HEADER HYDROLASE(O-GLYCOSYL) 21-AUG-89 2LZT TITLE REFINEMENT OF TRICLINIC LYSOZYME. II. THE METHOD OF STEREOCHEMICALLY TITLE 2 RESTRAINED LEAST-SQUARES 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 KEYWDS HYDROLASE(O-GLYCOSYL) EXPDTA X-RAY DIFFRACTION AUTHOR M.RAMANADHAM,L.C.SIEKER,L.H.JENSEN REVDAT 5 06-NOV-24 2LZT 1 REMARK REVDAT 4 05-JUN-24 2LZT 1 REMARK REVDAT 3 24-FEB-09 2LZT 1 VERSN REVDAT 2 01-APR-03 2LZT 1 JRNL REVDAT 1 15-JAN-90 2LZT 0 JRNL AUTH M.RAMANADHAM,L.C.SIEKER,L.H.JENSEN JRNL TITL REFINEMENT OF TRICLINIC LYSOZYME: II. THE METHOD OF JRNL TITL 2 STEREOCHEMICALLY RESTRAINED LEAST SQUARES. JRNL REF ACTA CRYSTALLOGR.,SECT.B V. 46 63 1990 JRNL REFN ISSN 0108-7681 JRNL PMID 2302327 JRNL DOI 10.1107/S0108768189009195 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.M.HODSDON,G.M.BROWN,L.C.SIEKER,L.H.JENSEN REMARK 1 TITL REFINEMENT OF TRICLINIC LYSOZYME. I. FOURIER AND LEAST REMARK 1 TITL 2 SQUARES METHODS REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH M.RAMANADHAM,L.C.SIEKER,L.H.JENSEN REMARK 1 TITL TRICLINIC LYSOZYME. SOME FEATURES OF THE STRUCTURE AT 2 REMARK 1 TITL 2 ANGSTROMS RESOLUTION REMARK 1 EDIT S.SMITH-GILL, E.SERCARZ REMARK 1 REF THE IMMUNE RESPONSE TO 15 1989 REMARK 1 REF 2 STRUCTURALLY DEFINED REMARK 1 REF 3 PROTEINS. THE LYSOZYME MODEL REMARK 1 PUBL ADENINE PRESS REMARK 1 REFN REMARK 1 REFERENCE 3 REMARK 1 AUTH M.RAMANADHAM,L.C.SIEKER,L.H.JENSEN REMARK 1 TITL SRLSQ REFINEMENT OF TRICLINIC LYSOZYME REMARK 1 REF ACTA CRYSTALLOGR.,SECT.A V. 43 13 1987 REMARK 1 REFN ISSN 0108-7673 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.RAMANADHAM,L.C.SIEKER,L.H.JENSEN REMARK 1 TITL STRUCTURE OF TRICLINIC LYSOZYME AND ITS CU2+ COMPLEX AT 2 REMARK 1 TITL 2 ANGSTROMS RESOLUTION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.A V. 37 33 1981 REMARK 1 REFN ISSN 0108-7673 REMARK 1 REFERENCE 5 REMARK 1 AUTH K.KURACHI,L.C.SIEKER,L.H.JENSEN REMARK 1 TITL STRUCTURES OF TRICLINIC MONO-AND DI-N-ACETYLGLUCOSAMINE. REMARK 1 TITL 2 LYSOZYME COMPLEXES-A CRYSTALLOGRAPHIC STUDY REMARK 1 REF J.MOL.BIOL. V. 101 11 1976 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 6 REMARK 1 AUTH K.KURACHI,L.C.SIEKER,L.H.JENSEN REMARK 1 TITL METAL ION BINDING IN TRICLINIC LYSOZYME REMARK 1 REF J.BIOL.CHEM. V. 250 7663 1975 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 1.97 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) : 1.97 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) : 0.124 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 : 1001 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 249 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) : 0.016 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.034 ; 0.030 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.047 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.018 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.140 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.170 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.238 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : 0.187 ; 0.300 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 4.400 ; 3.500 REMARK 3 STAGGERED (DEGREES) : 13.100; 12.500 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 2LZT 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_1000178327. 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 5 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 66 CB - CG - OD1 ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG A 73 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 114 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 128 NE - CZ - NH2 ANGL. DEV. = -3.6 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 ASP A 101 39.88 -90.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 130 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 131 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 132 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 133 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 134 DBREF 2LZT A 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 HET NO3 A 130 4 HET NO3 A 131 4 HET NO3 A 132 4 HET NO3 A 133 4 HET NO3 A 134 4 HETNAM NO3 NITRATE ION FORMUL 2 NO3 5(N O3 1-) FORMUL 7 HOH *249(H2 O) HELIX 1 1 GLY A 4 HIS A 15 1 12 HELIX 2 2 SER A 24 ASN A 37 1 14 HELIX 3 3 CYS A 80 SER A 85 5 6 HELIX 4 4 ILE A 88 ASP A 101 1 14 HELIX 5 5 GLY A 104 ALA A 107 5 4 HELIX 6 6 TRP A 108 CYS A 115 1 8 HELIX 7 7 ASP A 119 ILE A 124 5 6 SHEET 1 A 3 THR A 43 ARG A 45 0 SHEET 2 A 3 THR A 51 TYR A 53 -1 N ASP A 52 O ASN A 44 SHEET 3 A 3 ILE A 58 ASN A 59 -1 O ILE A 58 N TYR A 53 SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.06 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.04 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.00 SSBOND 4 CYS A 76 CYS A 94 1555 1555 1.94 SITE 1 AC1 7 ASN A 65 ASN A 74 ASN A 77 ILE A 78 SITE 2 AC1 7 PRO A 79 ARG A 112 LYS A 116 SITE 1 AC2 6 ARG A 21 ASP A 66 CYS A 80 SER A 81 SITE 2 AC2 6 HOH A 175 HOH A 187 SITE 1 AC3 6 LYS A 33 PHE A 38 ARG A 73 HOH A 305 SITE 2 AC3 6 HOH A 319 HOH A 340 SITE 1 AC4 6 ALA A 11 HIS A 15 ASP A 87 ILE A 88 SITE 2 AC4 6 HOH A 317 HOH A 349 SITE 1 AC5 7 SER A 24 LEU A 25 GLY A 26 GLN A 41 SITE 2 AC5 7 GLN A 121 ILE A 124 HOH A 193 CRYST1 27.283 31.980 34.291 88.53 108.57 111.85 P 1 1 ORIGX1 0.036653 0.014697 0.013943 0.00000 ORIGX2 0.000000 0.033690 0.003576 0.00000 ORIGX3 0.000000 0.000000 0.030937 0.00000 SCALE1 0.036653 0.014697 0.013943 0.00000 SCALE2 0.000000 0.033690 0.003576 0.00000 SCALE3 0.000000 0.000000 0.030937 0.00000