HEADER SUGAR BINDING PROTEIN 30-JAN-15 4XXA TITLE CRYSTAL STRUCTURE OF A RECOMBINANT VATAIREA MACROCARPA SEED LECTIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEED LECTIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: VML; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VATAIREA MACROCARPA; SOURCE 3 ORGANISM_TAXID: 77050; SOURCE 4 ORGAN: SEED; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS LEGUME, RECOMBINANT LECTIN, VATAIREA, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.L.SOUSA,J.C.SILVA-FILHO,P.KUMAR,A.LYSKOWSKI,G.A.BEZERRA, AUTHOR 2 P.DELATORRE,B.A.M.ROCHA,R.M.S.CUNHA,C.S.NAGANO,K.GRUBER,B.S.CAVADA REVDAT 3 27-SEP-23 4XXA 1 REMARK LINK REVDAT 2 27-JUL-16 4XXA 1 REMARK REVDAT 1 27-JAN-16 4XXA 0 JRNL AUTH B.L.SOUSA,J.C.SILVA-FILHO,P.KUMAR,A.LYSKOWSKI,G.A.BEZERRA, JRNL AUTH 2 P.DELATORRE,B.A.M.ROCHA,R.M.S.CUNHA,C.S.NAGANO,K.GRUBER, JRNL AUTH 3 B.S.CAVADA JRNL TITL CRYSTAL STRUCTURE OF A RECOMBINANT VATAIREA MACROCARPA SEED JRNL TITL 2 LECTIN JRNL REF INT.J.BIOCHEM.CELL BIOL. 2016 JRNL REFN ISSN 1357-2725 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0071 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 83.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 36221 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1764 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2490 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.2100 REMARK 3 BIN FREE R VALUE SET COUNT : 134 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3620 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 153 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.71000 REMARK 3 B22 (A**2) : -0.71000 REMARK 3 B33 (A**2) : 2.31000 REMARK 3 B12 (A**2) : -0.36000 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): 0.164 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.150 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.113 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.333 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3721 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3410 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5077 ; 1.942 ; 1.932 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7877 ; 0.876 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 466 ; 6.982 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 160 ;35.394 ;24.875 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 573 ;14.834 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;17.487 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 575 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4228 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 850 ; 0.001 ; 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): 1873 ; 1.778 ; 2.469 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1872 ; 1.779 ; 2.469 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2336 ; 2.144 ; 3.687 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 236 REMARK 3 ORIGIN FOR THE GROUP (A): 53.2180 8.8536 12.5340 REMARK 3 T TENSOR REMARK 3 T11: 0.0204 T22: 0.0630 REMARK 3 T33: 0.0242 T12: -0.0228 REMARK 3 T13: 0.0022 T23: 0.0188 REMARK 3 L TENSOR REMARK 3 L11: 1.4086 L22: 1.7982 REMARK 3 L33: 1.0081 L12: 0.2236 REMARK 3 L13: 0.0379 L23: -0.1485 REMARK 3 S TENSOR REMARK 3 S11: -0.0672 S12: 0.1770 S13: 0.0751 REMARK 3 S21: -0.1380 S22: 0.0325 S23: -0.1533 REMARK 3 S31: -0.0234 S32: 0.1799 S33: 0.0348 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 236 REMARK 3 ORIGIN FOR THE GROUP (A): 21.3380 4.5067 10.7918 REMARK 3 T TENSOR REMARK 3 T11: 0.0391 T22: 0.0346 REMARK 3 T33: 0.0982 T12: -0.0235 REMARK 3 T13: -0.0592 T23: 0.0384 REMARK 3 L TENSOR REMARK 3 L11: 1.0923 L22: 0.7969 REMARK 3 L33: 1.4149 L12: -0.0094 REMARK 3 L13: -0.0163 L23: 0.0697 REMARK 3 S TENSOR REMARK 3 S11: -0.0103 S12: 0.1194 S13: 0.0240 REMARK 3 S21: -0.0652 S22: 0.0098 S23: 0.1632 REMARK 3 S31: -0.0380 S32: -0.0827 S33: 0.0005 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 4XXA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000204593. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 - 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36249 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.898 REMARK 200 RESOLUTION RANGE LOW (A) : 83.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03900 REMARK 200 FOR THE DATA SET : 31.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 9.60 REMARK 200 R MERGE FOR SHELL (I) : 0.22700 REMARK 200 R SYM FOR SHELL (I) : 0.22700 REMARK 200 FOR SHELL : 3.400 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: 4U2A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CUBIC-LIKE CRYSTALS, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 28.36633 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 56.73267 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 56.73267 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 28.36633 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -115.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 56.73267 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 0 REMARK 465 ALA A 1 REMARK 465 SER A 114 REMARK 465 SER A 237 REMARK 465 ASP A 238 REMARK 465 ASP A 239 REMARK 465 SER A 240 REMARK 465 ASN A 241 REMARK 465 LEU A 242 REMARK 465 GLU A 243 REMARK 465 HIS A 244 REMARK 465 HIS A 245 REMARK 465 HIS A 246 REMARK 465 HIS A 247 REMARK 465 HIS A 248 REMARK 465 HIS A 249 REMARK 465 MET B 0 REMARK 465 LYS B 116 REMARK 465 SER B 117 REMARK 465 SER B 237 REMARK 465 ASP B 238 REMARK 465 ASP B 239 REMARK 465 SER B 240 REMARK 465 ASN B 241 REMARK 465 LEU B 242 REMARK 465 GLU B 243 REMARK 465 HIS B 244 REMARK 465 HIS B 245 REMARK 465 HIS B 246 REMARK 465 HIS B 247 REMARK 465 HIS B 248 REMARK 465 HIS B 249 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 PRO B 236 C - N - CA ANGL. DEV. = 9.7 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 ASP A 40 -135.44 57.73 REMARK 500 GLN A 102 -168.54 -111.77 REMARK 500 HIS A 218 71.97 -104.85 REMARK 500 TRP A 227 130.70 -177.11 REMARK 500 LYS B 103 153.28 -49.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1PE A 304 REMARK 610 1PE B 304 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 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 124 OE2 REMARK 620 2 ASP A 126 OD2 102.4 REMARK 620 3 ASP A 133 OD1 162.8 94.0 REMARK 620 4 HIS A 138 NE2 85.1 89.5 89.7 REMARK 620 5 HOH A 437 O 87.1 169.2 76.2 86.1 REMARK 620 6 HOH A 465 O 91.4 93.1 93.1 176.1 91.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 126 OD1 REMARK 620 2 ASP A 126 OD2 55.1 REMARK 620 3 PHE A 128 O 73.8 106.5 REMARK 620 4 ASP A 133 OD2 113.3 76.9 79.9 REMARK 620 5 HOH A 429 O 116.6 81.1 169.6 95.3 REMARK 620 6 HOH A 433 O 68.5 110.4 92.0 170.5 91.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 124 OE2 REMARK 620 2 ASP B 126 OD2 99.4 REMARK 620 3 ASP B 133 OD1 166.5 93.4 REMARK 620 4 HIS B 138 NE2 88.5 88.8 87.6 REMARK 620 5 HOH B 426 O 87.8 172.8 79.5 91.7 REMARK 620 6 HOH B 472 O 87.6 87.0 97.4 173.7 93.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 126 OD1 REMARK 620 2 ASP B 126 OD2 56.0 REMARK 620 3 PHE B 128 O 73.9 107.3 REMARK 620 4 ASP B 133 OD2 119.4 81.0 82.5 REMARK 620 5 HOH B 427 O 112.7 77.8 173.4 94.4 REMARK 620 6 HOH B 442 O 62.9 109.2 85.4 166.2 96.9 REMARK 620 N 1 2 3 4 5 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE B 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WV8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A RECOMBINANT VATAIREA MACROCARPA SEED LECTIN REMARK 900 COMPLEXED WITH LACTOSE REMARK 900 RELATED ID: 4XTM RELATED DB: PDB REMARK 900 RELATED ID: 4XTP RELATED DB: PDB DBREF 4XXA A 2 241 UNP P81371 LECS_VATMA 1 240 DBREF 4XXA B 2 241 UNP P81371 LECS_VATMA 1 240 SEQADV 4XXA MET A 0 UNP P81371 INITIATING METHIONINE SEQADV 4XXA ALA A 1 UNP P81371 EXPRESSION TAG SEQADV 4XXA LEU A 242 UNP P81371 EXPRESSION TAG SEQADV 4XXA GLU A 243 UNP P81371 EXPRESSION TAG SEQADV 4XXA HIS A 244 UNP P81371 EXPRESSION TAG SEQADV 4XXA HIS A 245 UNP P81371 EXPRESSION TAG SEQADV 4XXA HIS A 246 UNP P81371 EXPRESSION TAG SEQADV 4XXA HIS A 247 UNP P81371 EXPRESSION TAG SEQADV 4XXA HIS A 248 UNP P81371 EXPRESSION TAG SEQADV 4XXA HIS A 249 UNP P81371 EXPRESSION TAG SEQADV 4XXA MET B 0 UNP P81371 INITIATING METHIONINE SEQADV 4XXA ALA B 1 UNP P81371 EXPRESSION TAG SEQADV 4XXA LEU B 242 UNP P81371 EXPRESSION TAG SEQADV 4XXA GLU B 243 UNP P81371 EXPRESSION TAG SEQADV 4XXA HIS B 244 UNP P81371 EXPRESSION TAG SEQADV 4XXA HIS B 245 UNP P81371 EXPRESSION TAG SEQADV 4XXA HIS B 246 UNP P81371 EXPRESSION TAG SEQADV 4XXA HIS B 247 UNP P81371 EXPRESSION TAG SEQADV 4XXA HIS B 248 UNP P81371 EXPRESSION TAG SEQADV 4XXA HIS B 249 UNP P81371 EXPRESSION TAG SEQRES 1 A 250 MET ALA SER GLU VAL VAL SER PHE SER PHE THR LYS PHE SEQRES 2 A 250 ASN PRO ASN PRO LYS ASP ILE ILE LEU GLN GLY ASP ALA SEQRES 3 A 250 LEU VAL THR SER LYS GLY LYS LEU GLN LEU THR LYS VAL SEQRES 4 A 250 LYS ASP GLY LYS PRO VAL ASP HIS SER LEU GLY ARG ALA SEQRES 5 A 250 LEU TYR ALA ALA PRO ILE HIS ILE TRP ASP ASP SER THR SEQRES 6 A 250 ASP ARG VAL ALA SER PHE ALA THR SER PHE SER PHE VAL SEQRES 7 A 250 VAL GLU ALA PRO ASP GLU SER LYS THR ALA ASP GLY ILE SEQRES 8 A 250 ALA PHE PHE LEU ALA PRO PRO ASP THR GLN PRO GLN LYS SEQRES 9 A 250 ASP GLY GLY PHE LEU GLY LEU PHE ASN ASP SER ASN LYS SEQRES 10 A 250 SER ILE GLN THR VAL ALA VAL GLU PHE ASP THR PHE SER SEQRES 11 A 250 ASN THR TRP ASP PRO SER ALA ARG HIS ILE GLY ILE ASN SEQRES 12 A 250 VAL ASN SER ILE GLU SER MET LYS TYR VAL LYS TRP GLY SEQRES 13 A 250 TRP GLU ASN GLY LYS VAL ALA ASN VAL TYR ILE SER TYR SEQRES 14 A 250 GLU ALA SER THR LYS THR LEU THR ALA SER LEU THR TYR SEQRES 15 A 250 PRO SER ASN ALA THR SER TYR ILE VAL SER ALA ASN VAL SEQRES 16 A 250 ASP LEU LYS SER ALA LEU PRO GLU TRP VAL ARG VAL GLY SEQRES 17 A 250 PHE SER ALA THR SER GLY LEU SER ARG ASP HIS VAL GLU SEQRES 18 A 250 THR HIS ASP VAL LEU ASP TRP SER PHE THR SER THR LEU SEQRES 19 A 250 GLN ALA PRO SER ASP ASP SER ASN LEU GLU HIS HIS HIS SEQRES 20 A 250 HIS HIS HIS SEQRES 1 B 250 MET ALA SER GLU VAL VAL SER PHE SER PHE THR LYS PHE SEQRES 2 B 250 ASN PRO ASN PRO LYS ASP ILE ILE LEU GLN GLY ASP ALA SEQRES 3 B 250 LEU VAL THR SER LYS GLY LYS LEU GLN LEU THR LYS VAL SEQRES 4 B 250 LYS ASP GLY LYS PRO VAL ASP HIS SER LEU GLY ARG ALA SEQRES 5 B 250 LEU TYR ALA ALA PRO ILE HIS ILE TRP ASP ASP SER THR SEQRES 6 B 250 ASP ARG VAL ALA SER PHE ALA THR SER PHE SER PHE VAL SEQRES 7 B 250 VAL GLU ALA PRO ASP GLU SER LYS THR ALA ASP GLY ILE SEQRES 8 B 250 ALA PHE PHE LEU ALA PRO PRO ASP THR GLN PRO GLN LYS SEQRES 9 B 250 ASP GLY GLY PHE LEU GLY LEU PHE ASN ASP SER ASN LYS SEQRES 10 B 250 SER ILE GLN THR VAL ALA VAL GLU PHE ASP THR PHE SER SEQRES 11 B 250 ASN THR TRP ASP PRO SER ALA ARG HIS ILE GLY ILE ASN SEQRES 12 B 250 VAL ASN SER ILE GLU SER MET LYS TYR VAL LYS TRP GLY SEQRES 13 B 250 TRP GLU ASN GLY LYS VAL ALA ASN VAL TYR ILE SER TYR SEQRES 14 B 250 GLU ALA SER THR LYS THR LEU THR ALA SER LEU THR TYR SEQRES 15 B 250 PRO SER ASN ALA THR SER TYR ILE VAL SER ALA ASN VAL SEQRES 16 B 250 ASP LEU LYS SER ALA LEU PRO GLU TRP VAL ARG VAL GLY SEQRES 17 B 250 PHE SER ALA THR SER GLY LEU SER ARG ASP HIS VAL GLU SEQRES 18 B 250 THR HIS ASP VAL LEU ASP TRP SER PHE THR SER THR LEU SEQRES 19 B 250 GLN ALA PRO SER ASP ASP SER ASN LEU GLU HIS HIS HIS SEQRES 20 B 250 HIS HIS HIS HET CA A 301 1 HET MN A 302 1 HET GOL A 303 6 HET 1PE A 304 11 HET CA B 301 1 HET MN B 302 1 HET GOL B 303 6 HET 1PE B 304 10 HETNAM CA CALCIUM ION HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN 1PE PEG400 FORMUL 3 CA 2(CA 2+) FORMUL 4 MN 2(MN 2+) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 6 1PE 2(C10 H22 O6) FORMUL 11 HOH *153(H2 O) HELIX 1 AA1 ASP A 62 ASP A 65 5 4 HELIX 2 AA2 ASP A 104 LEU A 108 5 5 HELIX 3 AA3 ASP A 195 LEU A 200 1 6 HELIX 4 AA4 ASP B 104 LEU B 108 5 5 HELIX 5 AA5 ALA B 170 THR B 172 5 3 HELIX 6 AA6 ASP B 195 LEU B 200 1 6 SHEET 1 AA1 4 GLU A 3 PHE A 9 0 SHEET 2 AA1 4 ASP A 223 GLN A 234 -1 O PHE A 229 N PHE A 7 SHEET 3 AA1 4 ARG A 66 VAL A 77 -1 N SER A 75 O LEU A 225 SHEET 4 AA1 4 TRP A 60 ASP A 61 -1 N ASP A 61 O ARG A 66 SHEET 1 AA2 7 LEU A 26 VAL A 27 0 SHEET 2 AA2 7 LEU A 33 GLN A 34 -1 O GLN A 34 N LEU A 26 SHEET 3 AA2 7 ASP A 223 GLN A 234 -1 O VAL A 224 N LEU A 33 SHEET 4 AA2 7 ARG A 66 VAL A 77 -1 N SER A 75 O LEU A 225 SHEET 5 AA2 7 ALA A 162 GLU A 169 -1 O VAL A 164 N PHE A 74 SHEET 6 AA2 7 THR A 174 TYR A 181 -1 O THR A 180 N ASN A 163 SHEET 7 AA2 7 THR A 186 ASN A 193 -1 O VAL A 190 N ALA A 177 SHEET 1 AA3 4 ILE A 19 GLY A 23 0 SHEET 2 AA3 4 LEU A 48 TYR A 53 -1 O LEU A 52 N ILE A 20 SHEET 3 AA3 4 TRP A 203 SER A 212 -1 O VAL A 206 N TYR A 53 SHEET 4 AA3 4 ILE A 57 HIS A 58 -1 N ILE A 57 O VAL A 204 SHEET 1 AA4 7 ILE A 19 GLY A 23 0 SHEET 2 AA4 7 LEU A 48 TYR A 53 -1 O LEU A 52 N ILE A 20 SHEET 3 AA4 7 TRP A 203 SER A 212 -1 O VAL A 206 N TYR A 53 SHEET 4 AA4 7 ASP A 88 ALA A 95 -1 N ALA A 95 O ARG A 205 SHEET 5 AA4 7 VAL A 121 ASP A 126 -1 O PHE A 125 N ILE A 90 SHEET 6 AA4 7 HIS A 138 VAL A 143 -1 O ASN A 142 N ALA A 122 SHEET 7 AA4 7 LYS A 150 LYS A 153 -1 O LYS A 150 N ILE A 141 SHEET 1 AA5 2 VAL A 38 LYS A 39 0 SHEET 2 AA5 2 LYS A 42 PRO A 43 -1 O LYS A 42 N LYS A 39 SHEET 1 AA6 4 GLU B 3 PHE B 9 0 SHEET 2 AA6 4 ASP B 223 LEU B 233 -1 O LEU B 233 N GLU B 3 SHEET 3 AA6 4 LEU B 33 GLN B 34 -1 N LEU B 33 O VAL B 224 SHEET 4 AA6 4 LEU B 26 VAL B 27 -1 N LEU B 26 O GLN B 34 SHEET 1 AA7 6 GLU B 3 PHE B 9 0 SHEET 2 AA7 6 ASP B 223 LEU B 233 -1 O LEU B 233 N GLU B 3 SHEET 3 AA7 6 SER B 69 VAL B 77 -1 N SER B 73 O SER B 228 SHEET 4 AA7 6 ALA B 162 GLU B 169 -1 O TYR B 168 N PHE B 70 SHEET 5 AA7 6 THR B 174 TYR B 181 -1 O THR B 176 N SER B 167 SHEET 6 AA7 6 THR B 186 ASN B 193 -1 O ALA B 192 N LEU B 175 SHEET 1 AA8 4 ILE B 19 GLY B 23 0 SHEET 2 AA8 4 LEU B 48 TYR B 53 -1 O LEU B 52 N ILE B 20 SHEET 3 AA8 4 TRP B 203 SER B 212 -1 O VAL B 206 N TYR B 53 SHEET 4 AA8 4 ILE B 57 HIS B 58 -1 N ILE B 57 O VAL B 204 SHEET 1 AA9 7 ILE B 19 GLY B 23 0 SHEET 2 AA9 7 LEU B 48 TYR B 53 -1 O LEU B 52 N ILE B 20 SHEET 3 AA9 7 TRP B 203 SER B 212 -1 O VAL B 206 N TYR B 53 SHEET 4 AA9 7 ASP B 88 ALA B 95 -1 N ALA B 91 O SER B 209 SHEET 5 AA9 7 VAL B 121 ASP B 126 -1 O PHE B 125 N ILE B 90 SHEET 6 AA9 7 HIS B 138 VAL B 143 -1 O ASN B 142 N ALA B 122 SHEET 7 AA9 7 LYS B 150 LYS B 153 -1 O LYS B 150 N ILE B 141 SHEET 1 AB1 2 VAL B 38 LYS B 39 0 SHEET 2 AB1 2 LYS B 42 PRO B 43 -1 O LYS B 42 N LYS B 39 SHEET 1 AB2 2 TRP B 60 ASP B 61 0 SHEET 2 AB2 2 ARG B 66 VAL B 67 -1 O ARG B 66 N ASP B 61 LINK OE2 GLU A 124 MN MN A 302 1555 1555 2.21 LINK OD1 ASP A 126 CA CA A 301 1555 1555 2.50 LINK OD2 ASP A 126 CA CA A 301 1555 1555 2.22 LINK OD2 ASP A 126 MN MN A 302 1555 1555 2.33 LINK O PHE A 128 CA CA A 301 1555 1555 2.36 LINK OD2 ASP A 133 CA CA A 301 1555 1555 2.34 LINK OD1 ASP A 133 MN MN A 302 1555 1555 2.32 LINK NE2 HIS A 138 MN MN A 302 1555 1555 2.15 LINK CA CA A 301 O HOH A 429 1555 1555 2.54 LINK CA CA A 301 O HOH A 433 1555 1555 2.34 LINK MN MN A 302 O HOH A 437 1555 1555 2.25 LINK MN MN A 302 O HOH A 465 1555 1555 2.05 LINK OE2 GLU B 124 MN MN B 302 1555 1555 2.25 LINK OD1 ASP B 126 CA CA B 301 1555 1555 2.49 LINK OD2 ASP B 126 CA CA B 301 1555 1555 2.15 LINK OD2 ASP B 126 MN MN B 302 1555 1555 2.40 LINK O PHE B 128 CA CA B 301 1555 1555 2.26 LINK OD2 ASP B 133 CA CA B 301 1555 1555 2.37 LINK OD1 ASP B 133 MN MN B 302 1555 1555 2.25 LINK NE2 HIS B 138 MN MN B 302 1555 1555 2.29 LINK CA CA B 301 O HOH B 427 1555 1555 2.44 LINK CA CA B 301 O HOH B 442 1555 1555 2.58 LINK MN MN B 302 O HOH B 426 1555 1555 2.20 LINK MN MN B 302 O HOH B 472 1555 1555 2.24 CISPEP 1 ALA A 87 ASP A 88 0 -8.66 CISPEP 2 ALA B 87 ASP B 88 0 -6.54 SITE 1 AC1 6 ASP A 126 PHE A 128 ASN A 130 ASP A 133 SITE 2 AC1 6 HOH A 429 HOH A 433 SITE 1 AC2 6 GLU A 124 ASP A 126 ASP A 133 HIS A 138 SITE 2 AC2 6 HOH A 437 HOH A 465 SITE 1 AC3 7 ASP A 88 GLY A 106 PHE A 128 ASN A 130 SITE 2 AC3 7 GLY A 213 LEU A 214 SER A 215 SITE 1 AC4 5 HIS A 46 ASP A 104 LEU A 214 HOH A 405 SITE 2 AC4 5 1PE B 304 SITE 1 AC5 6 ASP B 126 PHE B 128 ASN B 130 ASP B 133 SITE 2 AC5 6 HOH B 427 HOH B 442 SITE 1 AC6 6 GLU B 124 ASP B 126 ASP B 133 HIS B 138 SITE 2 AC6 6 HOH B 426 HOH B 472 SITE 1 AC7 8 ASP B 88 GLY B 106 ASP B 113 PHE B 128 SITE 2 AC7 8 ASN B 130 GLY B 213 LEU B 214 HOH B 401 SITE 1 AC8 5 1PE A 304 HOH A 405 GLU B 79 ASN B 158 SITE 2 AC8 5 HOH B 486 CRYST1 96.083 96.083 85.099 90.00 90.00 120.00 P 31 2 1 12 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 0.010408 0.006009 0.000000 0.00000 SCALE2 0.000000 0.012018 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011751 0.00000