HEADER LECTIN 13-OCT-93 1HLC TITLE X-RAY CRYSTAL STRUCTURE OF THE HUMAN DIMERIC S-LAC LECTIN, L-14-II, IN TITLE 2 COMPLEX WITH LACTOSE AT 2.9 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN LECTIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CDNA KEYWDS LECTIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.D.LOBSANOV,M.A.GITT,H.LEFFLER,S.BARONDES,J.M.RINI REVDAT 6 07-FEB-24 1HLC 1 HETSYN REVDAT 5 29-JUL-20 1HLC 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 21-JUL-09 1HLC 1 HETATM REVDAT 3 24-FEB-09 1HLC 1 VERSN REVDAT 2 01-APR-03 1HLC 1 JRNL REVDAT 1 30-APR-94 1HLC 0 JRNL AUTH Y.D.LOBSANOV,M.A.GITT,H.LEFFLER,S.H.BARONDES,J.M.RINI JRNL TITL X-RAY CRYSTAL STRUCTURE OF THE HUMAN DIMERIC S-LAC LECTIN, JRNL TITL 2 L-14-II, IN COMPLEX WITH LACTOSE AT 2.9-A RESOLUTION. JRNL REF J.BIOL.CHEM. V. 268 27034 1993 JRNL REFN ISSN 0021-9258 JRNL PMID 8262940 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.D.LOBSANOV,M.A.GITT,H.LEFFLER,S.BARONDES,J.M.RINI REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION ANALYSIS REMARK 1 TITL 2 OF THE HUMAN DIMERIC S-LAC LECTIN (L-14-II) REMARK 1 REF J.MOL.BIOL. V. 233 553 1993 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 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 : 5469 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) : 0.177 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 2020 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.600 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 1HLC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173893. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 21.80000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.10000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.10000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.80000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.90000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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: 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 CYS B 57 CA - CB - SG ANGL. DEV. = 7.3 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 SER A 53 61.95 61.36 REMARK 500 ASP A 61 77.28 -118.11 REMARK 500 CYS A 75 49.30 -106.18 REMARK 500 SER A 115 -11.41 -151.81 REMARK 500 ASP B 99 34.82 -97.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE ADVISORY NOTICE: REMARK 999 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. REMARK 999 REMARK 999 SWISS-PROT ENTRY NAME: LEG1_HUMAN REMARK 999 REMARK 999 SWISS-PROT RESIDUE PDB ATOMS RECORDS REMARK 999 NAME NUMBER NAME CHAIN SEQ REMARK 999 ILE 116 VAL 116 REMARK 999 REMARK 999 THE SEQUENCE REPORTED HERE IS CORRECT AS CONFIRMED BY REMARK 999 PROTEIN SEQUENCING. THERE IS AN ERROR IN THE DNA SEQUENCE REMARK 999 DATA BASE. DBREF 1HLC A 4 132 UNP P05162 LEG2_HUMAN 4 132 DBREF 1HLC B 4 132 UNP P05162 LEG2_HUMAN 4 132 SEQRES 1 A 129 GLU LEU GLU VAL LYS ASN MET ASP MET LYS PRO GLY SER SEQRES 2 A 129 THR LEU LYS ILE THR GLY SER ILE ALA ASP GLY THR ASP SEQRES 3 A 129 GLY PHE VAL ILE ASN LEU GLY GLN GLY THR ASP LYS LEU SEQRES 4 A 129 ASN LEU HIS PHE ASN PRO ARG PHE SER GLU SER THR ILE SEQRES 5 A 129 VAL CYS ASN SER LEU ASP GLY SER ASN TRP GLY GLN GLU SEQRES 6 A 129 GLN ARG GLU ASP HIS LEU CYS PHE SER PRO GLY SER GLU SEQRES 7 A 129 VAL LYS PHE THR VAL THR PHE GLU SER ASP LYS PHE LYS SEQRES 8 A 129 VAL LYS LEU PRO ASP GLY HIS GLU LEU THR PHE PRO ASN SEQRES 9 A 129 ARG LEU GLY HIS SER HIS LEU SER TYR LEU SER VAL ARG SEQRES 10 A 129 GLY GLY PHE ASN MET SER SER PHE LYS LEU LYS GLU SEQRES 1 B 129 GLU LEU GLU VAL LYS ASN MET ASP MET LYS PRO GLY SER SEQRES 2 B 129 THR LEU LYS ILE THR GLY SER ILE ALA ASP GLY THR ASP SEQRES 3 B 129 GLY PHE VAL ILE ASN LEU GLY GLN GLY THR ASP LYS LEU SEQRES 4 B 129 ASN LEU HIS PHE ASN PRO ARG PHE SER GLU SER THR ILE SEQRES 5 B 129 VAL CYS ASN SER LEU ASP GLY SER ASN TRP GLY GLN GLU SEQRES 6 B 129 GLN ARG GLU ASP HIS LEU CYS PHE SER PRO GLY SER GLU SEQRES 7 B 129 VAL LYS PHE THR VAL THR PHE GLU SER ASP LYS PHE LYS SEQRES 8 B 129 VAL LYS LEU PRO ASP GLY HIS GLU LEU THR PHE PRO ASN SEQRES 9 B 129 ARG LEU GLY HIS SER HIS LEU SER TYR LEU SER VAL ARG SEQRES 10 B 129 GLY GLY PHE ASN MET SER SER PHE LYS LEU LYS GLU HET BGC C 1 12 HET GAL C 2 11 HET BGC D 1 12 HET GAL D 2 11 HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE FORMUL 3 BGC 2(C6 H12 O6) FORMUL 3 GAL 2(C6 H12 O6) SHEET 1 A10 PHE A 105 PRO A 106 0 SHEET 2 A10 LYS A 92 LYS A 96 -1 N PHE A 93 O PHE A 105 SHEET 3 A10 GLU A 81 THR A 87 -1 O THR A 85 N LYS A 96 SHEET 4 A10 THR A 17 ILE A 24 -1 N LEU A 18 O VAL A 86 SHEET 5 A10 PHE A 123 LYS A 131 -1 O ASN A 124 N SER A 23 SHEET 6 A10 PHE B 123 LYS B 131 -1 O SER B 126 N LEU A 130 SHEET 7 A10 THR B 17 ILE B 24 -1 N THR B 17 O LYS B 131 SHEET 8 A10 GLU B 81 GLU B 89 -1 O VAL B 82 N GLY B 22 SHEET 9 A10 LYS B 92 LYS B 96 -1 O LYS B 92 N GLU B 89 SHEET 10 A10 GLU B 102 PRO B 106 -1 N LEU B 103 O VAL B 95 LINK O4 BGC C 1 C1 GAL C 2 1555 1555 1.39 LINK O4 BGC D 1 C1 GAL D 2 1555 1555 1.39 CRYST1 43.600 57.800 108.200 90.00 90.00 90.00 P 21 21 21 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 0.022936 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017301 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009242 0.00000