HEADER HYDROLASE 22-NOV-17 6F1P TITLE TETRAGONAL LYSOZYME CRYSTALLIZED AT 298 K AND PH 4.5 WITH PHOSPHATE TITLE 2 BOUND 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 6F1P 1 LINK ATOM REVDAT 1 09-MAY-18 6F1P 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. 1.12 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) : 1.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 44863 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 4199 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 18.6914 - 3.4730 0.99 2694 124 0.1557 0.1410 REMARK 3 2 3.4730 - 2.7595 1.00 2690 133 0.1680 0.1996 REMARK 3 3 2.7595 - 2.4115 1.00 2686 137 0.1613 0.1788 REMARK 3 4 2.4115 - 2.1914 1.00 2709 140 0.1480 0.1559 REMARK 3 5 2.1914 - 2.0345 1.00 2676 148 0.1486 0.1712 REMARK 3 6 2.0345 - 1.9147 1.00 2687 128 0.1488 0.2048 REMARK 3 7 1.9147 - 1.8189 1.00 2702 142 0.1526 0.1447 REMARK 3 8 1.8189 - 1.7398 1.00 2698 139 0.1421 0.1850 REMARK 3 9 1.7398 - 1.6728 1.00 2649 162 0.1406 0.1519 REMARK 3 10 1.6728 - 1.6151 1.00 2671 182 0.1330 0.1443 REMARK 3 11 1.6151 - 1.5647 1.00 2687 144 0.1390 0.1360 REMARK 3 12 1.5647 - 1.5200 1.00 2701 138 0.1318 0.1506 REMARK 3 13 1.5200 - 1.4800 1.00 2659 146 0.1323 0.1791 REMARK 3 14 1.4800 - 1.4439 1.00 2701 136 0.1345 0.1528 REMARK 3 15 1.4439 - 1.4111 1.00 2627 194 0.1370 0.1564 REMARK 3 16 1.4111 - 1.3810 1.00 2699 138 0.1391 0.1608 REMARK 3 17 1.3810 - 1.3534 1.00 2723 120 0.1508 0.1775 REMARK 3 18 1.3534 - 1.3279 1.00 2646 149 0.1504 0.2009 REMARK 3 19 1.3279 - 1.3042 1.00 2734 125 0.1516 0.2003 REMARK 3 20 1.3042 - 1.2821 1.00 2656 146 0.1521 0.1876 REMARK 3 21 1.2821 - 1.2614 1.00 2725 152 0.1522 0.1575 REMARK 3 22 1.2614 - 1.2420 1.00 2680 122 0.1539 0.2057 REMARK 3 23 1.2420 - 1.2237 1.00 2687 149 0.1556 0.1574 REMARK 3 24 1.2237 - 1.2065 1.00 2701 146 0.1538 0.1582 REMARK 3 25 1.2065 - 1.1902 1.00 2685 142 0.1571 0.1554 REMARK 3 26 1.1902 - 1.1747 1.00 2721 120 0.1706 0.1921 REMARK 3 27 1.1747 - 1.1601 1.00 2664 125 0.1706 0.2309 REMARK 3 28 1.1601 - 1.1461 1.00 2705 110 0.1941 0.2301 REMARK 3 29 1.1461 - 1.1328 0.97 2595 126 0.2091 0.1630 REMARK 3 30 1.1328 - 1.1200 0.95 2610 136 0.2247 0.2850 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.60 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 : 0.006 1095 REMARK 3 ANGLE : 0.850 1490 REMARK 3 CHIRALITY : 0.080 151 REMARK 3 PLANARITY : 0.006 198 REMARK 3 DIHEDRAL : 17.383 410 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 6F1P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007634. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-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 : 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) : 0.97926 REMARK 200 MONOCHROMATOR : CHANNEL-CUT MONOCHROMATOR AND A REMARK 200 KIRKPATRICK-BAEZ (KB) FOCUSING REMARK 200 SYSTEM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44928 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.120 REMARK 200 RESOLUTION RANGE LOW (A) : 19.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.62800 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: 4E3U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 0.1 M SODIUM REMARK 280 ACETATE, 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 19.19350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.52800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.52800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.79025 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.52800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.52800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.59675 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.52800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.52800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.79025 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.52800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.52800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.59675 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 19.19350 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 335 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 417 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 426 LIES ON A SPECIAL POSITION. 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 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 60 O REMARK 620 2 CYS A 64 O 84.1 REMARK 620 3 SER A 72 OG 111.8 162.3 REMARK 620 4 ARG A 73 O 99.9 95.1 89.7 REMARK 620 5 HOH A 301 O 164.7 108.7 54.4 87.4 REMARK 620 6 HOH A 371 O 86.6 87.7 85.8 173.1 85.8 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 PO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 205 DBREF 6F1P 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 PO4 A 201 5 HET CL A 202 1 HET CL A 203 1 HET CL A 204 1 HET NA A 205 1 HETNAM PO4 PHOSPHATE ION HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION FORMUL 2 PO4 O4 P 3- FORMUL 3 CL 3(CL 1-) FORMUL 6 NA NA 1+ FORMUL 7 HOH *127(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 2.07 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.05 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.04 LINK O SER A 60 NA A NA A 205 1555 1555 2.31 LINK O CYS A 64 NA A NA A 205 1555 1555 2.44 LINK OG ASER A 72 NA A NA A 205 1555 1555 2.38 LINK O AARG A 73 NA A NA A 205 1555 1555 2.61 LINK NA A NA A 205 O AHOH A 301 1555 1555 2.32 LINK NA A NA A 205 O HOH A 371 1555 1555 2.28 SITE 1 AC1 4 HIS A 15 ASN A 93 LYS A 96 HOH A 317 SITE 1 AC2 3 SER A 24 GLY A 26 GLN A 121 SITE 1 AC3 2 TYR A 23 ASN A 113 SITE 1 AC4 6 ASN A 65 GLY A 67 ARG A 68 THR A 69 SITE 2 AC4 6 SER A 72 HOH A 371 SITE 1 AC5 7 SER A 60 CYS A 64 SER A 72 ARG A 73 SITE 2 AC5 7 HOH A 301 HOH A 307 HOH A 371 CRYST1 77.056 77.056 38.387 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 0.012978 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012978 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026050 0.00000