HEADER HYDROLASE 15-DEC-17 6FA0
TITLE LYSOZYME CRYSTALLIZED IN PRESENCE OF 100 MM AMMONIUM SULPHATE AT PH
TITLE 2 4.5
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSOZYME C;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C,ALLERGEN GAL D IV;
COMPND 5 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 A.CAMARA-ARTIGAS
REVDAT 2 17-JAN-24 6FA0 1 REMARK
REVDAT 1 09-MAY-18 6FA0 0
JRNL AUTH M.PLAZA-GARRIDO,M.C.SALINAS-GARCIA,A.CAMARA-ARTIGAS
JRNL TITL ORTHORHOMBIC LYSOZYME CRYSTALLIZATION AT ACIDIC PH VALUES
JRNL TITL 2 DRIVEN BY PHOSPHATE BINDING.
JRNL REF ACTA CRYSTALLOGR D STRUCT V. 74 480 2018
JRNL REF 2 BIOL
JRNL REFN ISSN 2059-7983
JRNL PMID 29717719
JRNL DOI 10.1107/S205979831800517X
REMARK 2
REMARK 2 RESOLUTION. 1.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.79
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.090
REMARK 3 COMPLETENESS FOR RANGE (%) : 88.5
REMARK 3 NUMBER OF REFLECTIONS : 28443
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.153
REMARK 3 R VALUE (WORKING SET) : 0.151
REMARK 3 FREE R VALUE : 0.188
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910
REMARK 3 FREE R VALUE TEST SET COUNT : 2562
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 19.7898 - 3.4017 0.90 2795 157 0.1585 0.1919
REMARK 3 2 3.4017 - 2.7022 0.97 3032 149 0.1564 0.1763
REMARK 3 3 2.7022 - 2.3613 0.95 2946 165 0.1492 0.1878
REMARK 3 4 2.3613 - 2.1457 0.76 2365 118 0.1404 0.1449
REMARK 3 5 2.1457 - 1.9920 0.77 2424 109 0.1355 0.1636
REMARK 3 6 1.9920 - 1.8747 0.71 2218 92 0.1355 0.1978
REMARK 3 7 1.8747 - 1.7808 0.97 3080 143 0.1281 0.1934
REMARK 3 8 1.7808 - 1.7034 0.77 2389 127 0.1239 0.2140
REMARK 3 9 1.7034 - 1.6378 0.98 3049 188 0.1197 0.1404
REMARK 3 10 1.6378 - 1.5813 0.98 3037 155 0.1204 0.1715
REMARK 3 11 1.5813 - 1.5319 0.97 3098 139 0.1302 0.2115
REMARK 3 12 1.5319 - 1.4881 0.65 2012 118 0.1445 0.2024
REMARK 3 13 1.4881 - 1.4490 0.63 1963 96 0.1652 0.2406
REMARK 3 14 1.4490 - 1.4136 0.98 3051 187 0.1799 0.2358
REMARK 3 15 1.4136 - 1.3815 0.99 3073 163 0.1835 0.2214
REMARK 3 16 1.3815 - 1.3521 0.95 2997 139 0.2513 0.2942
REMARK 3 17 1.3521 - 1.3251 0.99 3115 151 0.2097 0.2176
REMARK 3 18 1.3251 - 1.3001 0.98 3024 166 0.2418 0.2567
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.180
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 14.62
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.98
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 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.007 1046
REMARK 3 ANGLE : 0.884 1425
REMARK 3 CHIRALITY : 0.074 147
REMARK 3 PLANARITY : 0.005 186
REMARK 3 DIHEDRAL : 19.192 390
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 6FA0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-DEC-17.
REMARK 100 THE DEPOSITION ID IS D_1200007999.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 24-JUL-17
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 4.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : MASSIF-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.966
REMARK 200 MONOCHROMATOR : DIAMOND
REMARK 200 OPTICS : COMPOUND REFRACTIVE LENS
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28509
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300
REMARK 200 RESOLUTION RANGE LOW (A) : 19.790
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0
REMARK 200 DATA REDUNDANCY : 4.300
REMARK 200 R MERGE (I) : 0.04800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6
REMARK 200 DATA REDUNDANCY IN SHELL : 4.60
REMARK 200 R MERGE FOR SHELL (I) : 0.69700
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
REMARK 200 STARTING MODEL: 4E3U
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.20
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM AMMONIUM SULPHATE, 0.4 M SODIUM
REMARK 280 CHLORIDE, 0.1 M SODIUM ACETATE, PH 4.5, VAPOR DIFFUSION, HANGING
REMARK 280 DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
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
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 15.04400
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.60400
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.14100
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.60400
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.04400
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.14100
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 290 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 6350 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202
DBREF 6FA0 A 1 127 UNP P00698 LYSC_CHICK 19 145
SEQRES 1 A 127 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS
SEQRES 2 A 127 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY
SEQRES 3 A 127 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN
SEQRES 4 A 127 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP
SEQRES 5 A 127 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN
SEQRES 6 A 127 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE
SEQRES 7 A 127 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER
SEQRES 8 A 127 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY
SEQRES 9 A 127 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY
SEQRES 10 A 127 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS
HET CL A 201 1
HET SO4 A 202 5
HETNAM CL CHLORIDE ION
HETNAM SO4 SULFATE ION
FORMUL 2 CL CL 1-
FORMUL 3 SO4 O4 S 2-
FORMUL 4 HOH *172(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 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
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
SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.03
SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.04
SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.03
SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.03
SITE 1 AC1 5 ASN A 65 ASP A 66 SER A 81 ARG A 125
SITE 2 AC1 5 HOH A 400
SITE 1 AC2 5 ARG A 14 HIS A 15 HOH A 305 HOH A 306
SITE 2 AC2 5 HOH A 322
CRYST1 30.088 56.282 73.208 90.00 90.00 90.00 P 21 21 21 4
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 0.033236 0.000000 0.000000 0.00000
SCALE2 0.000000 0.017768 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013660 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
