10 20 30 40 50 60 70 80 3LYT - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE(O-GLYCOSYL) 20-MAR-92 3LYT
TITLE COMPARISON OF RADIATION-INDUCED DECAY AND STRUCTURE TITLE 2 REFINEMENT FROM X-RAY DATA COLLECTED FROM LYSOZYME TITLE 3 CRYSTALS AT LOW AND AMBIENT TEMPERATURES
COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEN EGG WHITE LYSOZYME; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.2.1.17; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031
KEYWDS HYDROLASE(O-GLYCOSYL)
EXPDTA X-RAY DIFFRACTION
AUTHOR J.C.DEWAN,A.C.M.YOUNG,R.F.TILTON
REVDAT 2 24-FEB-09 3LYT 1 VERSN REVDAT 1 31-OCT-93 3LYT 0
JRNL AUTH A.C.M.YOUNG,J.C.DEWAN,C.NAVE,R.F.TILTON JRNL TITL COMPARISON OF RADIATION-INDUCED DECAY AND JRNL TITL 2 STRUCTURE REFINEMENT FROM X-RAY DATA COLLECTED JRNL TITL 3 FROM LYSOZYME CRYSTALS AT LOW AND AMBIENT JRNL TITL 4 TEMPERATURES JRNL REF J.APPL.CRYSTALLOGR. V. 26 309 1993 JRNL REFN ISSN 0021-8898
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.T.RAO,J.HOGLE,M.SUNDARALINGAM REMARK 1 TITL STUDIES OF MONOCLINIC HEN EGG WHITE LYSOZYME. II. REMARK 1 TITL 2 THE REFINEMENT AT 2.5 ANGSTROMS REMARK 1 TITL 3 RESOLUTION-CONFORMATIONAL VARIABILITY BETWEEN THE REMARK 1 TITL 4 TWO INDEPENDENT MOLECULES REMARK 1 REF ACTA CRYSTALLOGR.,SECT.C V. 39 237 1983 REMARK 1 REFN ISSN 0108-2701 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.HOGLE REMARK 1 TITL THE STRUCTURE OF THE MONOCLINIC CRYSTAL FORM OF REMARK 1 TITL 2 HEN EGG WHITE LYSOZYME AT 2.5 ANGSTROMS REMARK 1 TITL 3 RESOLUTION. COMPARISON OF A PROTEIN STRUCTURE IN REMARK 1 TITL 4 SEVERAL CRYSTALLINE ENVIRONMENTS REMARK 1 REF THESIS 1978 REMARK 1 REFN ISSN 0378-0546 REMARK 1 REFERENCE 3 REMARK 1 AUTH J.HOGLE,S.T.RAO,M.MALLIKARJUNAN,C.BEDDELL, REMARK 1 AUTH 2 R.K.MCMULLAN,M.SUNDARALINGAM REMARK 1 TITL STUDIES OF MONOCLINIC HEN EGG WHITE LYSOZYME. I. REMARK 1 TITL 2 STRUCTURE SOLUTION AT 4 ANGSTROMS RESOLUTION AND REMARK 1 TITL 3 MOLECULAR-PACKING COMPARISONS WITH TETRAGONAL AND REMARK 1 TITL 4 TRICLINIC LYSOZYMES REMARK 1 REF ACTA CRYSTALLOGR.,SECT.B V. 37 591 1981 REMARK 1 REFN ISSN 0108-7681
REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL 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 + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : NULL 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 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2002 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 406 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.020 ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 3LYT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
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 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 31.33000 REMARK 290 SMTRY3 2 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 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 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 156 DISTANCE = 14.37 ANGSTROMS REMARK 525 HOH B 163 DISTANCE = 26.06 ANGSTROMS REMARK 525 HOH B 185 DISTANCE = 12.95 ANGSTROMS REMARK 525 HOH B 217 DISTANCE = 7.04 ANGSTROMS REMARK 525 HOH A 258 DISTANCE = 7.25 ANGSTROMS REMARK 525 HOH A 269 DISTANCE = 10.91 ANGSTROMS REMARK 525 HOH B 281 DISTANCE = 12.90 ANGSTROMS REMARK 525 HOH A 303 DISTANCE = 5.17 ANGSTROMS REMARK 525 HOH B 302 DISTANCE = 7.91 ANGSTROMS REMARK 525 HOH A 359 DISTANCE = 6.98 ANGSTROMS REMARK 525 HOH B 337 DISTANCE = 13.04 ANGSTROMS REMARK 525 HOH A 391 DISTANCE = 5.62 ANGSTROMS REMARK 525 HOH B 386 DISTANCE = 8.39 ANGSTROMS REMARK 525 HOH B 392 DISTANCE = 13.53 ANGSTROMS REMARK 525 HOH B 414 DISTANCE = 14.85 ANGSTROMS REMARK 525 HOH B 441 DISTANCE = 14.18 ANGSTROMS REMARK 525 HOH A 466 DISTANCE = 16.49 ANGSTROMS
DBREF 3LYT A 1 129 UNP P00698 LYSC_CHICK 19 147 DBREF 3LYT B 1 129 UNP P00698 LYSC_CHICK 19 147
SEQRES 1 A 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 A 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 A 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 A 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 A 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 A 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE SEQRES 7 A 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 A 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY SEQRES 9 A 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 A 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU SEQRES 1 B 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 B 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 B 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 B 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 B 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 B 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE SEQRES 7 B 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 B 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY SEQRES 9 B 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 B 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU
FORMUL 3 HOH *406(H2 O)
HELIX 1 AA ARG A 5 HIS A 15 1 11 HELIX 2 BA LEU A 25 GLU A 35 1 11 HELIX 3 CA CYS A 80 LEU A 84 5 5 HELIX 4 DA THR A 89 LYS A 96 1 8 HELIX 5 AB ARG B 5 HIS B 15 1 11 HELIX 6 BB LEU B 25 GLU B 35 1 11 HELIX 7 CB CYS B 80 LEU B 84 5 5 HELIX 8 DB THR B 89 LYS B 96 1 8
SHEET 1 S1A 2 LYS A 1 PHE A 3 0 SHEET 2 S1A 2 PHE A 38 THR A 40 -1 N THR A 40 O LYS A 1 SHEET 1 S2A 3 ALA A 42 ASN A 46 0 SHEET 2 S2A 3 SER A 50 GLY A 54 -1 O SER A 50 N ASN A 46 SHEET 3 S2A 3 GLN A 57 SER A 60 -1 O ILE A 58 N TYR A 53 SHEET 1 S1B 2 LYS B 1 PHE B 3 0 SHEET 2 S1B 2 PHE B 38 THR B 40 -1 N THR B 40 O LYS B 1 SHEET 1 S2B 3 ALA B 42 ASN B 46 0 SHEET 2 S2B 3 SER B 50 GLY B 54 -1 O SER B 50 N ASN B 46 SHEET 3 S2B 3 GLN B 57 SER B 60 -1 O ILE B 58 N TYR B 53
SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.29 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.06 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.27 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.47 SSBOND 5 CYS B 6 CYS B 127 1555 1555 2.28 SSBOND 6 CYS B 30 CYS B 115 1555 1555 2.35 SSBOND 7 CYS B 64 CYS B 80 1555 1555 2.34 SSBOND 8 CYS B 76 CYS B 94 1555 1555 2.32
CRYST1 27.510 62.660 59.660 90.00 89.57 90.00 P 1 21 1 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 0.036350 0.000000 -0.000273 0.00000
SCALE2 0.000000 0.015959 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016762 0.00000