HEADER HYDROLASE 14-DEC-20 7B9J TITLE LYSOZYME CRYSTALLIZED IN THE PRESENCE OF THE HYDRATED DEEP EUTECTIC TITLE 2 SOLVENT CHOLINE CHLORIDE-UREA 1:2 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_TAXID: 9031 KEYWDS COMPLEX, LYSOZYME, HYDRATED DEEP EUTECTIC SOLVENTS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.D.BELVISO,R.CALIANDRO,B.CARROZZINI REVDAT 3 31-JAN-24 7B9J 1 REMARK REVDAT 2 26-JAN-22 7B9J 1 REMARK REVDAT 1 20-OCT-21 7B9J 0 JRNL AUTH B.D.BELVISO,F.M.PERNA,B.CARROZZINI,M.TROTTA,V.CAPRIATI, JRNL AUTH 2 R.CALIANDRO JRNL TITL INTRODUCING PROTEIN CRYSTALLIZATION IN HYDRATED DEEP JRNL TITL 2 EUTECTIC SOLVENTS JRNL REF ACS SUSTAIN CHEM ENG V. 9 8435 2021 JRNL REFN ESSN 2168-0485 JRNL DOI 10.1021/ACSSUSCHEMENG.1C01230 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 6444 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.590 REMARK 3 FREE R VALUE TEST SET COUNT : 296 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 56.6040 - 2.7721 1.00 3167 141 0.1747 0.2081 REMARK 3 2 2.2630 - 2.2003 1.00 2981 155 0.1863 0.2580 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.97 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 7B9J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292112906. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-19 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6448 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 56.604 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 24.90 REMARK 200 R MERGE (I) : 0.14100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 26.20 REMARK 200 R MERGE FOR SHELL (I) : 0.57800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SIR2014 REMARK 200 STARTING MODEL: 4N9R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CHLORIDE, SODIUM ACETATE, DES: REMARK 280 CHOLINE CHLORIDE/UREA, PH 4.5, VAPOR DIFFUSION, SITTING DROP, 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 18.38450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.02500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.02500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.57675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.02500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.02500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.19225 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.02500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.02500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.57675 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.02500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.02500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.19225 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 18.38450 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: 3470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -149.0 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 CL CL A 215 LIES ON A SPECIAL POSITION. REMARK 375 C URE A 222 LIES ON A SPECIAL POSITION. REMARK 375 O URE A 222 LIES ON A SPECIAL POSITION. REMARK 375 C URE A 223 LIES ON A SPECIAL POSITION. REMARK 375 O URE A 223 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 220 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 35 OE1 REMARK 620 2 HOH A 312 O 98.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 217 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 60 O REMARK 620 2 CYS A 64 O 86.0 REMARK 620 3 SER A 72 OG 94.4 175.0 REMARK 620 4 ARG A 73 O 89.0 83.3 101.7 REMARK 620 5 HOH A 319 O 171.9 102.0 77.9 90.5 REMARK 620 6 HOH A 328 O 101.7 87.5 87.6 165.4 80.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 218 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 67 O REMARK 620 2 HOH A 358 O 111.6 REMARK 620 3 HOH A 382 O 107.2 99.6 REMARK 620 N 1 2 DBREF 7B9J 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 ACT A 201 4 HET CHT A 202 7 HET CHT A 203 7 HET CL A 204 1 HET CL A 205 1 HET CL A 206 1 HET CL A 207 1 HET CL A 208 1 HET CL A 209 1 HET CL A 210 1 HET CL A 211 1 HET CL A 212 1 HET CL A 213 1 HET CL A 214 1 HET CL A 215 1 HET CL A 216 1 HET NA A 217 1 HET NA A 218 1 HET NA A 219 1 HET NA A 220 1 HET NA A 221 1 HET URE A 222 4 HET URE A 223 4 HET URE A 224 4 HET URE A 225 4 HETNAM ACT ACETATE ION HETNAM CHT CHOLINE ION HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETNAM URE UREA FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 CHT 2(C5 H14 N O 1+) FORMUL 5 CL 13(CL 1-) FORMUL 18 NA 5(NA 1+) FORMUL 23 URE 4(C H4 N2 O) FORMUL 27 HOH *100(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 ASP A 101 GLY A 102 5 2 HELIX 7 AA7 ASN A 103 ALA A 107 5 5 HELIX 8 AA8 TRP A 108 CYS A 115 1 8 HELIX 9 AA9 ASP A 119 ILE A 124 5 6 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 2.04 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 OE1 GLU A 35 NA NA A 220 1555 1555 2.65 LINK O SER A 60 NA NA A 217 1555 1555 2.46 LINK O CYS A 64 NA NA A 217 1555 1555 2.44 LINK O GLY A 67 NA NA A 218 1555 1555 2.73 LINK OG SER A 72 NA NA A 217 1555 1555 2.31 LINK O ARG A 73 NA NA A 217 1555 1555 2.65 LINK NA NA A 217 O HOH A 319 1555 1555 2.51 LINK NA NA A 217 O HOH A 328 1555 1555 2.28 LINK NA NA A 218 O HOH A 358 1555 7556 3.12 LINK NA NA A 218 O HOH A 382 1555 7556 2.91 LINK NA NA A 220 O HOH A 312 1555 1555 2.85 CRYST1 80.050 80.050 36.769 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 0.012492 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012492 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027197 0.00000