HEADER HYDROLASE 09-SEP-20 7D04 TITLE LYSOZYME STRUCTURE SS3 FROM SS MODE 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; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 GENE: LYZ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LYSOZYME, XFEL, SFX, SELF-SEEDED MODE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.S.KANG,S.J.LEE REVDAT 2 29-NOV-23 7D04 1 JRNL REVDAT 1 31-MAR-21 7D04 0 JRNL AUTH I.NAM,C.K.MIN,B.OH,G.KIM,D.NA,Y.J.SUH,H.YANG,M.H.CHO,C.KIM, JRNL AUTH 2 M.J.KIM,C.H.SHIM,J.H.KO,H.HEO,J.PARK,J.KIM,S.PARK,G.PARK, JRNL AUTH 3 S.KIM,S.H.CHUN,H.HYUN,J.H.LEE,K.S.KIM,I.EOM,S.RAH,D.SHU, JRNL AUTH 4 K.J.KIM,S.TERENTYEV,V.BLANK,Y.SHVYDKO,S.J.LEE,H.S.KANG JRNL TITL HIGH-BRIGHTNESS SELF-SEEDED X-RAY FREE-ELECTRON LASER JRNL TITL 2 COVERING THE 3.5 KEV TO 14.6 KEV RANGE JRNL REF NAT PHOTONICS 2021 JRNL REFN ESSN 1749-4893 JRNL DOI 10.1038/S41566-021-00777-Z REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 25111 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1249 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 27.8900 - 3.5400 1.00 2649 138 0.2290 0.2636 REMARK 3 2 3.5300 - 2.8100 1.00 2650 133 0.2138 0.2257 REMARK 3 3 2.8100 - 2.4500 1.00 2658 144 0.2079 0.2424 REMARK 3 4 2.4500 - 2.2300 1.00 2639 131 0.1907 0.2145 REMARK 3 5 2.2300 - 2.0700 1.00 2648 141 0.1885 0.2553 REMARK 3 6 2.0700 - 1.9500 1.00 2656 143 0.1875 0.2361 REMARK 3 7 1.9500 - 1.8500 1.00 2649 139 0.2113 0.2278 REMARK 3 8 1.8500 - 1.7700 1.00 2643 140 0.2437 0.3246 REMARK 3 9 1.7700 - 1.7000 1.00 2670 140 0.2626 0.3164 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 1021 REMARK 3 ANGLE : 1.050 1381 REMARK 3 CHIRALITY : 0.059 144 REMARK 3 PLANARITY : 0.009 181 REMARK 3 DIHEDRAL : 15.511 143 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 7D04 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300018506. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : NCI REMARK 200 X-RAY GENERATOR MODEL : PAL-XFEL BEAMLINE NCI REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2782 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL V0.9.1 REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL V0.9.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25173 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 27.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 140.6 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.5200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 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 : 1.560 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX V1.18.2_3874 REMARK 200 STARTING MODEL: 1VDS REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE (PH 4.0), 6% REMARK 280 (W/V) POLYETHYLENE GLYCOL 8,000, AND 3.5 M NACL, BATCH MODE, REMARK 280 TEMPERATURE 293K 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 18.90550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.44750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.44750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.35825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.44750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.44750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.45275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.44750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.44750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.35825 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.44750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.44750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.45275 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 18.90550 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 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 214 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 238 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 272 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: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 91 0.09 SIDE CHAIN REMARK 500 ARG A 146 0.29 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 7D04 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 FORMUL 2 HOH *72(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 2.02 SSBOND 2 CYS A 48 CYS A 133 1555 1555 2.02 SSBOND 3 CYS A 82 CYS A 98 1555 1555 2.05 SSBOND 4 CYS A 94 CYS A 112 1555 1555 2.03 CRYST1 78.895 78.895 37.811 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 0.012675 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012675 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026447 0.00000