HEADER SUGAR BINDING PROTEIN 22-APR-05 1ZGS TITLE PARKIA PLATYCEPHALA SEED LECTIN IN COMPLEX WITH 5-BROMO-4-CHLORO-3- TITLE 2 INDOLYL-A-D-MANNOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MANNOSE/GLUCOSE-SPECIFIC LECTIN; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARKIA PLATYCEPHALA; SOURCE 3 ORGANISM_TAXID: 185447; SOURCE 4 TISSUE: SEEDS KEYWDS BETA PRISM, LECTIN, X-MAN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.GALLEGO DEL SOL,B.S.CAVADA,J.J.CALVETE REVDAT 4 29-JUL-20 1ZGS 1 COMPND REMARK HETNAM SITE REVDAT 3 24-FEB-09 1ZGS 1 VERSN REVDAT 2 01-NOV-05 1ZGS 1 JRNL REVDAT 1 11-OCT-05 1ZGS 0 JRNL AUTH F.GALLEGO DEL SOL,C.NAGANO,B.S.CAVADA,J.J.CALVETE JRNL TITL THE FIRST CRYSTAL STRUCTURE OF A MIMOSOIDEAE LECTIN REVEALS JRNL TITL 2 A NOVEL QUATERNARY ARRANGEMENT OF A WIDESPREAD DOMAIN. JRNL REF J.MOL.BIOL. V. 353 574 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16185708 JRNL DOI 10.1016/J.JMB.2005.08.055 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 39474 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3929 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2868 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 284 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6668 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 138 REMARK 3 SOLVENT ATOMS : 203 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.43000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : 0.51000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.88000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.415 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.264 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.924 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6940 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9436 ; 3.160 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 874 ; 7.273 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 273 ;35.847 ;24.359 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1009 ;18.694 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;18.920 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1005 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5332 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2997 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4732 ; 0.320 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 356 ; 0.145 ; 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): 14 ; 0.142 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.294 ; 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): 4298 ; 1.074 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6893 ; 1.915 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2642 ; 2.541 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2543 ; 3.793 ; 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZGS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000032703. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-04 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 : BM16 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91995, 0.91932, 0.92191 REMARK 200 MONOCHROMATOR : SINCHROTRON 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 : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43436 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 69.673 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : 0.04000 REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.17000 REMARK 200 R SYM FOR SHELL (I) : 0.13800 REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM DIHYDROGEN PHOSPHATE, REMARK 280 0.1M TRIS-HYDROCHLORIDE, 3MM, PH 8.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 57.08850 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 SER A 1 REMARK 465 LEU A 2 REMARK 465 THR A 445 REMARK 465 ALA A 446 REMARK 465 VAL A 447 REMARK 465 SER B 1 REMARK 465 LEU B 2 REMARK 465 THR B 445 REMARK 465 ALA B 446 REMARK 465 VAL B 447 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 VAL A 297 CG1 CG2 REMARK 470 VAL B 297 CG1 CG2 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 LYS A 3 REMARK 475 VAL A 297 REMARK 475 GLU A 298 REMARK 475 LYS B 3 REMARK 475 VAL B 297 REMARK 475 GLU B 298 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 61 CG CD OE1 OE2 REMARK 480 LYS A 64 CG CD CE NZ REMARK 480 LEU A 223 CD1 CD2 REMARK 480 GLN A 381 CD OE1 NE2 REMARK 480 GLU B 61 CD OE1 OE2 REMARK 480 LYS B 64 CG CD CE NZ 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 GLU A 298 N GLY A 299 1.43 REMARK 500 O GLU B 298 N GLY B 299 1.44 REMARK 500 CA GLU B 298 N GLY B 299 1.65 REMARK 500 CA GLU A 298 N GLY A 299 1.66 REMARK 500 C GLU B 298 CA GLY B 299 1.68 REMARK 500 C GLU A 298 CA GLY A 299 1.68 REMARK 500 O HOH B 551 O HOH B 552 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 3 C GLY A 4 N -0.146 REMARK 500 VAL A 292 CB VAL A 292 CG1 -0.132 REMARK 500 ASP A 296 C VAL A 297 N -0.418 REMARK 500 GLU A 298 C GLY A 299 N -1.034 REMARK 500 VAL B 292 CB VAL B 292 CG1 -0.146 REMARK 500 VAL B 292 CB VAL B 292 CG2 -0.167 REMARK 500 ASP B 296 C VAL B 297 N -0.419 REMARK 500 GLU B 298 C GLY B 299 N -1.013 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 3 CA - C - N ANGL. DEV. = 22.2 DEGREES REMARK 500 LYS A 3 O - C - N ANGL. DEV. = -19.6 DEGREES REMARK 500 GLY A 4 C - N - CA ANGL. DEV. = 21.8 DEGREES REMARK 500 ASP A 194 CB - CG - OD2 ANGL. DEV. = 7.4 DEGREES REMARK 500 LYS A 202 N - CA - C ANGL. DEV. = -25.7 DEGREES REMARK 500 LEU A 223 CB - CG - CD2 ANGL. DEV. = 11.9 DEGREES REMARK 500 VAL A 297 N - CA - C ANGL. DEV. = -16.4 DEGREES REMARK 500 GLN A 381 CB - CG - CD ANGL. DEV. = -15.7 DEGREES REMARK 500 LYS B 3 CA - C - N ANGL. DEV. = 22.4 DEGREES REMARK 500 LYS B 3 O - C - N ANGL. DEV. = -19.6 DEGREES REMARK 500 GLY B 4 C - N - CA ANGL. DEV. = 21.0 DEGREES REMARK 500 ASP B 88 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ALA B 183 O - C - N ANGL. DEV. = 10.6 DEGREES REMARK 500 ASP B 194 CB - CG - OD2 ANGL. DEV. = 6.9 DEGREES REMARK 500 LYS B 202 N - CA - C ANGL. DEV. = -26.6 DEGREES 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 LYS A 35 -75.13 -140.10 REMARK 500 GLU A 117 115.67 -164.15 REMARK 500 ALA A 163 -166.21 -105.23 REMARK 500 ASN A 169 114.83 -175.54 REMARK 500 SER A 174 -99.78 -120.88 REMARK 500 ASP A 184 -82.16 -115.24 REMARK 500 LYS A 237 46.04 38.72 REMARK 500 GLU A 298 142.96 139.67 REMARK 500 GLU A 320 -100.04 -129.09 REMARK 500 ASN A 332 -164.73 -121.48 REMARK 500 SER A 374 172.96 173.04 REMARK 500 PHE A 384 -79.77 -114.14 REMARK 500 LYS B 35 -69.35 -137.65 REMARK 500 ASN B 62 20.03 -69.46 REMARK 500 ALA B 163 -164.31 -106.06 REMARK 500 ASN B 169 114.73 -177.88 REMARK 500 SER B 174 -99.51 -128.58 REMARK 500 ASP B 184 -79.95 -139.22 REMARK 500 ASP B 194 166.98 -48.46 REMARK 500 LYS B 237 45.28 39.38 REMARK 500 GLU B 298 139.54 141.61 REMARK 500 GLU B 320 -99.64 -129.95 REMARK 500 ASN B 332 -165.79 -122.58 REMARK 500 SER B 374 175.94 173.24 REMARK 500 PHE B 384 -82.76 -112.65 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 GLY A 201 LYS A 202 116.98 REMARK 500 GLY B 201 LYS B 202 117.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP A 296 10.50 REMARK 500 GLU A 298 10.28 REMARK 500 ASP B 296 10.48 REMARK 500 GLU B 298 13.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZGR RELATED DB: PDB REMARK 900 NATIVE PARKIA PLATYCEPHALA SEED LECTIN DBREF 1ZGS A 1 447 UNP P83304 LEC_PARPC 1 447 DBREF 1ZGS B 1 447 UNP P83304 LEC_PARPC 1 447 SEQRES 1 A 447 SER LEU LYS GLY MET ILE SER VAL GLY PRO TRP GLY GLY SEQRES 2 A 447 SER GLY GLY ASN TYR TRP SER PHE LYS ALA ASN HIS ALA SEQRES 3 A 447 ILE THR GLU ILE VAL ILE HIS VAL LYS ASP ASN ILE LYS SEQRES 4 A 447 SER ILE SER PHE LYS ASP ALA SER GLY ASP ILE SER GLY SEQRES 5 A 447 THR PHE GLY GLY LYS ASP PRO ARG GLU ASN GLU LYS GLY SEQRES 6 A 447 ASP GLU LYS LYS ILE LYS ILE HIS TRP PRO THR GLU TYR SEQRES 7 A 447 LEU LYS SER ILE SER GLY SER TYR GLY ASP TYR ASN GLY SEQRES 8 A 447 VAL LEU VAL ILE ARG SER LEU SER PHE ILE THR ASN LEU SEQRES 9 A 447 THR THR TYR GLY PRO PHE GLY SER THR SER GLY GLY GLU SEQRES 10 A 447 SER PHE SER ILE PRO ILE ALA ASP SER VAL VAL VAL GLY SEQRES 11 A 447 PHE HIS GLY ARG ALA GLY TYR TYR LEU ASP ALA LEU GLY SEQRES 12 A 447 ILE PHE VAL GLN PRO VAL PRO HIS GLY THR ILE SER PHE SEQRES 13 A 447 GLY PRO TRP GLY GLY PRO ALA GLY ASP ASP ALA PHE ASN SEQRES 14 A 447 PHE LYS VAL GLY SER TRP ILE LYS ASP ILE ILE ILE TYR SEQRES 15 A 447 ALA ASP ALA ALA ILE ASN SER ILE ALA PHE LYS ASP ALA SEQRES 16 A 447 ASN GLY HIS CYS TYR GLY LYS PHE GLY GLY GLN ASP PRO SEQRES 17 A 447 ASN ASP ILE GLY VAL GLU LYS LYS VAL GLU ILE ASP GLY SEQRES 18 A 447 ASN LEU GLU HIS LEU LYS SER ILE SER GLY THR TYR GLY SEQRES 19 A 447 ASN TYR LYS GLY PHE GLU VAL VAL THR SER LEU SER PHE SEQRES 20 A 447 ILE THR ASN VAL THR LYS HIS GLY PRO PHE GLY ILE ALA SEQRES 21 A 447 SER GLY THR SER PHE SER ILE PRO ILE GLU GLY SER LEU SEQRES 22 A 447 VAL THR GLY PHE HIS GLY LYS SER GLY TYR TYR LEU ASP SEQRES 23 A 447 SER ILE GLY ILE TYR VAL LYS PRO ARG ASP VAL GLU GLY SEQRES 24 A 447 SER ILE SER ILE GLY PRO TRP GLY GLY SER GLY GLY ASP SEQRES 25 A 447 PRO TRP SER TYR THR ALA ASN GLU GLY ILE ASN GLN ILE SEQRES 26 A 447 ILE ILE TYR ALA GLY SER ASN ILE LYS SER VAL ALA PHE SEQRES 27 A 447 LYS ASP THR SER GLY LEU ASP SER ALA THR PHE GLY GLY SEQRES 28 A 447 VAL ASN PRO LYS ASP THR GLY GLU LYS ASN THR VAL SER SEQRES 29 A 447 ILE ASN TRP PRO SER GLU TYR LEU THR SER ILE SER GLY SEQRES 30 A 447 THR TYR GLY GLN TYR LYS PHE LYS ASP VAL PHE THR THR SEQRES 31 A 447 ILE THR SER LEU SER PHE THR THR ASN LEU ALA THR TYR SEQRES 32 A 447 GLY PRO PHE GLY LYS ALA SER ALA THR SER PHE SER ILE SEQRES 33 A 447 PRO ILE HIS ASN ASN MET VAL VAL GLY PHE HIS GLY ARG SEQRES 34 A 447 ALA GLY ASP TYR LEU ASP ALA ILE GLY ILE PHE VAL LYS SEQRES 35 A 447 PRO ASP THR ALA VAL SEQRES 1 B 447 SER LEU LYS GLY MET ILE SER VAL GLY PRO TRP GLY GLY SEQRES 2 B 447 SER GLY GLY ASN TYR TRP SER PHE LYS ALA ASN HIS ALA SEQRES 3 B 447 ILE THR GLU ILE VAL ILE HIS VAL LYS ASP ASN ILE LYS SEQRES 4 B 447 SER ILE SER PHE LYS ASP ALA SER GLY ASP ILE SER GLY SEQRES 5 B 447 THR PHE GLY GLY LYS ASP PRO ARG GLU ASN GLU LYS GLY SEQRES 6 B 447 ASP GLU LYS LYS ILE LYS ILE HIS TRP PRO THR GLU TYR SEQRES 7 B 447 LEU LYS SER ILE SER GLY SER TYR GLY ASP TYR ASN GLY SEQRES 8 B 447 VAL LEU VAL ILE ARG SER LEU SER PHE ILE THR ASN LEU SEQRES 9 B 447 THR THR TYR GLY PRO PHE GLY SER THR SER GLY GLY GLU SEQRES 10 B 447 SER PHE SER ILE PRO ILE ALA ASP SER VAL VAL VAL GLY SEQRES 11 B 447 PHE HIS GLY ARG ALA GLY TYR TYR LEU ASP ALA LEU GLY SEQRES 12 B 447 ILE PHE VAL GLN PRO VAL PRO HIS GLY THR ILE SER PHE SEQRES 13 B 447 GLY PRO TRP GLY GLY PRO ALA GLY ASP ASP ALA PHE ASN SEQRES 14 B 447 PHE LYS VAL GLY SER TRP ILE LYS ASP ILE ILE ILE TYR SEQRES 15 B 447 ALA ASP ALA ALA ILE ASN SER ILE ALA PHE LYS ASP ALA SEQRES 16 B 447 ASN GLY HIS CYS TYR GLY LYS PHE GLY GLY GLN ASP PRO SEQRES 17 B 447 ASN ASP ILE GLY VAL GLU LYS LYS VAL GLU ILE ASP GLY SEQRES 18 B 447 ASN LEU GLU HIS LEU LYS SER ILE SER GLY THR TYR GLY SEQRES 19 B 447 ASN TYR LYS GLY PHE GLU VAL VAL THR SER LEU SER PHE SEQRES 20 B 447 ILE THR ASN VAL THR LYS HIS GLY PRO PHE GLY ILE ALA SEQRES 21 B 447 SER GLY THR SER PHE SER ILE PRO ILE GLU GLY SER LEU SEQRES 22 B 447 VAL THR GLY PHE HIS GLY LYS SER GLY TYR TYR LEU ASP SEQRES 23 B 447 SER ILE GLY ILE TYR VAL LYS PRO ARG ASP VAL GLU GLY SEQRES 24 B 447 SER ILE SER ILE GLY PRO TRP GLY GLY SER GLY GLY ASP SEQRES 25 B 447 PRO TRP SER TYR THR ALA ASN GLU GLY ILE ASN GLN ILE SEQRES 26 B 447 ILE ILE TYR ALA GLY SER ASN ILE LYS SER VAL ALA PHE SEQRES 27 B 447 LYS ASP THR SER GLY LEU ASP SER ALA THR PHE GLY GLY SEQRES 28 B 447 VAL ASN PRO LYS ASP THR GLY GLU LYS ASN THR VAL SER SEQRES 29 B 447 ILE ASN TRP PRO SER GLU TYR LEU THR SER ILE SER GLY SEQRES 30 B 447 THR TYR GLY GLN TYR LYS PHE LYS ASP VAL PHE THR THR SEQRES 31 B 447 ILE THR SER LEU SER PHE THR THR ASN LEU ALA THR TYR SEQRES 32 B 447 GLY PRO PHE GLY LYS ALA SER ALA THR SER PHE SER ILE SEQRES 33 B 447 PRO ILE HIS ASN ASN MET VAL VAL GLY PHE HIS GLY ARG SEQRES 34 B 447 ALA GLY ASP TYR LEU ASP ALA ILE GLY ILE PHE VAL LYS SEQRES 35 B 447 PRO ASP THR ALA VAL HET XMM A 450 23 HET XMM A 451 23 HET XMM A 452 23 HET XMM B 453 23 HET XMM B 454 23 HET XMM B 455 23 HETNAM XMM 5-BROMO-4-CHLORO-1H-INDOL-3-YL ALPHA-D-MANNOPYRANOSIDE HETSYN XMM (5-BROMO-4-CHLORO-3-INDOLYL)-A-D-MANNOSE FORMUL 3 XMM 6(C14 H15 BR CL N O6) FORMUL 9 HOH *203(H2 O) HELIX 1 1 ARG A 60 LYS A 64 5 5 HELIX 2 2 ARG B 60 LYS B 64 5 5 SHEET 1 A 5 ASN A 17 LYS A 22 0 SHEET 2 A 5 SER A 126 ALA A 135 -1 O PHE A 131 N PHE A 21 SHEET 3 A 5 LEU A 139 PRO A 148 -1 O GLY A 143 N HIS A 132 SHEET 4 A 5 ILE A 6 GLY A 12 -1 N VAL A 8 O ILE A 144 SHEET 5 A 5 ILE A 269 GLU A 270 -1 O GLU A 270 N SER A 7 SHEET 1 B 4 PHE A 54 GLY A 55 0 SHEET 2 B 4 ILE A 38 ASP A 45 -1 N ILE A 41 O PHE A 54 SHEET 3 B 4 ILE A 27 VAL A 34 -1 N THR A 28 O LYS A 44 SHEET 4 B 4 ASP A 66 LYS A 71 -1 O ASP A 66 N VAL A 34 SHEET 1 C 4 THR A 106 GLY A 111 0 SHEET 2 C 4 VAL A 92 THR A 102 -1 N PHE A 100 O TYR A 107 SHEET 3 C 4 LEU A 79 TYR A 89 -1 N SER A 85 O ARG A 96 SHEET 4 C 4 GLU A 117 PHE A 119 -1 O PHE A 119 N GLY A 84 SHEET 1 D 5 ILE A 123 ALA A 124 0 SHEET 2 D 5 ILE A 154 GLY A 160 -1 O SER A 155 N ALA A 124 SHEET 3 D 5 LEU A 285 PRO A 294 -1 O ILE A 288 N TRP A 159 SHEET 4 D 5 SER A 272 SER A 281 -1 N HIS A 278 O GLY A 289 SHEET 5 D 5 ASP A 166 LYS A 171 -1 N ASP A 166 O SER A 281 SHEET 1 E 4 CYS A 199 GLY A 204 0 SHEET 2 E 4 ILE A 187 ASP A 194 -1 N PHE A 192 O TYR A 200 SHEET 3 E 4 ILE A 176 ALA A 183 -1 N LYS A 177 O LYS A 193 SHEET 4 E 4 GLU A 214 GLU A 218 -1 O LYS A 215 N ILE A 181 SHEET 1 F 4 LYS A 253 GLY A 258 0 SHEET 2 F 4 PHE A 239 THR A 249 -1 N PHE A 247 O HIS A 254 SHEET 3 F 4 LEU A 226 TYR A 236 -1 N TYR A 236 O PHE A 239 SHEET 4 F 4 THR A 263 PHE A 265 -1 O THR A 263 N TYR A 233 SHEET 1 G 5 ASP A 312 THR A 317 0 SHEET 2 G 5 ASN A 421 ALA A 430 -1 O PHE A 426 N TYR A 316 SHEET 3 G 5 ALA A 436 PRO A 443 -1 O GLY A 438 N HIS A 427 SHEET 4 G 5 ILE A 301 GLY A 307 -1 N ILE A 301 O VAL A 441 SHEET 5 G 5 ILE B 418 HIS B 419 -1 O HIS B 419 N SER A 302 SHEET 1 H 4 PHE A 349 GLY A 350 0 SHEET 2 H 4 ILE A 333 ASP A 340 -1 N VAL A 336 O PHE A 349 SHEET 3 H 4 ILE A 322 ALA A 329 -1 N ASN A 323 O LYS A 339 SHEET 4 H 4 GLU A 359 SER A 364 -1 O GLU A 359 N ALA A 329 SHEET 1 I 4 THR A 402 GLY A 407 0 SHEET 2 I 4 VAL A 387 THR A 398 -1 N PHE A 396 O TYR A 403 SHEET 3 I 4 LEU A 372 LYS A 383 -1 N SER A 374 O THR A 397 SHEET 4 I 4 THR A 412 PHE A 414 -1 O THR A 412 N TYR A 379 SHEET 1 J 5 ILE A 418 HIS A 419 0 SHEET 2 J 5 ILE B 301 GLY B 307 -1 O SER B 302 N HIS A 419 SHEET 3 J 5 ALA B 436 PRO B 443 -1 O VAL B 441 N ILE B 301 SHEET 4 J 5 ASN B 421 ALA B 430 -1 N HIS B 427 O GLY B 438 SHEET 5 J 5 ASP B 312 THR B 317 -1 N TYR B 316 O PHE B 426 SHEET 1 K 5 ASN B 17 LYS B 22 0 SHEET 2 K 5 SER B 126 ALA B 135 -1 O PHE B 131 N PHE B 21 SHEET 3 K 5 ALA B 141 PRO B 148 -1 O GLY B 143 N HIS B 132 SHEET 4 K 5 ILE B 6 GLY B 12 -1 N VAL B 8 O ILE B 144 SHEET 5 K 5 ILE B 269 GLU B 270 -1 O GLU B 270 N SER B 7 SHEET 1 L 4 PHE B 54 GLY B 55 0 SHEET 2 L 4 ILE B 38 ASP B 45 -1 N ILE B 41 O PHE B 54 SHEET 3 L 4 ILE B 27 VAL B 34 -1 N THR B 28 O LYS B 44 SHEET 4 L 4 ASP B 66 LYS B 71 -1 O ASP B 66 N VAL B 34 SHEET 1 M 4 THR B 106 GLY B 111 0 SHEET 2 M 4 VAL B 92 THR B 102 -1 N PHE B 100 O TYR B 107 SHEET 3 M 4 LEU B 79 TYR B 89 -1 N SER B 85 O ARG B 96 SHEET 4 M 4 GLU B 117 PHE B 119 -1 O GLU B 117 N TYR B 86 SHEET 1 N 5 ILE B 123 ALA B 124 0 SHEET 2 N 5 ILE B 154 GLY B 160 -1 O SER B 155 N ALA B 124 SHEET 3 N 5 LEU B 285 PRO B 294 -1 O ILE B 288 N TRP B 159 SHEET 4 N 5 SER B 272 SER B 281 -1 N HIS B 278 O GLY B 289 SHEET 5 N 5 ASP B 166 LYS B 171 -1 N ASP B 166 O SER B 281 SHEET 1 O 4 CYS B 199 GLY B 204 0 SHEET 2 O 4 ILE B 187 ASP B 194 -1 N PHE B 192 O TYR B 200 SHEET 3 O 4 ILE B 176 ALA B 183 -1 N ILE B 180 O ALA B 191 SHEET 4 O 4 VAL B 213 GLU B 218 -1 O LYS B 215 N ILE B 181 SHEET 1 P 4 LYS B 253 GLY B 258 0 SHEET 2 P 4 PHE B 239 THR B 249 -1 N PHE B 247 O HIS B 254 SHEET 3 P 4 LEU B 226 TYR B 236 -1 N TYR B 236 O PHE B 239 SHEET 4 P 4 THR B 263 PHE B 265 -1 O THR B 263 N TYR B 233 SHEET 1 Q 4 PHE B 349 GLY B 350 0 SHEET 2 Q 4 ILE B 333 ASP B 340 -1 N VAL B 336 O PHE B 349 SHEET 3 Q 4 ILE B 322 ALA B 329 -1 N ASN B 323 O LYS B 339 SHEET 4 Q 4 GLU B 359 SER B 364 -1 O GLU B 359 N ALA B 329 SHEET 1 R 4 THR B 402 GLY B 407 0 SHEET 2 R 4 VAL B 387 THR B 398 -1 N PHE B 396 O TYR B 403 SHEET 3 R 4 LEU B 372 LYS B 383 -1 N SER B 374 O THR B 397 SHEET 4 R 4 THR B 412 PHE B 414 -1 O THR B 412 N TYR B 379 CISPEP 1 GLY A 9 PRO A 10 0 1.64 CISPEP 2 TRP A 74 PRO A 75 0 9.41 CISPEP 3 GLY A 108 PRO A 109 0 3.83 CISPEP 4 GLY A 157 PRO A 158 0 0.63 CISPEP 5 GLY A 255 PRO A 256 0 4.99 CISPEP 6 GLY A 304 PRO A 305 0 6.84 CISPEP 7 TRP A 367 PRO A 368 0 6.60 CISPEP 8 GLY A 404 PRO A 405 0 10.80 CISPEP 9 GLY B 9 PRO B 10 0 0.19 CISPEP 10 TRP B 74 PRO B 75 0 9.70 CISPEP 11 GLY B 108 PRO B 109 0 5.74 CISPEP 12 GLY B 157 PRO B 158 0 1.44 CISPEP 13 GLY B 255 PRO B 256 0 5.95 CISPEP 14 GLY B 304 PRO B 305 0 4.79 CISPEP 15 TRP B 367 PRO B 368 0 6.85 CISPEP 16 GLY B 404 PRO B 405 0 11.79 CRYST1 80.239 114.177 80.304 90.00 119.88 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012463 0.000000 0.007160 0.00000 SCALE2 0.000000 0.008758 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014361 0.00000 MASTER 433 0 6 2 78 0 0 6 0 0 0 70 END