HEADER HYDROLASE 26-AUG-20 7CVJ TITLE CRYSTAL STRUCTURE OF LYSOZYME BY FIXED-TARGET SERIAL SYNCHROTRON TITLE 2 CRYSTALLOGRAPHY (100 MS) 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 ROOM TEMPERATURE STRUCTURE, SERIAL CRYSTALLOGRAPHY, SERIAL KEYWDS 2 SYNCHROTRON CRYSTALLOGRAPHY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.H.NAM REVDAT 5 23-OCT-24 7CVJ 1 REMARK REVDAT 4 29-NOV-23 7CVJ 1 REMARK REVDAT 3 06-SEP-23 7CVJ 1 REMARK REVDAT 2 23-MAR-22 7CVJ 1 JRNL REVDAT 1 09-SEP-20 7CVJ 0 JRNL AUTH S.Y.PARK,H.CHOI,C.EO,Y.CHO,K.H.NAM JRNL TITL FIXED-TARGET SERIAL SYNCHROTRON CRYSTALLOGRAPHY USING NYLON JRNL TITL 2 MESH AND ENCLOSED FILM-BASED SAMPLE HOLDER JRNL REF CRYSTALS V. 10 2020 JRNL REFN ESSN 2073-4352 JRNL DOI 10.3390/CRYST10090803 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20256 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.870 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 56.1800 - 3.6200 1.00 1434 157 0.1647 0.1745 REMARK 3 2 3.6100 - 2.8700 1.00 1351 147 0.1670 0.1846 REMARK 3 3 2.8700 - 2.5100 1.00 1319 145 0.1632 0.1680 REMARK 3 4 2.5100 - 2.2800 1.00 1299 143 0.1515 0.1652 REMARK 3 5 2.2800 - 2.1100 1.00 1312 143 0.1482 0.1816 REMARK 3 6 2.1100 - 1.9900 1.00 1303 142 0.1493 0.1861 REMARK 3 7 1.9900 - 1.8900 1.00 1285 142 0.1555 0.1591 REMARK 3 8 1.8900 - 1.8100 1.00 1286 140 0.1721 0.2413 REMARK 3 9 1.8100 - 1.7400 1.00 1289 141 0.1721 0.1870 REMARK 3 10 1.7400 - 1.6800 1.00 1275 140 0.1870 0.2287 REMARK 3 11 1.6800 - 1.6300 1.00 1285 141 0.1868 0.2026 REMARK 3 12 1.6300 - 1.5800 1.00 1278 139 0.1979 0.2283 REMARK 3 13 1.5800 - 1.5400 1.00 1278 141 0.2392 0.2770 REMARK 3 14 1.5400 - 1.5000 1.00 1262 139 0.2755 0.2824 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.30 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7CVJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1300018311. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 298.15 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 11C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97942 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20320 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 80.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 427.0 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 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 FOR SHELL : 2.240 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6JXQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, PEG 8000, NACL, SMALL REMARK 280 TUBES, TEMPERATURE 293.5K 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 19.22500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.72500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.72500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.83750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.72500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.72500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.61250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.72500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.72500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.83750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.72500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.72500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.61250 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 19.22500 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: 6570 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 334 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 347 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 383 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 MET A 1 REMARK 465 ARG A 2 REMARK 465 SER A 3 REMARK 465 LEU A 4 REMARK 465 LEU A 5 REMARK 465 ILE A 6 REMARK 465 LEU A 7 REMARK 465 VAL A 8 REMARK 465 LEU A 9 REMARK 465 CYS A 10 REMARK 465 PHE A 11 REMARK 465 LEU A 12 REMARK 465 PRO A 13 REMARK 465 LEU A 14 REMARK 465 ALA A 15 REMARK 465 ALA A 16 REMARK 465 LEU A 17 REMARK 465 GLY A 18 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 HE ARG A 130 O HOH A 301 1.35 REMARK 500 OE1 GLN A 139 HH21 ARG A 143 1.40 REMARK 500 OE1 GLN A 139 NH2 ARG A 143 2.09 REMARK 500 NE ARG A 130 O HOH A 301 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 78 O REMARK 620 2 CYS A 82 O 87.8 REMARK 620 3 SER A 90 OG 91.7 163.4 REMARK 620 4 ARG A 91 O 96.1 95.0 101.5 REMARK 620 N 1 2 3 DBREF 7CVJ A 1 147 UNP P00698 LYSC_CHICK 1 147 SEQRES 1 A 147 MET ARG SER LEU LEU ILE LEU VAL LEU CYS PHE LEU PRO SEQRES 2 A 147 LEU ALA ALA LEU GLY LYS VAL PHE GLY ARG CYS GLU LEU SEQRES 3 A 147 ALA ALA ALA MET LYS ARG HIS GLY LEU ASP ASN TYR ARG SEQRES 4 A 147 GLY TYR SER LEU GLY ASN TRP VAL CYS ALA ALA LYS PHE SEQRES 5 A 147 GLU SER ASN PHE ASN THR GLN ALA THR ASN ARG ASN THR SEQRES 6 A 147 ASP GLY SER THR ASP TYR GLY ILE LEU GLN ILE ASN SER SEQRES 7 A 147 ARG TRP TRP CYS ASN ASP GLY ARG THR PRO GLY SER ARG SEQRES 8 A 147 ASN LEU CYS ASN ILE PRO CYS SER ALA LEU LEU SER SER SEQRES 9 A 147 ASP ILE THR ALA SER VAL ASN CYS ALA LYS LYS ILE VAL SEQRES 10 A 147 SER ASP GLY ASN GLY MET ASN ALA TRP VAL ALA TRP ARG SEQRES 11 A 147 ASN ARG CYS LYS GLY THR ASP VAL GLN ALA TRP ILE ARG SEQRES 12 A 147 GLY CYS ARG LEU HET NA A 201 1 HET CL A 202 1 HET CL A 203 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 2 NA NA 1+ FORMUL 3 CL 2(CL 1-) FORMUL 5 HOH *83(H2 O) HELIX 1 AA1 GLY A 22 HIS A 33 1 12 HELIX 2 AA2 ASN A 37 TYR A 41 5 5 HELIX 3 AA3 SER A 42 ASN A 55 1 14 HELIX 4 AA4 PRO A 97 SER A 103 5 7 HELIX 5 AA5 ILE A 106 SER A 118 1 13 HELIX 6 AA6 ASN A 121 ALA A 125 5 5 HELIX 7 AA7 TRP A 126 CYS A 133 1 8 HELIX 8 AA8 ASP A 137 ARG A 143 5 7 SHEET 1 AA1 3 THR A 61 ARG A 63 0 SHEET 2 AA1 3 THR A 69 TYR A 71 -1 O ASP A 70 N ASN A 62 SHEET 3 AA1 3 ILE A 76 ASN A 77 -1 O ILE A 76 N TYR A 71 SSBOND 1 CYS A 24 CYS A 145 1555 1555 1.99 SSBOND 2 CYS A 48 CYS A 133 1555 1555 2.04 SSBOND 3 CYS A 82 CYS A 98 1555 1555 2.03 SSBOND 4 CYS A 94 CYS A 112 1555 1555 2.04 LINK O SER A 78 NA NA A 201 1555 1555 2.39 LINK O CYS A 82 NA NA A 201 1555 1555 2.37 LINK OG SER A 90 NA NA A 201 1555 1555 2.51 LINK O ARG A 91 NA NA A 201 1555 1555 2.49 CRYST1 79.450 79.450 38.450 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 0.012587 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012587 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026008 0.00000