PDB Short entry for 1LZ4 HEADER HYDROLASE(O-GLYCOSYL) 03-FEB-93 1LZ4 TITLE ENTHALPIC DESTABILIZATION OF A MUTANT HUMAN LYSOZYME LACKING A TITLE 2 DISULFIDE BRIDGE BETWEEN CYSTEINE-77 AND CYSTEINE-95 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.17; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS HYDROLASE(O-GLYCOSYL) EXPDTA X-RAY DIFFRACTION AUTHOR K.INAKA,M.MATSUSHIMA,R.KUROKI,Y.TANIYAMA,M.KIKUCHI REVDAT 4 29-NOV-17 1LZ4 1 HELIX REVDAT 3 24-FEB-09 1LZ4 1 VERSN REVDAT 2 01-APR-03 1LZ4 1 JRNL REVDAT 1 31-OCT-93 1LZ4 0 JRNL AUTH R.KUROKI,K.INAKA,Y.TANIYAMA,S.KIDOKORO,M.MATSUSHIMA, JRNL AUTH 2 M.KIKUCHI,K.YUTANI JRNL TITL ENTHALPIC DESTABILIZATION OF A MUTANT HUMAN LYSOZYME LACKING JRNL TITL 2 A DISULFIDE BRIDGE BETWEEN CYSTEINE-77 AND CYSTEINE-95. JRNL REF BIOCHEMISTRY V. 31 8323 1992 JRNL REFN ISSN 0006-2960 JRNL PMID 1525170 JRNL DOI 10.1021/BI00150A028 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.INAKA,Y.TANIYAMA,M.KIKUCHI,K.MORIKAWA,M.MATSUSHIMA REMARK 1 TITL THE CRYSTAL STRUCTURE OF A MUTANT HUMAN LYSOZYME REMARK 1 TITL 2 C77(SLASH)95A WITH INCREASED SECRETION EFFICIENCY IN YEAST REMARK 1 REF J.BIOL.CHEM. V. 266 12599 1991 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 10265 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) : 0.188 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 : 1016 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 57 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) : NULL ; 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: REMARK 3 THE ELECTRON DENSITIES OF THE LOOP BETWEEN ALA 73 AND HIS REMARK 3 78 ARE VERY WEAK AND THE ATOMS OF THE LOOP HAVE LARGE B REMARK 3 FACTORS. THEN THE LOOP CAN BE VERY FLEXIBLE. REMARK 4 REMARK 4 1LZ4 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_1000174877. 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 (%): 37.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 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 28.41000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.66500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.43000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 16.66500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.41000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.43000 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 14 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 41 CG CD NE CZ NH1 NH2 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 GLU A 4 OE1 - CD - OE2 ANGL. DEV. = 8.2 DEGREES REMARK 500 GLU A 7 CG - CD - OE1 ANGL. DEV. = 12.5 DEGREES REMARK 500 GLU A 7 CG - CD - OE2 ANGL. DEV. = -14.7 DEGREES REMARK 500 ARG A 10 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ASP A 18 CB - CG - OD1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 21 NE - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 50 CD - NE - CZ ANGL. DEV. = 14.8 DEGREES REMARK 500 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 50 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 53 CB - CG - OD2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ARG A 62 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 62 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP A 87 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 98 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 98 NE - CZ - NH2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ASP A 102 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 107 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 107 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 113 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 115 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 115 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 119 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 119 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 120 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1LZ4 A 1 130 UNP P61626 LYSC_HUMAN 19 148 SEQADV 1LZ4 ALA A 77 UNP P61626 CYS 95 CONFLICT SEQRES 1 A 130 LYS VAL PHE GLU ARG CYS GLU LEU ALA ARG THR LEU LYS SEQRES 2 A 130 ARG LEU GLY MET ASP GLY TYR ARG GLY ILE SER LEU ALA SEQRES 3 A 130 ASN TRP MET CYS LEU ALA LYS TRP GLU SER GLY TYR ASN SEQRES 4 A 130 THR ARG ALA THR ASN TYR ASN ALA GLY ASP ARG SER THR SEQRES 5 A 130 ASP TYR GLY ILE PHE GLN ILE ASN SER ARG TYR TRP CYS SEQRES 6 A 130 ASN ASP GLY LYS THR PRO GLY ALA VAL ASN ALA ALA HIS SEQRES 7 A 130 LEU SER CYS SER ALA LEU LEU GLN ASP ASN ILE ALA ASP SEQRES 8 A 130 ALA VAL ALA CYS ALA LYS ARG VAL VAL ARG ASP PRO GLN SEQRES 9 A 130 GLY ILE ARG ALA TRP VAL ALA TRP ARG ASN ARG CYS GLN SEQRES 10 A 130 ASN ARG ASP VAL ARG GLN TYR VAL GLN GLY CYS GLY VAL FORMUL 2 HOH *57(H2 O) HELIX 1 A ARG A 5 ARG A 14 1 10 HELIX 2 B LEU A 25 GLU A 35 1 11 HELIX 3 E SER A 80 LEU A 85 5 6 HELIX 4 C ALA A 90 VAL A 99 1 10 HELIX 5 D VAL A 110 CYS A 116 1 7 SHEET 1 A 2 LYS A 1 PHE A 3 0 SHEET 2 A 2 TYR A 38 THR A 40 -1 N THR A 40 O LYS A 1 SHEET 1 B 3 ALA A 42 ASN A 46 0 SHEET 2 B 3 SER A 51 GLY A 55 -1 N GLY A 55 O ALA A 42 SHEET 3 B 3 ILE A 59 SER A 61 -1 N SER A 61 O THR A 52 SSBOND 1 CYS A 6 CYS A 128 1555 1555 2.03 SSBOND 2 CYS A 30 CYS A 116 1555 1555 2.06 SSBOND 3 CYS A 65 CYS A 81 1555 1555 2.07 CRYST1 56.820 60.860 33.330 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 0.017599 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016431 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030003 0.00000