HEADER HYDROLASE 08-OCT-14 4WM6
TITLE HIGH PRESSURE PROTEIN CRYSTALLOGRAPHY OF HEN EGG WHITE LYSOZYME AT 950
TITLE 2 MPA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSOZYME C;
COMPND 3 CHAIN: A, B, C, D;
COMPND 4 FRAGMENT: UNP RESIDUES 19-147;
COMPND 5 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C,ALLERGEN GAL D IV;
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
KEYWDS HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR H.YAMADA,N.WATANABE,T.NAGAE
REVDAT 3 24-JUL-19 4WM6 1 SOURCE REMARK LINK SITE
REVDAT 3 2 1 ATOM
REVDAT 2 22-APR-15 4WM6 1 JRNL
REVDAT 1 08-APR-15 4WM6 0
JRNL AUTH H.YAMADA,T.NAGAE,N.WATANABE
JRNL TITL HIGH-PRESSURE PROTEIN CRYSTALLOGRAPHY OF HEN EGG-WHITE
JRNL TITL 2 LYSOZYME
JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 742 2015
JRNL REFN ESSN 1399-0047
JRNL PMID 25849385
JRNL DOI 10.1107/S1399004715000292
REMARK 2
REMARK 2 RESOLUTION. 1.85 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.7.0032
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.76
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 88.0
REMARK 3 NUMBER OF REFLECTIONS : 30495
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) : 0.204
REMARK 3 R VALUE (WORKING SET) : 0.199
REMARK 3 FREE R VALUE : 0.284
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1606
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) : 1.85
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1949
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.46
REMARK 3 BIN R VALUE (WORKING SET) : 0.2940
REMARK 3 BIN FREE R VALUE SET COUNT : 109
REMARK 3 BIN FREE R VALUE : 0.4190
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4004
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 4
REMARK 3 SOLVENT ATOMS : 615
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.90
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.02000
REMARK 3 B22 (A**2) : 0.02000
REMARK 3 B33 (A**2) : -0.04000
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): 0.243
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.218
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.162
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.599
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.863
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4110 ; 0.015 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 3798 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5571 ; 1.728 ; 1.903
REMARK 3 BOND ANGLES OTHERS (DEGREES): 8608 ; 0.945 ; 3.007
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 514 ; 6.906 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 201 ;37.363 ;23.035
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 666 ;17.727 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;20.089 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 577 ; 0.101 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4842 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 1086 ; 0.001 ; 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): 2065 ; 1.225 ; 1.609
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2064 ; 1.225 ; 1.609
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2576 ; 1.992 ; 2.406
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2577 ; 1.992 ; 2.406
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2045 ; 1.511 ; 1.828
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2045 ; 1.511 ; 1.828
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2995 ; 2.485 ; 2.668
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5893 ; 4.956 ;14.575
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5692 ; 4.761 ;14.205
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 : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
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 4WM6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-OCT-14.
REMARK 100 THE DEPOSITION ID IS D_1000204055.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-FEB-13
REMARK 200 TEMPERATURE (KELVIN) : 298
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PHOTON FACTORY
REMARK 200 BEAMLINE : AR-NW12A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.71
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36471
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 200 DATA REDUNDANCY : 4.000
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
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: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 33.56
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CHLORIDE, BATCH MODE,
REMARK 280 TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43
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,X,Z+3/4
REMARK 290 4555 Y,-X,Z+1/4
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 18.44550
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.66825
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.22275
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2, 3, 4
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 130 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 6390 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 6420 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL
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 350
REMARK 350 BIOMOLECULE: 3
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 130 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 6450 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C
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: 4
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 6400 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: D
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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 NH2 ARG A 21 OD1 ASN D 113 2.05
REMARK 500
REMARK 500 REMARK: NULL
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 O HOH C 307 O HOH C 369 4555 1.75
REMARK 500 O HOH B 392 O HOH B 439 4565 2.10
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 21 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 ARG A 114 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 ARG B 112 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 ARG B 114 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 ARG B 114 NE - CZ - NH2 ANGL. DEV. = -3.5 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 ARG A 68 37.24 -149.34
REMARK 500 CYS A 115 -52.07 -139.83
REMARK 500 ASN B 19 18.92 52.31
REMARK 500 GLN B 57 68.49 36.20
REMARK 500 ASP B 119 69.24 -66.49
REMARK 500 ASN C 74 67.42 -155.94
REMARK 500 PHE D 38 16.90 59.39
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 473 DISTANCE = 6.52 ANGSTROMS
REMARK 525 HOH C 427 DISTANCE = 5.83 ANGSTROMS
REMARK 525 HOH C 428 DISTANCE = 6.33 ANGSTROMS
REMARK 525 HOH C 429 DISTANCE = 7.00 ANGSTROMS
REMARK 525 HOH D 459 DISTANCE = 6.35 ANGSTROMS
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 201 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SER A 60 O
REMARK 620 2 CYS A 64 O 88.0
REMARK 620 3 SER A 72 OG 91.4 161.4
REMARK 620 4 ARG A 73 O 90.4 98.8 99.8
REMARK 620 5 HOH A 356 O 170.9 100.8 79.5 90.6
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA B 201 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SER B 60 O
REMARK 620 2 CYS B 64 O 73.6
REMARK 620 3 SER B 72 OG 77.4 105.0
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA C 201 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SER C 60 O
REMARK 620 2 CYS C 64 O 89.0
REMARK 620 3 SER C 72 OG 94.7 166.2
REMARK 620 4 ARG C 73 O 108.5 97.3 94.2
REMARK 620 5 HOH C 333 O 82.4 90.7 76.6 166.5
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA D 201 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SER D 60 O
REMARK 620 2 ARG D 61 O 78.8
REMARK 620 3 CYS D 64 O 73.4 150.2
REMARK 620 4 ARG D 73 O 150.1 72.3 136.3
REMARK 620 5 HOH D 410 O 91.1 117.8 73.7 95.5
REMARK 620 N 1 2 3 4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA C 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA D 201
DBREF 4WM6 A 1 129 UNP P00698 LYSC_CHICK 19 147
DBREF 4WM6 B 1 129 UNP P00698 LYSC_CHICK 19 147
DBREF 4WM6 C 1 129 UNP P00698 LYSC_CHICK 19 147
DBREF 4WM6 D 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
SEQRES 1 B 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS
SEQRES 2 B 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY
SEQRES 3 B 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN 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 ASN
SEQRES 6 B 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE
SEQRES 7 B 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER
SEQRES 8 B 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY
SEQRES 9 B 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY
SEQRES 10 B 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU
SEQRES 1 C 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS
SEQRES 2 C 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY
SEQRES 3 C 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN
SEQRES 4 C 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP
SEQRES 5 C 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN
SEQRES 6 C 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE
SEQRES 7 C 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER
SEQRES 8 C 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY
SEQRES 9 C 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY
SEQRES 10 C 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU
SEQRES 1 D 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS
SEQRES 2 D 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY
SEQRES 3 D 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN
SEQRES 4 D 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP
SEQRES 5 D 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN
SEQRES 6 D 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE
SEQRES 7 D 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER
SEQRES 8 D 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY
SEQRES 9 D 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY
SEQRES 10 D 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU
HET NA A 201 1
HET NA B 201 1
HET NA C 201 1
HET NA D 201 1
HETNAM NA SODIUM ION
FORMUL 5 NA 4(NA 1+)
FORMUL 9 HOH *615(H2 O)
HELIX 1 AA1 GLY A 4 HIS A 15 1 12
HELIX 2 AA2 ASN A 19 TYR A 23 5 5
HELIX 3 AA3 SER A 24 ASN A 37 1 14
HELIX 4 AA4 PRO A 79 SER A 85 5 7
HELIX 5 AA5 ILE A 88 SER A 100 1 13
HELIX 6 AA6 ASP A 101 GLY A 102 5 2
HELIX 7 AA7 ASN A 103 ALA A 107 5 5
HELIX 8 AA8 TRP A 108 CYS A 115 1 8
HELIX 9 AA9 ASP A 119 ILE A 124 5 6
HELIX 10 AB1 GLY B 4 HIS B 15 1 12
HELIX 11 AB2 ASN B 19 TYR B 23 5 5
HELIX 12 AB3 SER B 24 ASN B 37 1 14
HELIX 13 AB4 PRO B 79 SER B 85 5 7
HELIX 14 AB5 ILE B 88 SER B 100 1 13
HELIX 15 AB6 ASN B 103 ALA B 107 5 5
HELIX 16 AB7 TRP B 108 CYS B 115 1 8
HELIX 17 AB8 ASP B 119 ARG B 125 5 7
HELIX 18 AB9 GLY C 4 GLY C 16 1 13
HELIX 19 AC1 ASN C 19 TYR C 23 5 5
HELIX 20 AC2 SER C 24 ASN C 37 1 14
HELIX 21 AC3 PRO C 79 LEU C 84 5 6
HELIX 22 AC4 ILE C 88 SER C 100 1 13
HELIX 23 AC5 ASN C 103 ALA C 107 5 5
HELIX 24 AC6 TRP C 108 CYS C 115 1 8
HELIX 25 AC7 ASP C 119 ARG C 125 5 7
HELIX 26 AC8 GLY D 4 HIS D 15 1 12
HELIX 27 AC9 ASN D 19 TYR D 23 5 5
HELIX 28 AD1 SER D 24 ASN D 37 1 14
HELIX 29 AD2 SER D 81 SER D 85 5 5
HELIX 30 AD3 ILE D 88 SER D 100 1 13
HELIX 31 AD4 ASN D 103 ALA D 107 5 5
HELIX 32 AD5 TRP D 108 CYS D 115 1 8
HELIX 33 AD6 ASP D 119 ARG D 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
SHEET 1 AA3 3 THR C 43 ARG C 45 0
SHEET 2 AA3 3 THR C 51 TYR C 53 -1 O ASP C 52 N ASN C 44
SHEET 3 AA3 3 ILE C 58 ASN C 59 -1 O ILE C 58 N TYR C 53
SHEET 1 AA4 3 THR D 43 ARG D 45 0
SHEET 2 AA4 3 THR D 51 TYR D 53 -1 O ASP D 52 N ASN D 44
SHEET 3 AA4 3 ILE D 58 ASN D 59 -1 O ILE D 58 N TYR D 53
SSBOND 1 CYS A 6 CYS A 127 1555 1555 1.97
SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.00
SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.00
SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.07
SSBOND 5 CYS B 6 CYS B 127 1555 1555 1.99
SSBOND 6 CYS B 30 CYS B 115 1555 1555 1.98
SSBOND 7 CYS B 64 CYS B 80 1555 1555 2.02
SSBOND 8 CYS B 76 CYS B 94 1555 1555 2.06
SSBOND 9 CYS C 6 CYS C 127 1555 1555 2.02
SSBOND 10 CYS C 30 CYS C 115 1555 1555 1.96
SSBOND 11 CYS C 64 CYS C 80 1555 1555 2.06
SSBOND 12 CYS C 76 CYS C 94 1555 1555 2.05
SSBOND 13 CYS D 6 CYS D 127 1555 1555 2.00
SSBOND 14 CYS D 30 CYS D 115 1555 1555 2.02
SSBOND 15 CYS D 64 CYS D 80 1555 1555 2.01
SSBOND 16 CYS D 76 CYS D 94 1555 1555 2.04
LINK O SER A 60 NA NA A 201 1555 1555 2.23
LINK O CYS A 64 NA NA A 201 1555 1555 2.31
LINK OG SER A 72 NA NA A 201 1555 1555 2.50
LINK O ARG A 73 NA NA A 201 1555 1555 2.40
LINK O SER B 60 NA NA B 201 1555 1555 2.58
LINK O CYS B 64 NA NA B 201 1555 1555 2.45
LINK OG SER B 72 NA NA B 201 1555 1555 2.68
LINK O SER C 60 NA NA C 201 1555 1555 2.26
LINK O CYS C 64 NA NA C 201 1555 1555 2.16
LINK OG SER C 72 NA NA C 201 1555 1555 2.33
LINK O ARG C 73 NA NA C 201 1555 1555 2.38
LINK O SER D 60 NA NA D 201 1555 1555 2.72
LINK O ARG D 61 NA NA D 201 1555 1555 3.18
LINK O CYS D 64 NA NA D 201 1555 1555 2.79
LINK O ARG D 73 NA NA D 201 1555 1555 2.32
LINK NA NA A 201 O HOH A 356 1555 1555 2.46
LINK NA NA C 201 O HOH C 333 1555 1555 2.45
LINK NA NA D 201 O HOH D 410 1555 1555 3.05
SITE 1 AC1 5 SER A 60 CYS A 64 SER A 72 ARG A 73
SITE 2 AC1 5 HOH A 356
SITE 1 AC2 7 SER B 60 ARG B 61 TRP B 63 CYS B 64
SITE 2 AC2 7 SER B 72 ARG B 73 ASN B 74
SITE 1 AC3 6 SER C 60 CYS C 64 ASN C 65 SER C 72
SITE 2 AC3 6 ARG C 73 HOH C 333
SITE 1 AC4 9 SER D 60 ARG D 61 TRP D 62 TRP D 63
SITE 2 AC4 9 CYS D 64 SER D 72 ARG D 73 ASN D 74
SITE 3 AC4 9 HOH D 410
CRYST1 107.269 107.269 36.891 90.00 90.00 90.00 P 43 16
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 0.009322 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009322 0.000000 0.00000
SCALE3 0.000000 0.000000 0.027107 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
