEU THR TRP ASN GLY HIS SEQRES 12 B 254 ILE SER LEU ARG CYS GLU PHE TYR THR GLN PRO VAL GLN SEQRES 13 B 254 SER SER VAL THR GLN VAL GLY ALA ASP ILE TYR THR GLY SEQRES 14 B 254 ASP ASN CYS ALA LEU ASN THR GLY SER GLY LYS ARG GLU SEQRES 15 B 254 VAL VAL VAL PRO VAL LYS PHE GLN PHE GLU PHE ALA THR SEQRES 16 B 254 LEU PRO LYS VAL ALA LEU ASN PHE ASP GLN ILE ASP CYS SEQRES 17 B 254 THR ASP ALA THR ASN GLN THR ARG ILE GLY VAL GLN PRO SEQRES 18 B 254 ARG ASN ILE THR THR LYS GLY PHE ASP CYS VAL PHE TYR SEQRES 19 B 254 THR TRP ASN GLU ASN LYS VAL TYR SER LEU ARG ALA ASP SEQRES 20 B 254 TYR ILE ALA THR ALA LEU GLU SEQRES 1 C 254 ALA MET SER THR GLN GLY LEU VAL GLN LEU LEU ALA ASN SEQRES 2 C 254 ALA GLN CYS HIS LEU ARG THR SER THR ASN TYR ASN GLY SEQRES 3 C 254 VAL HIS THR GLN PHE ASN SER ALA LEU ASN TYR LYS ASN SEQRES 4 C 254 ASN GLY THR ASN THR ILE ASP GLY SER GLU ALA TRP CYS SEQRES 5 C 254 SER SER ILE VAL ASP THR ASN GLN TYR ILE VAL ALA GLY SEQRES 6 C 254 CYS GLU VAL PRO ARG THR PHE MET CYS VAL ALA LEU GLN SEQRES 7 C 254 GLY ARG GLY ASP ALA ASP GLN TRP VAL THR SER TYR LYS SEQRES 8 C 254 ILE ARG TYR SER LEU ASP ASN VAL SER TRP PHE GLU TYR SEQRES 9 C 254 ARG ASN GLY ALA ALA VAL THR GLY VAL THR ASP ARG ASN SEQRES 10 C 254 THR VAL VAL ASN HIS PHE PHE ASP THR PRO ILE ARG ALA SEQRES 11 C 254 ARG SER ILE ALA ILE HIS PRO LEU THR TRP ASN GLY HIS SEQRES 12 C 254 ILE SER LEU ARG CYS GLU PHE TYR THR GLN PRO VAL GLN SEQRES 13 C 254 SER SER VAL THR GLN VAL GLY ALA ASP ILE TYR THR GLY SEQRES 14 C 254 ASP ASN CYS ALA LEU ASN THR GLY SER GLY LYS ARG GLU SEQRES 15 C 254 VAL VAL VAL PRO VAL LYS PHE GLN PHE GLU PHE ALA THR SEQRES 16 C 254 LEU PRO LYS VAL ALA LEU ASN PHE ASP GLN ILE ASP CYS SEQRES 17 C 254 THR ASP ALA THR ASN GLN THR ARG ILE GLY VAL GLN PRO SEQRES 18 C 254 ARG ASN ILE THR THR LYS GLY PHE ASP CYS VAL PHE TYR SEQRES 19 C 254 THR TRP ASN GLU ASN LYS VAL TYR SER LEU ARG ALA ASP SEQRES 20 C 254 TYR ILE ALA THR ALA LEU GLU HET MPD A1254 8 HET MPD A1255 8 HET SO4 A1256 5 HET CA A1257 1 HET NI A1258 1 HET SO4 A1259 5 HET MPD B1254 8 HET SO4 B1255 5 HET CA B1256 1 HET MRD C1254 8 HET MRD C1255 8 HET SO4 C1256 5 HET CA C1257 1 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM SO4 SULFATE ION HETNAM CA CALCIUM ION HETNAM NI NICKEL (II) ION HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL FORMUL 4 MPD 3(C6 H14 O2) FORMUL 6 SO4 4(O4 S 2-) FORMUL 7 CA 3(CA 2+) FORMUL 8 NI NI 2+ FORMUL 13 MRD 2(C6 H14 O2) FORMUL 17 HOH *981(H2 O) HELIX 1 1 LEU A 9 ASN A 12 1 4 HELIX 2 1 LEU B 9 ASN B 12 1 4 HELIX 3 1 LEU C 9 ASN C 12 1 4 SHEET 1 AA 6 HIS A 16 THR A 19 0 SHEET 2 AA 6 ILE A 61 CYS A 65 -1 O VAL A 62 N ARG A 18 SHEET 3 AA 6 ILE A 127 ASN A 140 -1 O ILE A 132 N ALA A 63 SHEET 4 AA 6 TRP A 85 SER A 94 0 SHEET 5 AA 6 TRP A 100 TYR A 103 -1 O PHE A 101 N TYR A 93 SHEET 6 AA 6 VAL A 109 GLY A 111 -1 O VAL A 109 N TYR A 89 SHEET 1 AB 3 VAL A 119 PHE A 122 0 SHEET 2 AB 3 ARG A 69 GLN A 77 0 SHEET 3 AB 3 SER A 144 THR A 151 0 SHEET 1 AC 3 SER A 157 TYR A 166 0 SHEET 2 AC 3 VAL A 240 LEU A 252 -1 O ALA A 245 N ILE A 165 SHEET 3 AC 3 LYS A 197 THR A 208 -1 O LYS A 197 N THR A 250 SHEET 1 AD 3 ARG A 180 LYS A 187 0 SHEET 2 AD 3 GLY A 227 THR A 234 -1 O PHE A 228 N VAL A 186 SHEET 3 AD 3 GLY A 217 ARG A 221 -1 O GLY A 217 N TYR A 233 SHEET 1 BA 6 HIS B 16 THR B 19 0 SHEET 2 BA 6 ILE B 61 CYS B 65 -1 O VAL B 62 N ARG B 18 SHEET 3 BA 6 ILE B 127 ASN B 140 -1 O ILE B 132 N ALA B 63 SHEET 4 BA 6 TRP B 85 SER B 94 0 SHEET 5 BA 6 TRP B 100 TYR B 103 -1 O PHE B 101 N TYR B 93 SHEET 6 BA 6 VAL B 109 GLY B 111 -1 O VAL B 109 N TYR B 89 SHEET 1 BB 3 VAL B 119 PHE B 122 0 SHEET 2 BB 3 ARG B 69 GLN B 77 0 SHEET 3 BB 3 SER B 144 THR B 151 0 SHEET 1 BC 3 SER B 157 TYR B 166 0 SHEET 2 BC 3 VAL B 240 LEU B 252 -1 O ALA B 245 N ILE B 165 SHEET 3 BC 3 LYS B 197 THR B 208 -1 O LYS B 197 N THR B 250 SHEET 1 BD 3 ARG B 180 LYS B 187 0 SHEET 2 BD 3 GLY B 227 THR B 234 -1 O PHE B 228 N VAL B 186 SHEET 3 BD 3 GLY B 217 ARG B 221 -1 O GLY B 217 N TYR B 233 SHEET 1 CA 6 HIS C 16 THR C 19 0 SHEET 2 CA 6 ILE C 61 CYS C 65 -1 O VAL C 62 N ARG C 18 SHEET 3 CA 6 ILE C 127 ASN C 140 -1 O ILE C 132 N ALA C 63 SHEET 4 CA 6 TRP C 85 SER C 94 0 SHEET 5 CA 6 TRP C 100 TYR C 103 -1 O PHE C 101 N TYR C 93 SHEET 6 CA 6 VAL C 109 GLY C 111 -1 O VAL C 109 N TYR C 89 SHEET 1 CB 3 VAL C 119 PHE C 122 0 SHEET 2 CB 3 ARG C 69 GLN C 77 0 SHEET 3 CB 3 SER C 144 THR C 151 0 SHEET 1 CC 3 SER C 157 TYR C 166 0 SHEET 2 CC 3 VAL C 240 LEU C 252 -1 O ALA C 245 N ILE C 165 SHEET 3 CC 3 LYS C 197 THR C 208 -1 O LYS C 197 N THR C 250 SHEET 1 CD 3 ARG C 180 LYS C 187 0 SHEET 2 CD 3 GLY C 227 THR C 234 -1 O PHE C 228 N VAL C 186 SHEET 3 CD 3 GLY C 217 ARG C 221 -1 O GLY C 217 N TYR C 233 LINK ND1 HIS A 16 NI NI A1258 1555 1555 2.51 LINK OD1 ASP A 164 CA CA A1257 1555 1555 2.30 LINK OD2 ASP A 203 CA CA A1257 1555 1555 2.40 LINK OE1 GLN A 219 CA CA C1257 1555 1555 2.38 LINK OD2 ASP A 246 CA CA A1257 1555 1555 2.58 LINK OD1 ASP A 246 CA CA A1257 1555 1555 2.49 LINK CA CA A1257 OE1 GLN B 219 1555 1555 2.41 LINK CA CA A1257 O HOH B2281 1555 1555 2.37 LINK CA CA A1257 O HOH B2282 1555 1555 2.41 LINK NI NI A1258 ND1 HIS B 16 1555 1555 2.28 LINK NI NI A1258 ND1 HIS C 16 1555 1555 2.35 LINK O HOH A2288 CA CA C1257 1555 1555 2.36 LINK O HOH A2289 CA CA C1257 1555 1555 2.50 LINK OD1 ASP B 164 CA CA B1256 1555 1555 2.39 LINK OD2 ASP B 203 CA CA B1256 1555 1555 2.41 LINK OD2 ASP B 246 CA CA B1256 1555 1555 2.57 LINK OD1 ASP B 246 CA CA B1256 1555 1555 2.53 LINK CA CA B1256 OE1 GLN C 219 1555 1555 2.44 LINK CA CA B1256 O HOH C2263 1555 1555 2.38 LINK CA CA B1256 O HOH C2264 1555 1555 2.44 LINK OD1 ASP C 164 CA CA C1257 1555 1555 2.38 LINK OD2 ASP C 203 CA CA C1257 1555 1555 2.39 LINK OD2 ASP C 246 CA CA C1257 1555 1555 2.70 LINK OD1 ASP C 246 CA CA C1257 1555 1555 2.56 SITE 1 AC1 6 VAL A 62 ARG A 92 TRP A 100 HOH A2345 SITE 2 AC1 6 HOH A2346 ASN C 12 SITE 1 AC2 6 ARG A 79 GLN A 84 HIS A 142 HOH A2047 SITE 2 AC2 6 THR B 41 HOH B2075 SITE 1 AC3 5 ARG A 104 VAL A 109 THR A 110 HIS A 121 SITE 2 AC3 5 HOH A2347 SITE 1 AC4 6 ASP A 164 ASP A 203 ASP A 246 GLN B 219 SITE 2 AC4 6 HOH B2281 HOH B2282 SITE 1 AC5 4 HIS A 16 HIS B 16 HIS C 16 HOH C2035 SITE 1 AC6 7 SER A 157 VAL A 158 THR A 159 SER B 157 SITE 2 AC6 7 THR B 159 SER C 157 THR C 159 SITE 1 AC7 6 THR A 41 TYR B 23 ARG B 79 GLN B 84 SITE 2 AC7 6 HIS B 142 HOH B2042 SITE 1 AC8 4 ARG B 104 VAL B 109 THR B 110 HIS B 121 SITE 1 AC9 6 ASP B 164 ASP B 203 ASP B 246 GLN C 219 SITE 2 AC9 6 HOH C2263 HOH C2264 SITE 1 BC1 6 ARG C 18 VAL C 62 ARG C 92 TRP C 100 SITE 2 BC1 6 HIS C 135 HOH C2305 SITE 1 BC2 6 THR C 41 ASN C 42 ARG C 79 GLN C 84 SITE 2 BC2 6 HIS C 142 HOH C2075 SITE 1 BC3 6 ARG C 104 VAL C 109 THR C 110 HIS C 121 SITE 2 BC3 6 HOH C2165 HOH C2306 SITE 1 BC4 6 GLN A 219 HOH A2288 HOH A2289 ASP C 164 SITE 2 BC4 6 ASP C 203 ASP C 246 CRYST1 72.530 274.371 85.928 90.00 90.00 90.00 C 2 2 21 24 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 0.013787 0.000000 0.000000 0.00000 SCALE2 0.000000 0.003645 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011638 0.00000