HEADER HYDROLASE 19-AUG-97 1AT6 TITLE HEN EGG WHITE LYSOZYME WITH A ISOASPARTATE RESIDUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.17; COMPND 5 OTHER_DETAILS: ISOASPARTATE AT RESIDUE 101 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 ISOASPARTATE, HYDROLASE, O-GLYCOSYL HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.NOGUCHI,K.MIYAWAKI,Y.SATOW REVDAT 10 20-NOV-24 1AT6 1 REMARK REVDAT 9 02-AUG-23 1AT6 1 HETSYN REVDAT 8 29-JUL-20 1AT6 1 COMPND REMARK HETNAM LINK REVDAT 8 2 1 SITE ATOM REVDAT 7 29-NOV-17 1AT6 1 REMARK REVDAT 6 27-JUL-11 1AT6 1 HETNAM HETSYN REMARK REVDAT 5 13-JUL-11 1AT6 1 VERSN REVDAT 4 14-APR-10 1AT6 1 ATOM REVDAT 3 08-SEP-09 1AT6 1 HET REVDAT 2 24-FEB-09 1AT6 1 VERSN REVDAT 1 25-FEB-98 1AT6 0 JRNL AUTH S.NOGUCHI,K.MIYAWAKI,Y.SATOW JRNL TITL SUCCINIMIDE AND ISOASPARTATE RESIDUES IN THE CRYSTAL JRNL TITL 2 STRUCTURES OF HEN EGG-WHITE LYSOZYME COMPLEXED WITH JRNL TITL 3 TRI-N-ACETYLCHITOTRIOSE. JRNL REF J.MOL.BIOL. V. 278 231 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9571046 JRNL DOI 10.1006/JMBI.1998.1674 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.MIYAWAKI,S.NOGUCHI,S.HARADA,Y.SATOW REMARK 1 TITL CRYSTALLOGRAPHY OF SUCCINIMIDE HEN EGG-WHITE LYSOZYME AT LOW REMARK 1 TITL 2 TEMPERATURES REMARK 1 REF J.CRYST.GROWTH V. 168 292 1996 REMARK 1 REFN ISSN 0022-0248 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 10515 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : POSTERIORI REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 992 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 673 REMARK 3 BIN R VALUE (WORKING SET) : 0.2330 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 75 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 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 : 43 REMARK 3 SOLVENT ATOMS : 184 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.70 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.18 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.290 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.370 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) : 1.270 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.900 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.170 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.210 ; 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.PRO REMARK 3 PARAMETER FILE 2 : PARAM19X.SOL REMARK 3 PARAMETER FILE 3 : PARAM3.CHO REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : TOPH3.CHO REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 A BULK SOLVENT ANALYSIS, WITH MASK PARAMETERS K = 0.350 (ELECTRON/ REMARK 3 ANGSTROM**3) AND B = 73.6 (ANGSTROM**2), WAS APPLIED IN THE REMARK 3 REFINEMENT. REMARK 3 REMARK 3 ALTHOUGH BOND DISTANCES BETWEEN MET 12 SD AND CE AND REMARK 3 BETWEEN ARG 14 CG AND CD DEVIATE BY LARGER THAN 4.0*RMSD REMARK 3 FROM THE IDEAL VALUES, ALL THE ATOMS OF MET 12 AND ARG REMARK 3 14 ARE DEFINED IN THE ELECTRON DENSITIES. REMARK 4 REMARK 4 1AT6 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_1000171226. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAR-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2-7.5 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10515 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 34.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 39.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.14700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.843 REMARK 200 STARTING MODEL: PDB ENTRY 1LZB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE PREPARED AT 277 K FROM REMARK 280 THE DROPLET MIXTURE OF A 20 MG/ML PROTEIN SOLUTION CONTAINING 7 REMARK 280 MM TRI-N-ACETYLCHITOTRIOSE (NAG3) AND 50 MM ACETATE BUFFER PH REMARK 280 4.2 WITH EQUAL VOLUME OF A RESERVOIR SOLUTION CONTAINING 2.0 M REMARK 280 AMMONIUM FORMATE AND 100 MM N-(2-HYDROXYETHYL)PIPERAZINE-N'-(2- REMARK 280 ETHANESULFONIC ACID) (HEPES) BUFFER PH 7.5. PRIOR TO THE REMARK 280 DIFFRACTION DATA COLLECTION, THE CRYSTAL WAS SOAKED IN A REMARK 280 CRYOPROTECTANT SOLUTION CONTAINING 30 % (W/V) POLYETHYLENE REMARK 280 GLYCOL 20,000, 2.2 M AMMONIUM FORMATE, 100 MM HEPES BUFFER PH REMARK 280 7.5, AND 7 MM NAG3 FOR 2 MINUTES AT 277 K. 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 19.14500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.33000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.33000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.71750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.33000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.33000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.57250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.33000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.33000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.71750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.33000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.33000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.57250 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 19.14500 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, B 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 140 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 141 LIES ON A SPECIAL POSITION. DBREF 1AT6 A 1 129 UNP P00698 LYC_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 IAS 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 IAS A 101 8 HET NAG B 1 15 HET NAG B 2 14 HET NAG B 3 14 HETNAM IAS BETA-L-ASPARTIC ACID HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN IAS L-ASPARTIC ACID HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 1 IAS C4 H7 N O4 FORMUL 2 NAG 3(C8 H15 N O6) FORMUL 3 HOH *184(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 VAL A 99 1 11 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 GLN A 121 ILE A 124 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 2.03 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.03 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.04 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.02 LINK C SER A 100 N IAS A 101 1555 1555 1.33 LINK CG IAS A 101 N GLY A 102 1555 1555 1.35 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.39 LINK O4 NAG B 2 C1 NAG B 3 1555 1555 1.39 CRYST1 76.660 76.660 38.290 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 0.013045 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013045 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026116 0.00000