HEADER PLANT PROTEIN 20-FEB-00 1EHD TITLE CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ ISOLECTIN VI COMPND MOL_ID: 1; COMPND 2 MOLECULE: AGGLUTININ ISOLECTIN VI; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: URTICA DIOICA; SOURCE 3 ORGANISM_COMMON: GREAT NETTLE; SOURCE 4 ORGANISM_TAXID: 3501 KEYWDS TWO HOMOLOGOUS HEVEIN-LIKE DOMAINS, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.HARATA,M.MURAKI REVDAT 6 06-NOV-24 1EHD 1 REMARK REVDAT 5 25-DEC-19 1EHD 1 SEQADV SEQRES LINK REVDAT 4 18-APR-18 1EHD 1 REMARK REVDAT 3 04-OCT-17 1EHD 1 REMARK REVDAT 2 24-FEB-09 1EHD 1 VERSN REVDAT 1 05-APR-00 1EHD 0 JRNL AUTH K.HARATA,M.MURAKI JRNL TITL CRYSTAL STRUCTURES OF URTICA DIOICA AGGLUTININ AND ITS JRNL TITL 2 COMPLEX WITH TRI-N-ACETYLCHITOTRIOSE. JRNL REF J.MOL.BIOL. V. 297 673 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10731420 JRNL DOI 10.1006/JMBI.2000.3594 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 13142 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1212 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 641 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 54 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 3.010 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EHD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-00. REMARK 100 THE DEPOSITION ID IS D_1000010572. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-99 REMARK 200 TEMPERATURE (KELVIN) : 286 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR571 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS FAST REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MERGEF, MADNESS REMARK 200 DATA SCALING SOFTWARE : MERGEF REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19125 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 24.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : 0.03100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MIRPHS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG1000, SODIUM CITRATE, PH 5.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 15.96000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.22500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.64500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.22500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.96000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.64500 REMARK 290 SMTRY3 4 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: MONOMERIC 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 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 HIS A 67 NE2 HIS A 67 CD2 -0.066 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 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 16 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 TRP A 21 CD1 - CG - CD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 TRP A 21 CE2 - CD2 - CG ANGL. DEV. = -5.6 DEGREES REMARK 500 TRP A 23 CD1 - CG - CD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 TRP A 23 CE2 - CD2 - CG ANGL. DEV. = -6.1 DEGREES REMARK 500 TRP A 40 CD1 - CG - CD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 TRP A 40 CE2 - CD2 - CG ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 48 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 62 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 TRP A 69 CD1 - CG - CD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 TRP A 69 CE2 - CD2 - CG ANGL. DEV. = -5.8 DEGREES REMARK 500 TYR A 84 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 SER A 88 N - CA - C ANGL. DEV. = -17.4 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 THR A 34 30.29 -91.90 REMARK 500 HIS A 47 16.70 59.92 REMARK 500 SER A 87 52.06 22.55 REMARK 500 SER A 88 -99.58 151.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EHH RELATED DB: PDB REMARK 900 URTICA DIOICA AGGLUTININ IN COMPLEX WITH TRI-N-ACETYLCHITOTRIOSE DBREF 1EHD A 1 89 UNP Q9S7B3 Q9S7B3_URTDI 24 112 SEQADV 1EHD ALA A 10 UNP Q9S7B3 SER 33 CONFLICT SEQADV 1EHD LYS A 81 UNP Q9S7B3 ASN 104 CONFLICT SEQRES 1 A 89 PCA ARG CYS GLY SER GLN GLY GLY GLY ALA THR CYS PRO SEQRES 2 A 89 GLY LEU ARG CYS CYS SER ILE TRP GLY TRP CYS GLY ASP SEQRES 3 A 89 SER GLU PRO TYR CYS GLY ARG THR CYS GLU ASN LYS CYS SEQRES 4 A 89 TRP SER GLY GLU ARG SER ASP HIS ARG CYS GLY ALA ALA SEQRES 5 A 89 VAL GLY ASN PRO PRO CYS GLY GLN ASP ARG CYS CYS SER SEQRES 6 A 89 VAL HIS GLY TRP CYS GLY GLY GLY ASN ASP TYR CYS SER SEQRES 7 A 89 GLY GLY LYS CYS GLN TYR ARG CYS SER SER SER MODRES 1EHD PCA A 1 GLN PYROGLUTAMIC ACID HET PCA A 1 8 HETNAM PCA PYROGLUTAMIC ACID FORMUL 1 PCA C5 H7 N O3 FORMUL 2 HOH *54(H2 O) HELIX 1 1 GLY A 4 GLY A 8 5 5 HELIX 2 2 CYS A 12 ARG A 16 5 5 HELIX 3 3 SER A 27 GLY A 32 1 6 HELIX 4 4 CYS A 39 GLU A 43 5 5 HELIX 5 5 GLY A 50 GLY A 54 5 5 HELIX 6 6 GLY A 73 SER A 78 1 6 SHEET 1 A 3 CYS A 24 GLY A 25 0 SHEET 2 A 3 CYS A 17 SER A 19 -1 O CYS A 17 N GLY A 25 SHEET 3 A 3 CYS A 35 ASN A 37 -1 N GLU A 36 O CYS A 18 SHEET 1 B 3 CYS A 70 GLY A 71 0 SHEET 2 B 3 CYS A 63 SER A 65 -1 N CYS A 63 O GLY A 71 SHEET 3 B 3 CYS A 82 TYR A 84 -1 N GLN A 83 O CYS A 64 SSBOND 1 CYS A 3 CYS A 18 1555 1555 2.04 SSBOND 2 CYS A 12 CYS A 24 1555 1555 2.04 SSBOND 3 CYS A 17 CYS A 31 1555 1555 1.95 SSBOND 4 CYS A 35 CYS A 39 1555 1555 2.00 SSBOND 5 CYS A 49 CYS A 64 1555 1555 2.02 SSBOND 6 CYS A 58 CYS A 70 1555 1555 2.04 SSBOND 7 CYS A 63 CYS A 77 1555 1555 2.02 SSBOND 8 CYS A 82 CYS A 86 1555 1555 2.04 LINK C PCA A 1 N ARG A 2 1555 1555 1.31 CRYST1 31.920 41.290 76.450 90.00 90.00 90.00 P 21 21 21 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 0.031328 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024219 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013080 0.00000 HETATM 1 N PCA A 1 19.765 6.417 6.773 1.00 25.30 N HETATM 2 CA PCA A 1 18.807 5.895 5.825 1.00 24.18 C HETATM 3 CB PCA A 1 17.512 5.712 6.606 1.00 24.07 C HETATM 4 CG PCA A 1 17.773 6.405 7.906 1.00 24.61 C HETATM 5 CD PCA A 1 19.179 6.956 7.830 1.00 25.46 C HETATM 6 OE PCA A 1 19.785 7.402 8.804 1.00 25.42 O HETATM 7 C PCA A 1 18.623 6.787 4.609 1.00 22.03 C HETATM 8 O PCA A 1 19.360 7.742 4.362 1.00 20.55 O