HEADER CELL ADHESION 16-APR-99 2LIS TITLE HIGH RESOLUTION STRUCTURE OF THE RED ABALONE LYSIN MONOMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPERM LYSIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALIOTIS RUFESCENS; SOURCE 3 ORGANISM_COMMON: CALIFORNIA RED ABALONE; SOURCE 4 ORGANISM_TAXID: 6454; SOURCE 5 ORGAN: GONAD; SOURCE 6 CELL: SPERM; SOURCE 7 ORGANELLE: ACROSOME GRANULE KEYWDS ABALONE LYSIN, FERTILIZATION PROTEIN, GAMETE RECOGNITION PROTEIN, KEYWDS 2 CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR N.KRESGE,V.D.VACQUIER,C.D.STOUT REVDAT 6 27-DEC-23 2LIS 1 REMARK REVDAT 5 04-OCT-17 2LIS 1 REMARK REVDAT 4 24-FEB-09 2LIS 1 VERSN REVDAT 3 01-APR-03 2LIS 1 JRNL REVDAT 2 23-MAY-00 2LIS 1 DBREF REMARK REVDAT 1 21-JAN-00 2LIS 0 JRNL AUTH N.KRESGE,V.D.VACQUIER,C.D.STOUT JRNL TITL 1.35 AND 2.07 A RESOLUTION STRUCTURES OF THE RED ABALONE JRNL TITL 2 SPERM LYSIN MONOMER AND DIMER REVEAL FEATURES INVOLVED IN JRNL TITL 3 RECEPTOR BINDING. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 56 34 2000 JRNL REFN ISSN 0907-4449 JRNL PMID 10666624 JRNL DOI 10.1107/S0907444999014626 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : 5% OF REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.137 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.136 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2071 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 39350 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.135 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.134 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2007 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 38167 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1104 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 284 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1388.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1133.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 12587 REMARK 3 NUMBER OF RESTRAINTS : 14715 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.021 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.272 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.069 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.070 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.020 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REMARK 4 REMARK 4 2LIS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-99. REMARK 100 THE DEPOSITION ID IS D_1000000867. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-98 REMARK 200 TEMPERATURE (KELVIN) : 100.00 REMARK 200 PH : 9.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 41576 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 18.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 4.50000 REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 8.20000 REMARK 200 FOR SHELL : 8.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: REMARK 200 STRUCTURE WAS REFINED BY PHASE EXTENSION USING 1.9 A STRUCTURE OF REMARK 200 RED ABALONE REMARK 200 LYSIN MONOMER AS A STARTING POINT REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.26 M AMMONIUM SULFATE, 100 MM CHESS REMARK 280 PH 9.5, 200 MM NACL, PH 9.50 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 25.70500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.57000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.65500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.57000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.70500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.65500 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 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 ARG A 1 REMARK 465 SER A 2 REMARK 465 TRP A 3 REMARK 465 GLY A 135 REMARK 465 LYS A 136 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 40 NH1 - CZ - NH2 ANGL. DEV. = -6.7 DEGREES REMARK 500 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 55 CD - NE - CZ ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG A 56 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 87 CD - NE - CZ ANGL. DEV. = 10.5 DEGREES REMARK 500 ARG A 94 CD - NE - CZ ANGL. DEV. = 13.7 DEGREES REMARK 500 ARG A 94 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 123 CD - NE - CZ ANGL. DEV. = 12.7 DEGREES REMARK 500 ARG A 123 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 125 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2LYN RELATED DB: PDB REMARK 900 DIMER DBREF 2LIS A 1 136 UNP P04552 ELYS_HALRU 1 136 SEQRES 1 A 136 ARG SER TRP HIS TYR VAL GLU PRO LYS PHE LEU ASN LYS SEQRES 2 A 136 ALA PHE GLU VAL ALA LEU LYS VAL GLN ILE ILE ALA GLY SEQRES 3 A 136 PHE ASP ARG GLY LEU VAL LYS TRP LEU ARG VAL HIS GLY SEQRES 4 A 136 ARG THR LEU SER THR VAL GLN LYS LYS ALA LEU TYR PHE SEQRES 5 A 136 VAL ASN ARG ARG TYR MET GLN THR HIS TRP ALA ASN TYR SEQRES 6 A 136 MET LEU TRP ILE ASN LYS LYS ILE ASP ALA LEU GLY ARG SEQRES 7 A 136 THR PRO VAL VAL GLY ASP TYR THR ARG LEU GLY ALA GLU SEQRES 8 A 136 ILE GLY ARG ARG ILE ASP MET ALA TYR PHE TYR ASP PHE SEQRES 9 A 136 LEU LYS ASP LYS ASN MET ILE PRO LYS TYR LEU PRO TYR SEQRES 10 A 136 MET GLU GLU ILE ASN ARG MET ARG PRO ALA ASP VAL PRO SEQRES 11 A 136 VAL LYS TYR MET GLY LYS FORMUL 2 HOH *284(H2 O) HELIX 1 1 LYS A 13 THR A 41 1 29 HELIX 2 2 THR A 44 ASP A 74 1 31 HELIX 3 3 VAL A 82 ARG A 95 1 14 HELIX 4 4 MET A 98 ASP A 107 1 10 HELIX 5 5 PRO A 116 ARG A 123 1 8 HELIX 6 6 PRO A 126 ASP A 128 5 3 CRYST1 51.410 45.310 81.140 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 0.019451 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022070 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012324 0.00000