HEADER HYDROLASE(O-GLYCOSYL) 02-JUN-93 132L TITLE STRUCTURAL CONSEQUENCES OF REDUCTIVE METHYLATION OF LYSINE RESIDUES IN TITLE 2 HEN EGG WHITE LYSOZYME: AN X-RAY ANALYSIS AT 1.8 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEN EGG WHITE LYSOZYME; COMPND 3 CHAIN: A; 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; SOURCE 5 TISSUE: EGG WHITE KEYWDS HYDROLASE(O-GLYCOSYL) EXPDTA X-RAY DIFFRACTION AUTHOR I.RAYMENT,W.R.RYPNIEWSKI,H.M.HOLDEN REVDAT 4 29-NOV-17 132L 1 HELIX REVDAT 3 25-AUG-09 132L 1 SOURCE REVDAT 2 24-FEB-09 132L 1 VERSN REVDAT 1 31-OCT-93 132L 0 JRNL AUTH W.R.RYPNIEWSKI,H.M.HOLDEN,I.RAYMENT JRNL TITL STRUCTURAL CONSEQUENCES OF REDUCTIVE METHYLATION OF LYSINE JRNL TITL 2 RESIDUES IN HEN EGG WHITE LYSOZYME: AN X-RAY ANALYSIS AT JRNL TITL 3 1.8-A RESOLUTION. JRNL REF BIOCHEMISTRY V. 32 9851 1993 JRNL REFN ISSN 0006-2960 JRNL PMID 8373783 JRNL DOI 10.1021/BI00088A041 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 10796 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 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 USING ALL DATA, NO SIGMA CUTOFF. 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 : 1013 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 78 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.009 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 1.790 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 132L 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_1000170078. 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 (%): 44.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 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 15.30000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.60000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.60000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.30000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.15000 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 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 ASP A 18 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 18 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP A 52 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 66 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 87 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 87 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP A 119 CB - CG - OD2 ANGL. DEV. = -5.8 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 ARG A 68 13.51 -140.18 REMARK 500 ASN A 103 8.94 -67.07 REMARK 500 REMARK 500 REMARK: NULL DBREF 132L A 1 129 UNP P00698 LYSC_CHICK 19 147 SEQRES 1 A 129 DM0 VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET MLY 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 MLY 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 MLY LYS ILE VAL SER ASP GLY ASN GLY SEQRES 9 A 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS MLY GLY SEQRES 10 A 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU MODRES 132L DM0 A 1 LYS MODRES 132L MLY A 13 LYS N-DIMETHYL-LYSINE MODRES 132L MLY A 33 LYS N-DIMETHYL-LYSINE MODRES 132L MLY A 96 LYS N-DIMETHYL-LYSINE MODRES 132L MLY A 116 LYS N-DIMETHYL-LYSINE HET DM0 A 1 13 HET MLY A 13 11 HET MLY A 33 11 HET MLY A 96 11 HET MLY A 116 11 HETNAM DM0 N~2~,N~2~,N~6~,N~6~-TETRAMETHYL-L-LYSINE HETNAM MLY N-DIMETHYL-LYSINE FORMUL 1 DM0 C10 H22 N2 O2 FORMUL 1 MLY 4(C8 H18 N2 O2) FORMUL 2 HOH *78(H2 O) HELIX 1 1 ARG A 5 ARG A 14 1 10 HELIX 2 2 LEU A 25 GLU A 35 1 11 HELIX 3 3 THR A 89 SER A 100 1 12 HELIX 4 4 VAL A 109 ASN A 113 1 5 SHEET 1 1 3 THR A 43 ARG A 45 0 SHEET 2 1 3 SER A 50 TYR A 53 -1 SHEET 3 1 3 ILE A 58 ASN A 59 -1 SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.01 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.05 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.02 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.02 LINK C DM0 A 1 N VAL A 2 1555 1555 1.33 LINK C MET A 12 N MLY A 13 1555 1555 1.32 LINK C MLY A 13 N ARG A 14 1555 1555 1.32 LINK C ALA A 32 N MLY A 33 1555 1555 1.32 LINK C MLY A 33 N PHE A 34 1555 1555 1.34 LINK C ALA A 95 N MLY A 96 1555 1555 1.33 LINK C MLY A 96 N LYS A 97 1555 1555 1.34 LINK C CYS A 115 N MLY A 116 1555 1555 1.32 LINK C MLY A 116 N GLY A 117 1555 1555 1.33 CRYST1 30.600 56.300 73.200 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 0.032680 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017762 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013661 0.00000 HETATM 1 N DM0 A 1 -9.649 18.097 49.778 1.00 20.73 N HETATM 2 CA DM0 A 1 -8.887 17.726 48.556 1.00 18.01 C HETATM 3 CB DM0 A 1 -7.960 18.833 48.055 1.00 16.55 C HETATM 4 CG DM0 A 1 -7.182 18.316 46.859 1.00 14.36 C HETATM 5 CD DM0 A 1 -6.452 19.360 46.027 1.00 19.02 C HETATM 6 CE DM0 A 1 -5.602 18.751 44.900 1.00 39.83 C HETATM 7 NZ DM0 A 1 -5.025 19.729 43.942 1.00 40.59 N HETATM 8 CH1 DM0 A 1 -3.831 20.358 44.516 1.00 43.44 C HETATM 9 CH2 DM0 A 1 -6.071 20.253 43.059 1.00 42.19 C HETATM 10 C DM0 A 1 -8.095 16.434 48.729 1.00 25.07 C HETATM 11 O DM0 A 1 -7.335 16.282 49.666 1.00 19.20 O HETATM 12 CM1 DM0 A 1 -10.688 17.051 50.137 1.00 30.38 C HETATM 13 CM2 DM0 A 1 -10.258 19.415 49.535 1.00 45.70 C