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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
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