HEADER CARBOHYDRATE-BINDING PROTEIN 12-JAN-07 2JDZ TITLE CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GUIANENSIS LECTIN COMPLEXED TITLE 2 WITH 5-BROMO-4-CHLORO-3-INDOLYL-A-D-MANNOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LECTIN ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RDGUIA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DIOCLEA GUIANENSIS; SOURCE 3 ORGANISM_TAXID: 99571; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET32A; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: RDGUIA/PET32A KEYWDS CARBOHYDRATE-BINDING PROTEIN, METAL-BINDING, LEGUME LECTIN EXPDTA X-RAY DIFFRACTION AUTHOR C.S.NAGANO,L.SANZ,B.S.CAVADA,J.J.CALVETE REVDAT 7 13-DEC-23 2JDZ 1 HETSYN REVDAT 6 29-JUL-20 2JDZ 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE REVDAT 5 08-MAY-19 2JDZ 1 REMARK REVDAT 4 29-AUG-12 2JDZ 1 JRNL REMARK REVDAT 3 13-JUL-11 2JDZ 1 VERSN REVDAT 2 24-FEB-09 2JDZ 1 VERSN REVDAT 1 30-OCT-07 2JDZ 0 JRNL AUTH C.S.NAGANO,J.J.CALVETE,D.BARETTINO,A.PEREZ,B.S.CAVADA,L.SANZ JRNL TITL INSIGHTS INTO THE STRUCTURAL BASIS OF THE PH-DEPENDENT JRNL TITL 2 DIMER-TETRAMER EQUILIBRIUM THROUGH CRYSTALLOGRAPHIC ANALYSIS JRNL TITL 3 OF RECOMBINANT DIOCLEINAE LECTINS. JRNL REF BIOCHEM.J. V. 409 417 2008 JRNL REFN ISSN 0264-6021 JRNL PMID 17937659 JRNL DOI 10.1042/BJ20070942 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 11848 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.600 REMARK 3 FREE R VALUE TEST SET COUNT : 971 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 854 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1761 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 80 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.16 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) : -0.23000 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): 0.277 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.214 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.166 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.673 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1825 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2495 ; 1.658 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 232 ; 7.190 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 72 ;35.409 ;24.444 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 270 ;16.619 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;24.511 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 292 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1380 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 815 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1291 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 110 ; 0.229 ; 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): 45 ; 0.272 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.405 ; 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): 1181 ; 0.833 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1883 ; 1.452 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 741 ; 2.271 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 612 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 239 REMARK 3 RESIDUE RANGE : A 240 A 248 REMARK 3 RESIDUE RANGE : A 249 A 249 REMARK 3 RESIDUE RANGE : A 2001 A 2080 REMARK 3 ORIGIN FOR THE GROUP (A): 18.1149 2.0047 14.2788 REMARK 3 T TENSOR REMARK 3 T11: -0.1316 T22: -0.0250 REMARK 3 T33: -0.0788 T12: -0.0232 REMARK 3 T13: -0.0593 T23: 0.1177 REMARK 3 L TENSOR REMARK 3 L11: 2.2726 L22: 1.8375 REMARK 3 L33: 1.9645 L12: 0.2984 REMARK 3 L13: 0.0768 L23: -0.6653 REMARK 3 S TENSOR REMARK 3 S11: 0.1263 S12: -0.1638 S13: -0.1089 REMARK 3 S21: 0.1464 S22: -0.3750 S23: -0.3011 REMARK 3 S31: -0.0839 S32: 0.1979 S33: 0.2487 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. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. REMARK 4 REMARK 4 2JDZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1290031061. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-SEP-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9308 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12834 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 34.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.60 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1H9P REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN BY THE HANGING REMARK 280 DROP VAPOUR DIFFUSION METHOD USING 30% PEG 400, 0.1M MES, PH 6.5 REMARK 280 AND 0.1M CDCL2., VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 44.61100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 44.61100 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.03450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.61100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.51725 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.61100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 79.55175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.61100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 79.55175 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.61100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.51725 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 44.61100 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 44.61100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 53.03450 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 44.61100 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 44.61100 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 53.03450 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 44.61100 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 79.55175 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 44.61100 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 26.51725 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 44.61100 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 26.51725 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 44.61100 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 79.55175 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 44.61100 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 44.61100 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 53.03450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.4 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 ALA A 1 REMARK 465 MET A 2 REMARK 465 SER A 121 REMARK 465 ILE A 122 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 120 CA C O CB CG OD1 ND2 REMARK 470 ASP A 124 CG OD1 OD2 REMARK 470 SER A 146 CB OG REMARK 470 LYS A 186 CG CD CE NZ REMARK 470 ARG A 206 CG CD NE CZ NH1 NH2 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 2073 O HOH A 2075 1.72 REMARK 500 OE2 GLU A 185 O HOH A 2051 1.96 REMARK 500 NH1 ARG A 62 OD1 ASP A 80 2.17 REMARK 500 OD1 ASN A 84 O HOH A 2029 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 MN MN A 247 MN MN A 247 7545 1.25 REMARK 500 CD CD A 245 CD CD A 245 6555 1.31 REMARK 500 O HOH A 2076 O HOH A 2076 7545 1.93 REMARK 500 O HOH A 2032 O HOH A 2032 15555 2.17 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 45 77.85 -113.19 REMARK 500 SER A 146 -130.31 63.08 REMARK 500 LEU A 232 18.83 59.38 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 MN A 240 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 10 OE2 REMARK 620 2 ASP A 12 OD2 89.3 REMARK 620 3 ASP A 21 OD1 167.8 97.2 REMARK 620 4 HIS A 26 NE2 90.6 100.3 98.3 REMARK 620 5 HOH A2068 O 83.2 86.9 86.9 170.5 REMARK 620 6 HOH A2069 O 92.8 172.3 79.4 87.1 86.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 241 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 12 OD1 REMARK 620 2 ASP A 12 OD2 54.2 REMARK 620 3 TYR A 14 O 72.8 114.6 REMARK 620 4 ASN A 16 OD1 148.8 154.1 78.2 REMARK 620 5 ASP A 21 OD2 108.6 79.5 84.9 79.5 REMARK 620 6 HOH A2003 O 119.9 72.9 166.0 90.4 85.1 REMARK 620 7 HOH A2057 O 77.3 113.2 85.4 89.4 166.5 102.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 248 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 53 NE2 REMARK 620 2 HOH A2078 O 80.3 REMARK 620 3 HOH A2079 O 81.5 154.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 245 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 89 OE1 REMARK 620 2 GLU A 89 OE2 123.5 REMARK 620 3 GLU A 89 OE1 96.4 55.9 REMARK 620 4 GLU A 185 OE1 79.7 140.7 161.4 REMARK 620 5 GLU A 185 OE1 138.9 93.2 89.4 82.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 246 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 127 OG REMARK 620 2 HIS A 129 NE2 99.5 REMARK 620 3 HOH A2073 O 139.8 69.1 REMARK 620 4 HOH A2075 O 91.2 78.2 49.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 244 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 182 ND1 REMARK 620 2 HOH A2070 O 100.5 REMARK 620 3 HOH A2072 O 124.4 110.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 247 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 207 OD1 REMARK 620 2 HOH A2076 O 136.0 REMARK 620 N 1 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1H9P RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DIOCLEA GUIANENSIS SEED LECTIN REMARK 900 RELATED ID: 1H9W RELATED DB: PDB REMARK 900 NATIVE DIOCLEA GUIANENSIS SEED LECTIN REMARK 900 RELATED ID: 2JE7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GUIANENSIS LECTIN S131H REMARK 900 COMPLEXED WITH 5-BROMO-4-CHLORO-3-INDOLYL-A -D-MANNOSE REMARK 900 RELATED ID: 2JE9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GRANDIFLORA LECTIN REMARK 900 COMPLEXED WITH 5-BROMO-4-CHLORO-3-INDOLYL-A- D-MANNOSE REMARK 900 RELATED ID: 2JEC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GRANDIFLORA LECTIN MUTANT REMARK 900 E123A-H131N-K132Q COMPLEXED WITH 5-BROMO -4-CHLORO-3-INDOLYL-A-D- REMARK 900 MANNOSE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AMINO ACID SEQUENCE DEDUCED FROM CDNA PRESENTS CONFLICTS REMARK 999 WITH THE AMINO ACID SEQUENCE DETERMINED BY DIRECT METHOD. THE REMARK 999 DEDUCED SEQUENCE WAS CONFIRMED BY SEQUENCE OF ALL CLONES (FROM REMARK 999 CDNA AND GENOMIC DNA). THE INSERTIONS AT N-TERMINAL ARE DUE THE REMARK 999 NCOI RESTRICTION SITE OF THE PET-32A VECTOR. DBREF 2JDZ A 3 239 UNP P81637 LECA_DIOGU 1 237 SEQADV 2JDZ ALA A 1 UNP P81637 EXPRESSION TAG SEQADV 2JDZ MET A 2 UNP P81637 EXPRESSION TAG SEQADV 2JDZ SER A 70 UNP P81637 THR 68 SEE REMARK 999 SEQADV 2JDZ THR A 72 UNP P81637 SER 70 SEE REMARK 999 SEQADV 2JDZ SER A 133 UNP P81637 ASN 131 SEE REMARK 999 SEQADV 2JDZ GLN A 157 UNP P81637 GLU 155 SEE REMARK 999 SEQADV 2JDZ ARG A 160 UNP P81637 LYS 158 SEE REMARK 999 SEQADV 2JDZ ASP A 164 UNP P81637 SER 162 SEE REMARK 999 SEQADV 2JDZ SER A 166 UNP P81637 ASP 164 SEE REMARK 999 SEQADV 2JDZ SER A 192 UNP P81637 GLY 190 SEE REMARK 999 SEQRES 1 A 239 ALA MET ALA ASP THR ILE VAL ALA VAL GLU LEU ASP SER SEQRES 2 A 239 TYR PRO ASN THR ASP ILE GLY ASP PRO SER TYR PRO HIS SEQRES 3 A 239 ILE GLY ILE ASP ILE LYS SER ILE ARG SER LYS SER THR SEQRES 4 A 239 ALA ARG TRP ASN MET GLN THR GLY LYS VAL GLY THR ALA SEQRES 5 A 239 HIS ILE SER TYR ASN SER VAL ALA LYS ARG LEU SER ALA SEQRES 6 A 239 VAL VAL SER TYR SER GLY THR SER SER THR THR VAL SER SEQRES 7 A 239 TYR ASP VAL ASP LEU ASN ASN VAL LEU PRO GLU TRP VAL SEQRES 8 A 239 ARG VAL GLY LEU SER ALA THR THR GLY LEU TYR LYS GLU SEQRES 9 A 239 THR ASN THR ILE LEU SER TRP SER PHE THR SER LYS LEU SEQRES 10 A 239 LYS THR ASN SER ILE ALA ASP ALA ASN SER LEU HIS PHE SEQRES 11 A 239 SER PHE SER GLN PHE SER GLN ASN PRO LYS ASP LEU ILE SEQRES 12 A 239 LEU GLN SER ASP ALA THR THR ASP SER ASP GLY ASN LEU SEQRES 13 A 239 GLN LEU THR ARG VAL SER SER ASP GLY SER PRO GLN GLY SEQRES 14 A 239 SER SER VAL GLY ARG ALA LEU PHE TYR ALA PRO VAL HIS SEQRES 15 A 239 ILE TRP GLU LYS SER ALA VAL VAL ALA SER PHE ASP ALA SEQRES 16 A 239 THR PHE THR PHE LEU ILE LYS SER PRO ASP ARG ASP PRO SEQRES 17 A 239 ALA ASP GLY ILE THR PHE PHE ILE ALA ASN THR ASP THR SEQRES 18 A 239 SER ILE PRO SER GLY SER GLY GLY ARG LEU LEU GLY LEU SEQRES 19 A 239 PHE PRO ASP ALA ASN HET MN A 240 1 HET CA A 241 1 HET MN A 244 1 HET CD A 245 1 HET MN A 246 1 HET MN A 247 1 HET MN A 248 1 HET XMM A 249 23 HETNAM MN MANGANESE (II) ION HETNAM CA CALCIUM ION HETNAM CD CADMIUM ION HETNAM XMM 5-BROMO-4-CHLORO-1H-INDOL-3-YL ALPHA-D-MANNOPYRANOSIDE HETSYN XMM (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)- HETSYN 2 XMM TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL; (5- HETSYN 3 XMM BROMO-4-CHLORO-3-INDOLYL)-ALPHA-D-MANNOSE; 5-BROMO-4- HETSYN 4 XMM CHLORO-1H-INDOL-3-YL ALPHA-D-MANNOSIDE; 5-BROMO-4- HETSYN 5 XMM CHLORO-1H-INDOL-3-YL D-MANNOSIDE; 5-BROMO-4-CHLORO-1H- HETSYN 6 XMM INDOL-3-YL MANNOSIDE FORMUL 2 MN 5(MN 2+) FORMUL 3 CA CA 2+ FORMUL 5 CD CD 2+ FORMUL 9 XMM C14 H15 BR CL N O6 FORMUL 10 HOH *80(H2 O) HELIX 1 1 ASN A 16 GLY A 20 5 5 HELIX 2 2 ASP A 82 VAL A 86 5 5 HELIX 3 3 GLY A 228 LEU A 232 5 5 SHEET 1 AA 6 SER A 38 ARG A 41 0 SHEET 2 AA 6 HIS A 26 ILE A 31 -1 O ILE A 27 N ALA A 40 SHEET 3 AA 6 ILE A 6 ASP A 12 -1 O ALA A 8 N ASP A 30 SHEET 4 AA 6 GLY A 211 ASN A 218 -1 O ILE A 212 N LEU A 11 SHEET 5 AA 6 TRP A 90 THR A 98 -1 O ARG A 92 N ALA A 217 SHEET 6 AA 6 VAL A 181 HIS A 182 -1 O VAL A 181 N VAL A 91 SHEET 1 AB 7 SER A 38 ARG A 41 0 SHEET 2 AB 7 HIS A 26 ILE A 31 -1 O ILE A 27 N ALA A 40 SHEET 3 AB 7 ILE A 6 ASP A 12 -1 O ALA A 8 N ASP A 30 SHEET 4 AB 7 GLY A 211 ASN A 218 -1 O ILE A 212 N LEU A 11 SHEET 5 AB 7 TRP A 90 THR A 98 -1 O ARG A 92 N ALA A 217 SHEET 6 AB 7 VAL A 172 PHE A 177 -1 O GLY A 173 N ALA A 97 SHEET 7 AB 7 LEU A 142 SER A 146 -1 O ILE A 143 N LEU A 176 SHEET 1 AC 7 THR A 75 ASP A 80 0 SHEET 2 AC 7 ARG A 62 TYR A 69 -1 O LEU A 63 N TYR A 79 SHEET 3 AC 7 VAL A 49 ASN A 57 -1 O THR A 51 N SER A 68 SHEET 4 AC 7 VAL A 190 LEU A 200 -1 O PHE A 193 N TYR A 56 SHEET 5 AC 7 THR A 107 LYS A 118 -1 O THR A 107 N LEU A 200 SHEET 6 AC 7 LEU A 156 GLN A 157 -1 O LEU A 156 N ILE A 108 SHEET 7 AC 7 THR A 149 THR A 150 -1 O THR A 149 N GLN A 157 SHEET 1 AD 6 THR A 75 ASP A 80 0 SHEET 2 AD 6 ARG A 62 TYR A 69 -1 O LEU A 63 N TYR A 79 SHEET 3 AD 6 VAL A 49 ASN A 57 -1 O THR A 51 N SER A 68 SHEET 4 AD 6 VAL A 190 LEU A 200 -1 O PHE A 193 N TYR A 56 SHEET 5 AD 6 THR A 107 LYS A 118 -1 O THR A 107 N LEU A 200 SHEET 6 AD 6 ASN A 126 PHE A 132 -1 O ASN A 126 N LEU A 117 LINK OE2 GLU A 10 MN MN A 240 1555 1555 2.14 LINK OD2 ASP A 12 MN MN A 240 1555 1555 2.15 LINK OD1 ASP A 12 CA CA A 241 1555 1555 2.30 LINK OD2 ASP A 12 CA CA A 241 1555 1555 2.50 LINK O TYR A 14 CA CA A 241 1555 1555 2.36 LINK OD1 ASN A 16 CA CA A 241 1555 1555 2.42 LINK OD1 ASP A 21 MN MN A 240 1555 1555 2.30 LINK OD2 ASP A 21 CA CA A 241 1555 1555 2.37 LINK NE2 HIS A 26 MN MN A 240 1555 1555 2.17 LINK NE2 HIS A 53 MN MN A 248 1555 1555 2.25 LINK OE1 GLU A 89 CD CD A 245 1555 1555 2.76 LINK OE2 GLU A 89 CD CD A 245 6555 1555 2.38 LINK OE1 GLU A 89 CD CD A 245 6555 1555 2.39 LINK OG SER A 127 MN MN A 246 1555 1555 2.50 LINK NE2 HIS A 129 MN MN A 246 15555 1555 2.49 LINK ND1 HIS A 182 MN MN A 244 1555 1555 2.28 LINK OE1 GLU A 185 CD CD A 245 1555 1555 2.57 LINK OE1 GLU A 185 CD CD A 245 6555 1555 2.46 LINK OD1 ASP A 207 MN MN A 247 1555 1555 2.47 LINK MN MN A 240 O HOH A2068 1555 1555 1.92 LINK MN MN A 240 O HOH A2069 1555 1555 1.83 LINK CA CA A 241 O HOH A2003 1555 1555 2.23 LINK CA CA A 241 O HOH A2057 1555 1555 2.55 LINK MN MN A 244 O HOH A2070 1555 1555 2.47 LINK MN MN A 244 O HOH A2072 1555 1555 2.52 LINK MN MN A 246 O HOH A2073 1555 1555 2.21 LINK MN MN A 246 O HOH A2075 1555 1555 1.82 LINK MN MN A 247 O HOH A2076 1555 1555 2.15 LINK MN MN A 248 O HOH A2078 1555 1555 1.97 LINK MN MN A 248 O HOH A2079 1555 1555 2.40 CISPEP 1 ALA A 123 ASP A 124 0 -11.45 CISPEP 2 ALA A 209 ASP A 210 0 2.08 CRYST1 89.222 89.222 106.069 90.00 90.00 90.00 I 41 2 2 16 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 0.011208 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011208 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009428 0.00000