HEADER HYDROLASE 31-MAR-97 4LZT TITLE ATOMIC RESOLUTION REFINEMENT OF TRICLINIC HEW LYSOZYME AT 295K COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.17; COMPND 5 OTHER_DETAILS: NITRATE IONS PRESENT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 CELL: EGG; SOURCE 6 CELLULAR_LOCATION: CYTOPLASM (WHITE) KEYWDS HYDROLASE, O-GLYCOSYL, GLYCOSIDASE EXPDTA X-RAY DIFFRACTION AUTHOR M.A.WALSH,T.SCHNEIDER,L.C.SIEKER,Z.DAUTER,V.LAMZIN,K.S.WILSON REVDAT 5 16-OCT-24 4LZT 1 REMARK REVDAT 4 09-AUG-23 4LZT 1 REMARK REVDAT 3 24-FEB-09 4LZT 1 VERSN REVDAT 2 01-APR-03 4LZT 1 JRNL REVDAT 1 01-APR-98 4LZT 0 JRNL AUTH M.A.WALSH,T.R.SCHNEIDER,L.C.SIEKER,Z.DAUTER,V.S.LAMZIN, JRNL AUTH 2 K.S.WILSON JRNL TITL REFINEMENT OF TRICLINIC HEN EGG-WHITE LYSOZYME AT ATOMIC JRNL TITL 2 RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 54 522 1998 JRNL REFN ISSN 0907-4449 JRNL PMID 9761848 JRNL DOI 10.1107/S0907444997013656 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 REMARK 1 TITL 2 LEAST-SQUARES METHODS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.B V. 46 54 1990 REMARK 1 REFN ISSN 0108-7681 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.RAMANADHAM,L.C.SIEKER,L.H.JENSEN REMARK 1 TITL REFINEMENT OF TRICLINIC LYSOZYME: II. THE METHOD OF REMARK 1 TITL 2 STEREOCHEMICALLY RESTRAINED LEAST SQUARES REMARK 1 REF ACTA CRYSTALLOGR.,SECT.B V. 46 63 1990 REMARK 1 REFN ISSN 0108-7681 REMARK 2 REMARK 2 RESOLUTION. 0.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-96 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.108 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.114 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.147 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1870 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 61258 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.105 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.111 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.143 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 3.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1728 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 56149 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 : 24 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1123.7 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 920.89 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 15 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 10801 REMARK 3 NUMBER OF RESTRAINTS : 13288 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.033 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.014 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.390 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.128 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.152 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.044 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.007 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.071 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.095 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WATER OCCUPANCIES REFINED REMARK 3 REMARK 3 DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. REMARK 4 REMARK 4 4LZT 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_1000179365. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : DEC-96 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 4.5-4.6 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.862 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61265 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.950 REMARK 200 RESOLUTION RANGE LOW (A) : 21.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.27300 REMARK 200 R SYM FOR SHELL (I) : 0.27300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: STRUCTURE KNOWN REMARK 200 SOFTWARE USED: SHELXL-96 REMARK 200 STARTING MODEL: PDB ENTRY 2LZT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BATCH METHOD USED. 1% PROTEIN SOLUTION REMARK 280 IN 100MM SODIUM ACETATE PH 4.5-4.6. SODIUM NITRATE ADDED TO A REMARK 280 CONCENTRATION OF 20MGS/ML. CRYSTALS GROWN AT ROOM TEMPERATURE., REMARK 280 BATCH METHOD 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. = 4.9 DEGREES REMARK 500 ARG A 14 NH1 - CZ - NH2 ANGL. DEV. = 8.5 DEGREES REMARK 500 ARG A 14 NE - CZ - NH1 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 21 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 61 CD - NE - CZ ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG A 68 CD - NE - CZ ANGL. DEV. = 12.9 DEGREES REMARK 500 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP A 87 CB - CG - OD2 ANGL. DEV. = -8.9 DEGREES REMARK 500 THR A 89 CA - CB - CG2 ANGL. DEV. = 9.9 DEGREES REMARK 500 VAL A 99 O - C - N ANGL. DEV. = -11.0 DEGREES REMARK 500 GLY A 104 C - N - CA ANGL. DEV. = -12.6 DEGREES REMARK 500 ARG A 125 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 128 CD - NE - CZ ANGL. DEV. = 48.5 DEGREES REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 206 DBREF 4LZT 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 201 4 HET NO3 A 202 4 HET NO3 A 203 4 HET NO3 A 204 4 HET NO3 A 205 4 HET NO3 A 206 4 HETNAM NO3 NITRATE ION FORMUL 2 NO3 6(N O3 1-) FORMUL 8 HOH *139(H2 O) HELIX 1 1 ARG A 5 ARG A 14 1 10 HELIX 2 2 TYR A 20 GLY A 22 5 3 HELIX 3 3 LEU A 25 SER A 36 1 12 HELIX 4 4 CYS A 80 LEU A 84 5 5 HELIX 5 5 THR A 89 SER A 100 1 12 HELIX 6 6 MET A 105 ALA A 107 5 3 HELIX 7 7 VAL A 109 ARG A 114 1 6 HELIX 8 8 VAL A 120 TRP A 123 5 4 SHEET 1 A 2 THR A 43 ARG A 45 0 SHEET 2 A 2 THR A 51 TYR A 53 -1 N ASP A 52 O ASN A 44 SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.04 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.03 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.02 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.02 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 7 ARG A 21 ASN A 65 ASP A 66 PRO A 79 SITE 2 AC2 7 CYS A 80 SER A 81 HOH A1028 SITE 1 AC3 4 LYS A 33 PHE A 38 TRP A 62 ARG A 73 SITE 1 AC4 7 ALA A 11 HIS A 15 ASP A 87 ILE A 88 SITE 2 AC4 7 THR A 89 HOH A1129 HOH A1130 SITE 1 AC5 8 SER A 24 LEU A 25 GLY A 26 GLN A 41 SITE 2 AC5 8 VAL A 120 GLN A 121 ILE A 124 HOH A1107 SITE 1 AC6 6 TYR A 23 ARG A 45 ARG A 68 MET A 105 SITE 2 AC6 6 ASN A 106 HOH A1059 CRYST1 27.240 31.870 34.230 88.52 108.53 111.89 P 1 1 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 0.036711 0.014750 0.013936 0.00000 SCALE2 0.000000 0.033816 0.003581 0.00000 SCALE3 0.000000 0.000000 0.030984 0.00000