HEADER HYDROLASE 27-SEP-19 6SYD TITLE CRYSTAL STRUCTURE OF THE LYSOZYME IN PRESENCE OF BROMOPHENOL BLUE AT TITLE 2 PH 5.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 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, GLYCOSIDASE, DYE-SOAKING EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS,M.PLAZA-GARRIDO,M.C.SALINAS-GARCIA REVDAT 3 24-JAN-24 6SYD 1 REMARK REVDAT 2 16-SEP-20 6SYD 1 JRNL REVDAT 1 09-SEP-20 6SYD 0 JRNL AUTH M.PLAZA-GARRIDO,M.C.SALINAS-GARCIA,D.ALBA-ELENA, JRNL AUTH 2 J.C.MARTINEZ,A.CAMARA-ARTIGAS JRNL TITL LYSOZYME CRYSTALS DYED WITH BROMOPHENOL BLUE: WHERE HAS THE JRNL TITL 2 DYE GONE? JRNL REF ACTA CRYSTALLOGR D STRUCT V. 76 845 2020 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 32876060 JRNL DOI 10.1107/S2059798320008803 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 89752 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 4478 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 19.0400 - 3.4100 0.97 2800 132 0.1971 0.2441 REMARK 3 2 3.4100 - 2.7100 0.98 2788 147 0.1967 0.2108 REMARK 3 3 2.7100 - 2.3700 0.97 2802 154 0.1981 0.2290 REMARK 3 4 2.3700 - 2.1500 0.97 2804 148 0.1936 0.2430 REMARK 3 5 2.1500 - 2.0000 0.98 2820 136 0.1846 0.1699 REMARK 3 6 2.0000 - 1.8800 0.98 2811 123 0.1993 0.2162 REMARK 3 7 1.8800 - 1.7900 0.99 2805 160 0.2092 0.2368 REMARK 3 8 1.7900 - 1.7100 0.99 2847 144 0.2096 0.2565 REMARK 3 9 1.7100 - 1.6400 0.99 2862 126 0.2033 0.1983 REMARK 3 10 1.6400 - 1.5900 0.99 2895 147 0.2079 0.2195 REMARK 3 11 1.5900 - 1.5400 1.00 2825 156 0.2084 0.2682 REMARK 3 12 1.5400 - 1.4900 1.00 2888 146 0.2143 0.2117 REMARK 3 13 1.4900 - 1.4500 1.00 2829 167 0.2099 0.2352 REMARK 3 14 1.4500 - 1.4200 1.00 2882 143 0.2130 0.2297 REMARK 3 15 1.4200 - 1.3900 1.00 2862 126 0.2196 0.2251 REMARK 3 16 1.3900 - 1.3600 1.00 2862 156 0.2281 0.2399 REMARK 3 17 1.3600 - 1.3300 1.00 2840 153 0.2197 0.2493 REMARK 3 18 1.3300 - 1.3000 1.00 2917 128 0.2343 0.1943 REMARK 3 19 1.3000 - 1.2800 1.00 2825 148 0.2423 0.3075 REMARK 3 20 1.2800 - 1.2600 1.00 2874 132 0.2421 0.2803 REMARK 3 21 1.2600 - 1.2400 1.00 2871 147 0.2500 0.2225 REMARK 3 22 1.2400 - 1.2200 0.99 2880 110 0.2485 0.2502 REMARK 3 23 1.2200 - 1.2000 1.00 2853 168 0.2496 0.2761 REMARK 3 24 1.2000 - 1.1800 1.00 2827 167 0.2591 0.2562 REMARK 3 25 1.1800 - 1.1700 1.00 2824 173 0.2540 0.2998 REMARK 3 26 1.1700 - 1.1500 0.99 2838 185 0.2774 0.2981 REMARK 3 27 1.1500 - 1.1400 0.99 2845 151 0.2744 0.2795 REMARK 3 28 1.1400 - 1.1300 0.99 2810 179 0.2876 0.3113 REMARK 3 29 1.1300 - 1.1100 0.99 2855 161 0.2955 0.2946 REMARK 3 30 1.1100 - 1.1000 1.00 2833 165 0.2943 0.3075 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.112 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.44 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 : 0.005 1056 REMARK 3 ANGLE : 0.705 1434 REMARK 3 CHIRALITY : 0.066 145 REMARK 3 PLANARITY : 0.004 185 REMARK 3 DIHEDRAL : 16.229 166 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: THE LIGAND GEOMETRY VALIDATION IS NOT REMARK 3 ACCURATE BECAUSE THE MOLECULE IS A RESONANT FORM. REMARK 4 REMARK 4 6SYD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1292104540. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-18 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 : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 89752 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 19.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.89300 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 REMARK 200 STARTING MODEL: 6F1R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, 0.3-0.5 SODIUM REMARK 280 CHLORIDE AT PH 4.6. AFTER GROWTH, AND BEFORE MEASUREMENT, THESE REMARK 280 CRYSTALS WERE SOAKED IN THE DYE SOLUTION: SATURATED BROMOPHENOL REMARK 280 BLUE, 0.3 M SODIUM CHLORIDE, 0.1 M SODIUM ACETATE BUFFER AT PH REMARK 280 5.5., PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 18.67050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.24900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.24900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.00575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.24900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.24900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.33525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.24900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.24900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.00575 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.24900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.24900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.33525 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 18.67050 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: 130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6880 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 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 376 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 443 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LEU A 129 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 87.1 REMARK 620 3 SER A 72 OG 90.8 165.5 REMARK 620 4 ARG A 73 O 95.1 92.8 101.7 REMARK 620 5 HOH A 365 O 97.0 87.9 78.1 167.9 REMARK 620 6 HOH A 384 O 172.4 99.7 81.8 88.0 80.0 REMARK 620 N 1 2 3 4 5 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 LYE A 202 DBREF 6SYD A 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 HET NA A 201 1 HET LYE A 202 37 HETNAM NA SODIUM ION HETNAM LYE BROMOPHENOL BLUE FORMUL 2 NA NA 1+ FORMUL 3 LYE C19 H10 BR4 O5 S FORMUL 4 HOH *155(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 2.04 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.03 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.03 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.03 LINK O SER A 60 NA NA A 201 1555 1555 2.34 LINK O CYS A 64 NA NA A 201 1555 1555 2.34 LINK OG SER A 72 NA NA A 201 1555 1555 2.55 LINK O ARG A 73 NA NA A 201 1555 1555 2.51 LINK NA NA A 201 O HOH A 365 1555 1555 2.44 LINK NA NA A 201 O HOH A 384 1555 1555 2.39 SITE 1 AC1 6 SER A 60 CYS A 64 SER A 72 ARG A 73 SITE 2 AC1 6 HOH A 365 HOH A 384 SITE 1 AC2 12 ARG A 14 HIS A 15 TYR A 20 ARG A 21 SITE 2 AC2 12 THR A 47 LYS A 96 SER A 100 GLY A 126 SITE 3 AC2 12 ARG A 128 HOH A 308 HOH A 312 HOH A 434 CRYST1 78.498 78.498 37.341 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 0.012739 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012739 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026780 0.00000