HEADER CELL ADHESION 19-MAY-99 3LYN TITLE STRUCTURE OF GREEN ABALONE LYSIN DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPERM LYSIN; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALIOTIS FULGENS; SOURCE 3 ORGANISM_TAXID: 6456; SOURCE 4 ORGAN: GONAD; SOURCE 5 CELL: SPERM; SOURCE 6 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 4 27-DEC-23 3LYN 1 REMARK REVDAT 3 04-OCT-17 3LYN 1 REMARK REVDAT 2 24-FEB-09 3LYN 1 VERSN REVDAT 1 15-MAR-00 3LYN 0 JRNL AUTH N.KRESGE,V.D.VACQUIER,C.D.STOUT JRNL TITL THE HIGH RESOLUTION CRYSTAL STRUCTURE OF GREEN ABALONE SPERM JRNL TITL 2 LYSIN: IMPLICATIONS FOR SPECIES-SPECIFIC BINDING OF THE EGG JRNL TITL 3 RECEPTOR. JRNL REF J.MOL.BIOL. V. 296 1225 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10698629 JRNL DOI 10.1006/JMBI.2000.3533 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : 5% OF DATA REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.215 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.213 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2588 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 44062 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.200 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.198 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1947 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 38483 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2050 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 218 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2268.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 9088 REMARK 3 NUMBER OF RESTRAINTS : 8445 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.020 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.260 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.037 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.046 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.008 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)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: TER REMARK 3 LYS: C-TERMINAL RESIDUES OF CHAIN A ASN 133, HIS 134, GLY REMARK 3 135 AND LYS 136 WERE NOT SEEN IN DENSITY REMARK 3 HIS: C-TERMINAL RESIDUES OF CHAIN B GLY 135 AND LYS 136 REMARK 3 WERE NOT SEEN IN DENSITY REMARK 4 REMARK 4 3LYN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-99. REMARK 100 THE DEPOSITION ID IS D_1000001090. 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 REMARK 200 PH : 4.0 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 : 44479 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 REMARK 200 RESOLUTION RANGE LOW (A) : 25.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 5.10000 REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 38.7000 REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SOLVE, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.26 M AMMONIUM SULFATE 0.10 M SODIUM REMARK 280 ACETATE 0.20 M SODIUM CHLORIDE, PH 4.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 17.09667 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 34.19333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.64500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.74167 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 8.54833 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 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 ARG A 2 REMARK 465 TRP A 3 REMARK 465 THR A 4 REMARK 465 PHE A 5 REMARK 465 VAL A 6 REMARK 465 ARG A 7 REMARK 465 TYR A 8 REMARK 465 HIS A 9 REMARK 465 TYR A 10 REMARK 465 ASN A 133 REMARK 465 HIS A 134 REMARK 465 GLY A 135 REMARK 465 LYS A 136 REMARK 465 ARG B 1 REMARK 465 ARG B 2 REMARK 465 TRP B 3 REMARK 465 THR B 4 REMARK 465 PHE B 5 REMARK 465 VAL B 6 REMARK 465 ARG B 7 REMARK 465 TYR B 8 REMARK 465 HIS B 9 REMARK 465 TYR B 10 REMARK 465 GLY B 135 REMARK 465 LYS B 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 29 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 TYR A 57 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 78 CD - NE - CZ ANGL. DEV. = 11.0 DEGREES REMARK 500 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 108 NE - CZ - NH1 ANGL. DEV. = -4.0 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 ASN A 12 -64.60 -8.73 REMARK 500 ASN B 133 -13.77 -142.33 REMARK 500 REMARK 500 REMARK: NULL DBREF 3LYN A 1 136 UNP Q01381 ELYS_HALFU 19 154 DBREF 3LYN B 1 136 UNP Q01381 ELYS_HALFU 19 154 SEQRES 1 A 136 ARG ARG TRP THR PHE VAL ARG TYR HIS TYR ILE ASN LYS SEQRES 2 A 136 ALA TYR GLU VAL THR MET LYS ILE GLN ILE ILE SER GLY SEQRES 3 A 136 PHE ASP ARG GLN LEU THR ALA TRP LEU ARG VAL HIS GLY SEQRES 4 A 136 ARG ARG LEU THR ASN ASN GLN LYS LYS THR LEU PHE PHE SEQRES 5 A 136 VAL ASN ARG ARG TYR MET GLN THR HIS TRP GLN ASN TYR SEQRES 6 A 136 MET LEU TRP VAL LYS ARG LYS ILE LYS ALA LEU GLY ARG SEQRES 7 A 136 PRO ALA ALA VAL GLY ASP TYR THR ARG LEU GLY ALA GLU SEQRES 8 A 136 ILE GLY ARG ARG VAL ASP MET VAL PHE PHE TYR ASN PHE SEQRES 9 A 136 LEU SER GLY ARG LYS MET ILE PRO PRO TYR SER ALA TYR SEQRES 10 A 136 MET ALA LYS LEU ASN ALA LEU ARG PRO ALA ASP VAL PRO SEQRES 11 A 136 VAL LYS ASN HIS GLY LYS SEQRES 1 B 136 ARG ARG TRP THR PHE VAL ARG TYR HIS TYR ILE ASN LYS SEQRES 2 B 136 ALA TYR GLU VAL THR MET LYS ILE GLN ILE ILE SER GLY SEQRES 3 B 136 PHE ASP ARG GLN LEU THR ALA TRP LEU ARG VAL HIS GLY SEQRES 4 B 136 ARG ARG LEU THR ASN ASN GLN LYS LYS THR LEU PHE PHE SEQRES 5 B 136 VAL ASN ARG ARG TYR MET GLN THR HIS TRP GLN ASN TYR SEQRES 6 B 136 MET LEU TRP VAL LYS ARG LYS ILE LYS ALA LEU GLY ARG SEQRES 7 B 136 PRO ALA ALA VAL GLY ASP TYR THR ARG LEU GLY ALA GLU SEQRES 8 B 136 ILE GLY ARG ARG VAL ASP MET VAL PHE PHE TYR ASN PHE SEQRES 9 B 136 LEU SER GLY ARG LYS MET ILE PRO PRO TYR SER ALA TYR SEQRES 10 B 136 MET ALA LYS LEU ASN ALA LEU ARG PRO ALA ASP VAL PRO SEQRES 11 B 136 VAL LYS ASN HIS GLY LYS FORMUL 3 HOH *218(H2 O) HELIX 1 1 ASN A 12 ARG A 41 1 30 HELIX 2 2 ASN A 44 LEU A 76 1 33 HELIX 3 3 VAL A 82 ARG A 95 1 14 HELIX 4 4 MET A 98 GLY A 107 1 10 HELIX 5 5 ALA A 116 ALA A 123 1 8 HELIX 6 6 PRO A 126 ASP A 128 5 3 HELIX 7 7 LYS B 13 HIS B 38 1 26 HELIX 8 8 ASN B 44 THR B 60 1 17 HELIX 9 9 TRP B 62 LYS B 74 1 13 HELIX 10 10 VAL B 82 ARG B 95 1 14 HELIX 11 11 MET B 98 GLY B 107 1 10 HELIX 12 12 ALA B 116 ALA B 123 1 8 HELIX 13 13 PRO B 126 ASP B 128 5 3 CRYST1 119.170 119.170 51.290 90.00 90.00 120.00 P 61 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 0.008391 0.004845 0.000000 0.00000 SCALE2 0.000000 0.009689 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019497 0.00000