HEADER HYDROLASE 16-FEB-23 8CL6 TITLE LYSOZYME IN MATRIX OF HYDROXYETHYLCELLULOSE (HEC) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME, CHAIN A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPLENIUM BULBIFERUM SUBSP. BULBIFERUM; SOURCE 3 ORGANISM_TAXID: 241518; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LYSOZYME, LYSOZYME ACTIVITY, CATALYTIC ACTIVITY, HYDROLASE ACTIVITY, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.BERTRAND,M.W.KEPA,T.WEINERT,M.WRANIK,J.STANDFUSS REVDAT 1 13-DEC-23 8CL6 0 JRNL AUTH M.WRANIK,M.W.KEPA,E.V.BEALE,D.JAMES,Q.BERTRAND,T.WEINERT, JRNL AUTH 2 A.FURRER,H.GLOVER,D.GASHI,M.CARRILLO,Y.KONDO,R.T.STIPP, JRNL AUTH 3 G.KHUSAINOV,K.NASS,D.OZEROV,C.CIRELLI,P.J.M.JOHNSON, JRNL AUTH 4 F.DWORKOWSKI,J.H.BEALE,S.STUBBS,T.ZAMOFING,M.SCHNEIDER, JRNL AUTH 5 K.KRAUSKOPF,L.GAO,O.THORN-SESHOLD,C.BOSTEDT,C.BACELLAR, JRNL AUTH 6 M.O.STEINMETZ,C.MILNE,J.STANDFUSS JRNL TITL A MULTI-RESERVOIR EXTRUDER FOR TIME-RESOLVED SERIAL PROTEIN JRNL TITL 2 CRYSTALLOGRAPHY AND COMPOUND SCREENING AT X-RAY JRNL TITL 3 FREE-ELECTRON LASERS. JRNL REF NAT COMMUN V. 14 7956 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 38042952 JRNL DOI 10.1038/S41467-023-43523-5 REMARK 2 REMARK 2 RESOLUTION. 1.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 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) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 25665 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.124 REMARK 3 R VALUE (WORKING SET) : 0.121 REMARK 3 FREE R VALUE : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.790 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 13.5400 - 3.1800 1.00 1967 167 0.1243 0.1545 REMARK 3 2 3.1800 - 2.5300 1.00 1860 157 0.1316 0.1500 REMARK 3 3 2.5300 - 2.2100 1.00 1842 156 0.1141 0.1515 REMARK 3 4 2.2100 - 2.0100 1.00 1820 153 0.1067 0.1427 REMARK 3 5 2.0100 - 1.8600 1.00 1822 154 0.1013 0.1420 REMARK 3 6 1.8600 - 1.7500 1.00 1813 153 0.1019 0.1338 REMARK 3 7 1.7500 - 1.6700 1.00 1791 152 0.1043 0.1685 REMARK 3 8 1.6700 - 1.5900 1.00 1790 151 0.1008 0.1541 REMARK 3 9 1.5900 - 1.5300 1.00 1804 153 0.1046 0.1612 REMARK 3 10 1.5300 - 1.4800 1.00 1797 151 0.1164 0.1667 REMARK 3 11 1.4800 - 1.4300 1.00 1783 150 0.1420 0.2116 REMARK 3 12 1.4300 - 1.3900 1.00 1753 150 0.1753 0.1952 REMARK 3 13 1.3900 - 1.3600 0.83 1497 126 0.2312 0.2881 REMARK 3 14 1.3600 - 1.3200 0.18 326 27 0.2928 0.2784 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.590 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 : 0.014 NULL REMARK 3 ANGLE : 1.503 NULL REMARK 3 CHIRALITY : 0.106 166 REMARK 3 PLANARITY : 0.016 233 REMARK 3 DIHEDRAL : 13.224 196 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 8CL6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292128476. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 3.0 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 : ESA REMARK 200 X-RAY GENERATOR MODEL : SWISSFEL ARAMIS BEAMLINE ESA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI JUNGFRAU 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL 0.9.1 REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL 0.9.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25665 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 14.968 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 739.5 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.20_4459 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 MG/ML, 100 MM SODIUM ACETATE, REMARK 280 LYSOZYME SOLUTION ADDED TO 28% (W/V) SODIUM CHLORIDE, 8% (W/V) REMARK 280 PEG 6000, PH 3.0, BATCH MODE, TEMPERATURE 295K 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 18.84500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.95000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.26750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.95000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.95000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.42250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.95000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.95000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.26750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.95000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.95000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.42250 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 18.84500 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: 1180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 352 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 375 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 427 LIES ON A SPECIAL POSITION. REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 121 CD REMARK 480 ARG A 125 CZ REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1PE A 206 REMARK 610 1PE A 207 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 GLY A 49 O REMARK 620 2 THR A 51 OG1 97.9 REMARK 620 3 ASP A 66 OD2 155.4 95.9 REMARK 620 4 THR A 69 OG1 87.3 141.8 69.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 204 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 53 O REMARK 620 2 SER A 91 OG 123.2 REMARK 620 N 1 DBREF 8CL6 A 1 129 PDB 8CL6 8CL6 1 129 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 CL A 201 1 HET CL A 202 1 HET CL A 203 1 HET NA A 204 1 HET NA A 205 1 HET 1PE A 206 8 HET 1PE A 207 7 HET EDO A 208 4 HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM EDO 1,2-ETHANEDIOL HETSYN 1PE PEG400 HETSYN EDO ETHYLENE GLYCOL FORMUL 2 CL 3(CL 1-) FORMUL 5 NA 2(NA 1+) FORMUL 7 1PE 2(C10 H22 O6) FORMUL 9 EDO C2 H6 O2 FORMUL 10 HOH *129(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 2.02 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.01 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.03 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.00 LINK O GLY A 49 NA NA A 205 1555 1555 2.84 LINK OG1 THR A 51 NA NA A 205 1555 1555 2.64 LINK O TYR A 53 NA NA A 204 1555 1555 2.85 LINK OD2 ASP A 66 NA NA A 205 1555 1555 2.72 LINK OG1 THR A 69 NA NA A 205 1555 1555 3.03 LINK OG SER A 91 NA NA A 204 1555 1555 2.92 CRYST1 77.900 77.900 37.690 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 0.012837 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012837 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026532 0.00000