HEADER HYDROLASE 07-NOV-98 1B0D TITLE STRUCTURAL EFFECTS OF MONOVALENT ANIONS ON POLYMORPHIC LYSOZYME TITLE 2 CRYSTALS COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HEN (GALLUS GALLUS) EGG-WHITE LYSOZYME, MUCOPEPTIDE, N- COMPND 5 ACETYLMURAMYL HYDROLASE; COMPND 6 EC: 3.2.1.17 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; SOURCE 6 CELLULAR_LOCATION: CYTOPLASM (WHITE) KEYWDS HYDROLASE, O-GLYCOSYL EXPDTA X-RAY DIFFRACTION AUTHOR M.C.VANEY,I.BROUTIN,P.RETAILLEAU,S.LAFONT,C.HAMIAUX,T.PRANGE,M.RIES- AUTHOR 2 KAUTT,A.DUCRUIX REVDAT 5 27-DEC-23 1B0D 1 REMARK REVDAT 4 24-FEB-09 1B0D 1 VERSN REVDAT 3 29-MAR-05 1B0D 1 JRNL REVDAT 2 22-DEC-99 1B0D 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 11-NOV-98 1B0D 0 JRNL AUTH M.C.VANEY,I.BROUTIN,P.RETAILLEAU,A.DOUANGAMATH,S.LAFONT, JRNL AUTH 2 C.HAMIAUX,T.PRANGE,A.DUCRUIX,M.RIES-KAUTT JRNL TITL STRUCTURAL EFFECTS OF MONOVALENT ANIONS ON POLYMORPHIC JRNL TITL 2 LYSOZYME CRYSTALS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 57 929 2001 JRNL REFN ISSN 0907-4449 JRNL PMID 11418760 JRNL DOI 10.1107/S0907444901004504 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.A.WALSH,T.R.SCHNEIDER,L.C.SIEKER,Z.DAUTER,V.S.LAMZIN, REMARK 1 AUTH 2 K.S.WILSON REMARK 1 TITL REFINEMENT OF TRICLINIC HEN EGG-WHITE LYSOZYME AT ATOMIC REMARK 1 TITL 2 RESOLUTION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. D54 522 1998 REMARK 1 REFN ISSN 0907-4449 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.K.STEINRAUF REMARK 1 TITL STRUCTURES OF MONOCLINIC LYSOZYME IODIDE AT 1.6 ANG. AND OF REMARK 1 TITL 2 TRICLINIC LYSOZYME NITRATE AT 1.1 ANG REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. D54 767 1998 REMARK 1 REFN ISSN 0907-4449 REMARK 1 REFERENCE 3 REMARK 1 AUTH K.LIM,A.NADARAJAH,E.L.FORSYTHE,M.L.PUSEY REMARK 1 TITL LOCATIONS OF BROMIDE IONS IN TETRAGONAL LYSOZYME CRYSTALS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. D54 899 1998 REMARK 1 REFN ISSN 0907-4449 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.C.VANEY,S.MAIGNAN,M.RIES-KAUTT,A.DUCRUIX REMARK 1 TITL HIGH-RESOLUTION STRUCTURE (1.33 ANG.) OF A HEWL LYSOZYME REMARK 1 TITL 2 TETRAGONAL CRYSTAL GROWN IN THE APCF APPARATUS. DATA AND REMARK 1 TITL 3 STRUCTURAL COMPARISON WITH A CRYSTAL GROWN UNDER REMARK 1 TITL 4 MICROGRAVITY FROM SPACHAB-01 MISSION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. D52 505 1996 REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 10461 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1082 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.84 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.92 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1067 REMARK 3 BIN R VALUE (WORKING SET) : 0.3320 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.71 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 104 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 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 : 11 REMARK 3 SOLVENT ATOMS : 86 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.70 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.330 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.22 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.150 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.520 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.390 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.940 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.720 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PR REMARK 3 PARAMETER FILE 2 : PARAM11.WAT REMARK 3 PARAMETER FILE 3 : PARAMETER.PTS REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH11.WAT REMARK 3 TOPOLOGY FILE 3 : TOPOLOGY.PTS REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 SOME OF THE SIDE CHAIN ATOMS OF RESIDUES ARG 61, ARG 73, REMARK 3 ASN 77, LYS 97, ASP 101, ASN 103, GLN 121 AND ARG 125 HAVE REMARK 3 A POORLY DEFINED DENSITY. THESE ATOMS WERE BUILT USING REMARK 3 STEREOCHEMICAL CONSTRAINTS AND KEPT IN THE COORDINATE FILE. REMARK 4 REMARK 4 1B0D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000000044. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-94 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM, CCP4 REMARK 200 DATA SCALING SOFTWARE : CCP4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10462 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 13.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.13500 REMARK 200 FOR SHELL : 4.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MONOCHROMATIC REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE CRYSTAL WAS OBTAINED IN PRESENCE REMARK 280 OF NAPTS WITH A FINAL PROTEIN CONCENTRATION OF 40.5 MG/ML IN REMARK 280 HANGING DROPS USING VAPOR DIFFUSION METHOD. THE EQUILIBRATION AT REMARK 280 291K WAS DONE AGAINST A RESERVOIR SOLUTION CONTAINING 90 MM REMARK 280 NAPTS, 50 MM SODIUM ACETATE ADJUSTED AT PH 4.5., VAPOR DIFFUSION REMARK 280 - HANGING DROP, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.98500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.53000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.53000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.47750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.53000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.53000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.49250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.53000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.53000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.47750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.53000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.53000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.49250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 18.98500 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 150 LIES ON A SPECIAL POSITION. 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 -83.31 -50.83 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 TSU A 130 DBREF 1B0D 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 TSU A 130 11 HETNAM TSU PARA-TOLUENE SULFONATE FORMUL 2 TSU C7 H8 O3 S FORMUL 3 HOH *86(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 ASP A 101 1 13 HELIX 6 6 GLY A 104 ALA A 107 5 4 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 SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.03 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.02 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.04 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.03 SITE 1 AC1 10 ASN A 19 GLY A 22 LYS A 33 GLU A 35 SITE 2 AC1 10 ASN A 37 ALA A 42 ASN A 44 ARG A 45 SITE 3 AC1 10 ARG A 68 HOH A 133 CRYST1 79.060 79.060 37.970 90.00 90.00 90.00 P 43 21 2 8 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 0.012649 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012649 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026336 0.00000