HEADER HYDROLASE 22-MAR-17 5V94 TITLE PEKIN DUCK EGG LYSOZYME ISOFORM III (DEL-III), CUBIC FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME ISOFORM III; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DEL-III; COMPND 5 EC: 3.2.1.18 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANAS PLATYRHYNCHOS; SOURCE 3 ORGANISM_COMMON: MALLARD, PEKIN DUCK; SOURCE 4 ORGANISM_TAXID: 8839; SOURCE 5 TISSUE: EGG WHITE KEYWDS LYSOZYME, GLYCOSYL HYDROLASE, N-ACETYLMURAMIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.B.LANGLEY,D.CHRIST REVDAT 5 04-OCT-23 5V94 1 REMARK REVDAT 4 08-JAN-20 5V94 1 REMARK REVDAT 3 09-MAY-18 5V94 1 JRNL REVDAT 2 18-APR-18 5V94 1 JRNL REVDAT 1 15-NOV-17 5V94 0 JRNL AUTH D.B.LANGLEY,B.CROSSETT,P.SCHOFIELD,J.JACKSON,M.ZERAATI, JRNL AUTH 2 D.MALTBY,M.CHRISTIE,D.BURNETT,R.BRINK,C.GOODNOW,D.CHRIST JRNL TITL STRUCTURAL BASIS OF ANTIGEN RECOGNITION: CRYSTAL STRUCTURE JRNL TITL 2 OF DUCK EGG LYSOZYME. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 73 910 2017 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 29095163 JRNL DOI 10.1107/S2059798317013730 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 33669 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 + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1747 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2471 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE SET COUNT : 118 REMARK 3 BIN FREE R VALUE : 0.2400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1958 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 153 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.093 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.092 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.054 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.125 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2067 ; 0.015 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1809 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2815 ; 1.631 ; 1.936 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4146 ; 1.079 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 262 ; 6.366 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;35.169 ;22.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 317 ;10.974 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;13.549 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 297 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2335 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 466 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 129 REMARK 3 ORIGIN FOR THE GROUP (A): -25.8987 -12.2431 -1.7689 REMARK 3 T TENSOR REMARK 3 T11: 0.0087 T22: 0.0454 REMARK 3 T33: 0.0194 T12: 0.0013 REMARK 3 T13: 0.0109 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 0.9012 L22: 1.5199 REMARK 3 L33: 0.6764 L12: -0.4716 REMARK 3 L13: -0.2004 L23: -0.1978 REMARK 3 S TENSOR REMARK 3 S11: 0.0050 S12: -0.0433 S13: -0.0272 REMARK 3 S21: -0.0042 S22: -0.0357 S23: -0.0210 REMARK 3 S31: 0.0310 S32: 0.0308 S33: 0.0308 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 129 REMARK 3 ORIGIN FOR THE GROUP (A): -9.7054 14.1504 6.0742 REMARK 3 T TENSOR REMARK 3 T11: 0.0610 T22: 0.0601 REMARK 3 T33: 0.1018 T12: -0.0135 REMARK 3 T13: 0.0032 T23: 0.0363 REMARK 3 L TENSOR REMARK 3 L11: 1.8222 L22: 0.4036 REMARK 3 L33: 1.5638 L12: 0.5521 REMARK 3 L13: -1.4481 L23: -0.3560 REMARK 3 S TENSOR REMARK 3 S11: 0.0897 S12: 0.0920 S13: 0.2137 REMARK 3 S21: -0.0210 S22: -0.0180 S23: -0.0157 REMARK 3 S31: -0.1884 S32: -0.0162 S33: -0.0717 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5V94 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000227073. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.17 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35458 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 42.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 20.90 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 18.50 REMARK 200 R MERGE FOR SHELL (I) : 1.01500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.7 REMARK 200 STARTING MODEL: PDB ENTRY 1IEE REMARK 200 REMARK 200 REMARK: CUBIC REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM AMMONIUM PHOSPHATE DIBASIC, 100 REMARK 280 MM TRIS, PH 8.8, 45% MPD, EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+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 47.97500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.97500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.97500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.97500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.97500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.97500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 47.97500 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 47.97500 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 47.97500 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 47.97500 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 47.97500 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 47.97500 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 47.97500 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 47.97500 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 47.97500 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 47.97500 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 47.97500 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 47.97500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 P PO4 A 201 LIES ON A SPECIAL POSITION. REMARK 375 P PO4 A 204 LIES ON A SPECIAL POSITION. REMARK 375 P PO4 B 202 LIES ON A SPECIAL POSITION. REMARK 375 O4 PO4 B 202 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 302 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 415 LIES ON A SPECIAL POSITION. 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 45 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 125 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 14 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 45 CG CD NE CZ NH1 NH2 REMARK 470 THR B 47 OG1 CG2 REMARK 470 ARG B 61 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 71 CG CD NE CZ NH1 NH2 REMARK 470 SER B 72 OG REMARK 470 LYS B 73 CG CD CE NZ REMARK 470 ARG B 85 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 101 CG OD1 OD2 REMARK 470 ASN B 103 CG OD1 ND2 REMARK 470 ASN B 106 CG OD1 ND2 REMARK 470 ARG B 112 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 114 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 116 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O2 PO4 A 205 O2 PO4 A 205 5555 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 116 NE - CZ - NH1 ANGL. DEV. = 3.1 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 LYS A 68 14.74 -144.83 REMARK 500 ASN A 74 60.14 32.67 REMARK 500 ASP B 48 -176.59 -69.37 REMARK 500 ASN B 74 61.81 31.67 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 PO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MRD A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5V8G RELATED DB: PDB REMARK 900 PEKIN DUCK LYSOZYME ISOFORM I REMARK 900 RELATED ID: 5V92 RELATED DB: PDB REMARK 900 PEKIN DUCK EGG LYSOZYME ISOFORM III (DEL-III), ORTHORHOMBIC FORM DBREF 5V94 A 1 129 UNP U3J0P1 U3J0P1_ANAPL 19 147 DBREF 5V94 B 1 129 UNP U3J0P1 U3J0P1_ANAPL 19 147 SEQADV 5V94 ARG A 79 UNP U3J0P1 PRO 97 CONFLICT SEQADV 5V94 ARG A 100 UNP U3J0P1 SER 118 CONFLICT SEQADV 5V94 ARG B 79 UNP U3J0P1 PRO 97 CONFLICT SEQADV 5V94 ARG B 100 UNP U3J0P1 SER 118 CONFLICT SEQRES 1 A 129 LYS VAL TYR SER ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 A 129 ARG LEU GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 A 129 ASN TRP VAL CYS ALA ALA ASN TYR GLU SER GLY 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 ASP SEQRES 6 A 129 ASP GLY LYS THR PRO ARG SER LYS ASN ALA CYS GLY ILE SEQRES 7 A 129 ARG CYS SER VAL LEU LEU ARG SER ASP ILE THR GLU ALA SEQRES 8 A 129 VAL ARG CYS ALA LYS ARG ILE VAL ARG ASP GLY ASN GLY SEQRES 9 A 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS ARG GLY SEQRES 10 A 129 THR ASP VAL SER LYS TRP ILE ARG GLY CYS ARG LEU SEQRES 1 B 129 LYS VAL TYR SER ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 B 129 ARG LEU GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 B 129 ASN TRP VAL CYS ALA ALA ASN TYR GLU SER GLY PHE ASN SEQRES 4 B 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 B 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASP SEQRES 6 B 129 ASP GLY LYS THR PRO ARG SER LYS ASN ALA CYS GLY ILE SEQRES 7 B 129 ARG CYS SER VAL LEU LEU ARG SER ASP ILE THR GLU ALA SEQRES 8 B 129 VAL ARG CYS ALA LYS ARG ILE VAL ARG ASP GLY ASN GLY SEQRES 9 B 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS ARG GLY SEQRES 10 B 129 THR ASP VAL SER LYS TRP ILE ARG GLY CYS ARG LEU HET PO4 A 201 5 HET PO4 A 202 5 HET PO4 A 203 5 HET PO4 A 204 5 HET PO4 A 205 5 HET MRD A 206 8 HET TRS A 207 8 HET PO4 B 201 5 HET PO4 B 202 5 HETNAM PO4 PHOSPHATE ION HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 3 PO4 7(O4 P 3-) FORMUL 8 MRD C6 H14 O2 FORMUL 9 TRS C4 H12 N O3 1+ FORMUL 12 HOH *153(H2 O) HELIX 1 AA1 SER A 4 LEU A 15 1 12 HELIX 2 AA2 ASN A 19 TYR A 23 5 5 HELIX 3 AA3 SER A 24 GLY A 37 1 14 HELIX 4 AA4 ARG A 79 ARG A 85 5 7 HELIX 5 AA5 ILE A 88 ASP A 101 1 14 HELIX 6 AA6 ASN A 103 ALA A 107 5 5 HELIX 7 AA7 TRP A 108 CYS A 115 1 8 HELIX 8 AA8 ASP A 119 ARG A 125 5 7 HELIX 9 AA9 SER B 4 LEU B 15 1 12 HELIX 10 AB1 ASN B 19 TYR B 23 5 5 HELIX 11 AB2 SER B 24 GLY B 37 1 14 HELIX 12 AB3 ARG B 79 ARG B 85 5 7 HELIX 13 AB4 ILE B 88 ASP B 101 1 14 HELIX 14 AB5 GLY B 104 ALA B 107 5 4 HELIX 15 AB6 TRP B 108 CYS B 115 1 8 HELIX 16 AB7 ASP B 119 ARG B 125 5 7 SHEET 1 AA1 3 THR A 43 ARG A 45 0 SHEET 2 AA1 3 THR A 51 TYR A 53 -1 O ASP A 52 N ASN A 44 SHEET 3 AA1 3 ILE A 58 ASN A 59 -1 O ILE A 58 N TYR A 53 SHEET 1 AA2 3 THR B 43 ARG B 45 0 SHEET 2 AA2 3 THR B 51 TYR B 53 -1 O ASP B 52 N ASN B 44 SHEET 3 AA2 3 ILE B 58 ASN B 59 -1 O ILE B 58 N TYR B 53 SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.11 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.11 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.06 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.09 SSBOND 5 CYS B 6 CYS B 127 1555 1555 2.07 SSBOND 6 CYS B 30 CYS B 115 1555 1555 2.06 SSBOND 7 CYS B 64 CYS B 80 1555 1555 2.08 SSBOND 8 CYS B 76 CYS B 94 1555 1555 2.06 SITE 1 AC1 4 TYR A 34 ARG A 114 HOH A 302 HOH A 304 SITE 1 AC2 12 SER A 4 CYS A 6 GLU A 7 ARG A 112 SITE 2 AC2 12 ARG A 116 HOH A 313 HOH A 314 HOH A 320 SITE 3 AC2 12 HOH A 333 HOH A 348 HOH A 352 SER B 4 SITE 1 AC3 4 ARG A 85 SER A 86 HOH A 383 ARG B 79 SITE 1 AC4 5 ARG A 97 ARG A 100 PO4 A 205 HOH A 305 SITE 2 AC4 5 HOH A 308 SITE 1 AC5 7 ARG A 93 ARG A 97 ARG A 100 PO4 A 204 SITE 2 AC5 7 HOH A 307 HOH A 309 HOH A 319 SITE 1 AC6 7 ASN A 113 ARG A 114 THR A 118 LYS A 122 SITE 2 AC6 7 TRP A 123 HOH A 328 HOH A 345 SITE 1 AC7 9 GLU A 35 ASP A 52 GLN A 57 ALA A 107 SITE 2 AC7 9 TRP A 108 VAL A 109 HOH A 321 HOH A 381 SITE 3 AC7 9 ARG B 128 SITE 1 AC8 4 ARG A 79 ARG B 85 SER B 86 HOH B 330 SITE 1 AC9 2 ARG B 97 ARG B 100 CRYST1 95.950 95.950 95.950 90.00 90.00 90.00 P 21 3 24 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 0.010422 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010422 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010422 0.00000