HEADER SUGAR BINDING PROTEIN 12-SEP-03 1ULM TITLE CRYSTAL STRUCTURE OF POKEWEED LECTIN-D2 COMPLEXED WITH TRI-N- TITLE 2 ACETYLCHITOTRIOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LECTIN-D2; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYTOLACCA AMERICANA; SOURCE 3 ORGANISM_COMMON: AMERICAN POKEWEED; SOURCE 4 ORGANISM_TAXID: 3527; SOURCE 5 TISSUE: ROOTS KEYWDS LECTIN, CHITIN-BINDING, HEVEIN DOMAIN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.HAYASHIDA,T.FUJII,M.ISHIGURO,Y.HATA REVDAT 5 27-DEC-23 1ULM 1 HETSYN REVDAT 4 29-JUL-20 1ULM 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 13-JUL-11 1ULM 1 VERSN REVDAT 2 24-FEB-09 1ULM 1 VERSN REVDAT 1 23-DEC-03 1ULM 0 JRNL AUTH M.HAYASHIDA,T.FUJII,M.HAMASU,M.ISHIGURO,Y.HATA JRNL TITL SIMILARITY BETWEEN PROTEIN-PROTEIN AND PROTEIN-CARBOHYDRATE JRNL TITL 2 INTERACTIONS, REVEALED BY TWO CRYSTAL STRUCTURES OF LECTINS JRNL TITL 3 FROM THE ROOTS OF POKEWEED. JRNL REF J.MOL.BIOL. V. 334 551 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 14623194 JRNL DOI 10.1016/J.JMB.2003.09.076 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 889490.450 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 14699 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 SET) : 0.195 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1495 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2165 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE : 0.2990 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 223 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1246 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 122 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.93000 REMARK 3 B22 (A**2) : 3.28000 REMARK 3 B33 (A**2) : -1.34000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.12 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.760 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 37.50 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NAG.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NAG.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ULM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-SEP-03. REMARK 100 THE DEPOSITION ID IS D_1000005962. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (TRUNCATE) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14699 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 24.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.34200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, MAGNESIUM ACETATE, SODIUM REMARK 280 CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 49.28050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.14100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.28050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.14100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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: 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 O4 NAG D 2 C2 NAG D 3 2.15 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 75 98.88 49.79 REMARK 500 ASN B 115 8.35 57.97 REMARK 500 ASP B 175 74.03 63.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ULK RELATED DB: PDB REMARK 900 POKEWEED LECTIN-C DBREF 1ULM A 1 82 UNP P83790 LED2_PHYAM 1 82 DBREF 1ULM B 101 182 UNP P83790 LED2_PHYAM 1 82 SEQRES 1 A 82 ALA PRO GLU CYS GLY GLU ARG ALA SER GLY LYS ARG CYS SEQRES 2 A 82 PRO ASN GLY LYS CYS CYS SER GLN TRP GLY TYR CYS GLY SEQRES 3 A 82 THR THR ASP ASN TYR CYS GLY GLN GLY CYS GLN SER GLN SEQRES 4 A 82 CYS ASP TYR TRP ARG CYS GLY ARG ASP PHE GLY GLY ARG SEQRES 5 A 82 LEU CYS GLU GLU ASP MET CYS CYS SER LYS TYR GLY TRP SEQRES 6 A 82 CYS GLY TYR SER ASP ASP HIS CYS GLU ASP GLY CYS GLN SEQRES 7 A 82 SER GLN CYS ASP SEQRES 1 B 82 ALA PRO GLU CYS GLY GLU ARG ALA SER GLY LYS ARG CYS SEQRES 2 B 82 PRO ASN GLY LYS CYS CYS SER GLN TRP GLY TYR CYS GLY SEQRES 3 B 82 THR THR ASP ASN TYR CYS GLY GLN GLY CYS GLN SER GLN SEQRES 4 B 82 CYS ASP TYR TRP ARG CYS GLY ARG ASP PHE GLY GLY ARG SEQRES 5 B 82 LEU CYS GLU GLU ASP MET CYS CYS SER LYS TYR GLY TRP SEQRES 6 B 82 CYS GLY TYR SER ASP ASP HIS CYS GLU ASP GLY CYS GLN SEQRES 7 B 82 SER GLN CYS ASP HET NAG C 1 15 HET NAG C 2 14 HET NAG C 3 14 HET NAG D 1 15 HET NAG D 2 14 HET NAG D 3 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 3 NAG 6(C8 H15 N O6) FORMUL 5 HOH *122(H2 O) HELIX 1 1 GLY A 5 SER A 9 5 5 HELIX 2 2 CYS A 13 LYS A 17 5 5 HELIX 3 3 THR A 28 GLY A 33 1 6 HELIX 4 4 GLY A 46 GLY A 50 5 5 HELIX 5 5 SER A 69 GLU A 74 1 6 HELIX 6 6 GLY B 105 SER B 109 5 5 HELIX 7 7 CYS B 113 LYS B 117 5 5 HELIX 8 8 THR B 128 GLY B 133 1 6 HELIX 9 9 GLY B 146 GLY B 150 5 5 HELIX 10 10 SER B 169 GLU B 174 1 6 SHEET 1 A 2 CYS A 18 CYS A 19 0 SHEET 2 A 2 CYS A 25 GLY A 26 -1 O GLY A 26 N CYS A 18 SHEET 1 B 2 CYS A 59 CYS A 60 0 SHEET 2 B 2 CYS A 66 GLY A 67 -1 O GLY A 67 N CYS A 59 SHEET 1 C 2 CYS B 118 CYS B 119 0 SHEET 2 C 2 CYS B 125 GLY B 126 -1 O GLY B 126 N CYS B 118 SHEET 1 D 2 CYS B 159 CYS B 160 0 SHEET 2 D 2 CYS B 166 GLY B 167 -1 O GLY B 167 N CYS B 159 SSBOND 1 CYS A 4 CYS A 19 1555 1555 2.03 SSBOND 2 CYS A 13 CYS A 25 1555 1555 2.03 SSBOND 3 CYS A 18 CYS A 32 1555 1555 2.03 SSBOND 4 CYS A 36 CYS A 40 1555 1555 2.03 SSBOND 5 CYS A 45 CYS A 60 1555 1555 2.03 SSBOND 6 CYS A 54 CYS A 66 1555 1555 2.03 SSBOND 7 CYS A 59 CYS A 73 1555 1555 2.03 SSBOND 8 CYS A 77 CYS A 81 1555 1555 2.02 SSBOND 9 CYS B 104 CYS B 119 1555 1555 2.04 SSBOND 10 CYS B 113 CYS B 125 1555 1555 2.02 SSBOND 11 CYS B 118 CYS B 132 1555 1555 2.03 SSBOND 12 CYS B 136 CYS B 140 1555 1555 2.02 SSBOND 13 CYS B 145 CYS B 160 1555 1555 2.03 SSBOND 14 CYS B 154 CYS B 166 1555 1555 2.02 SSBOND 15 CYS B 159 CYS B 173 1555 1555 2.03 SSBOND 16 CYS B 177 CYS B 181 1555 1555 2.02 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.46 LINK O4 NAG C 2 C1 NAG C 3 1555 1555 1.43 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.48 LINK O4 NAG D 2 C1 NAG D 3 1555 1555 1.46 CRYST1 98.561 26.282 65.217 90.00 109.90 90.00 C 1 2 1 8 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 0.010146 0.000000 0.003673 0.00000 SCALE2 0.000000 0.038049 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016307 0.00000