HEADER HYDROLASE 24-OCT-22 8H8U TITLE ROOM-TEMPERATURE STRUCTURE OF LYSOZYME BY PINK-BEAM SERIAL TITLE 2 CRYSTALLOGRAPHY (50 MS, CENTER) 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 PINK-BEAM, SERIAL SYNCHROTRON CRYSTALLOGRAPHY, ROOM-TEMPERATURE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.KIM,K.H.NAM REVDAT 2 17-JAN-24 8H8U 1 JRNL REVDAT 1 01-NOV-23 8H8U 0 JRNL AUTH Y.KIM,K.H.NAM JRNL TITL DATA OF PINK-BEAM SERIAL SYNCHROTRON CRYSTALLOGRAPHY AT THE JRNL TITL 2 POHANG LIGHT SOURCE II. JRNL REF DATA BRIEF V. 52 09811 2024 JRNL REFN ESSN 2352-3409 JRNL PMID 38161663 JRNL DOI 10.1016/J.DIB.2023.109811 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.KIM,K.H.NAM REMARK 1 TITL PINK-BEAM SERIAL SYNCHROTRON CRYSTALLOGRAPHY AT POHANG LIGHT REMARK 1 TITL 2 SOURCE II REMARK 1 REF CRYSTALS V. 12 2022 REMARK 1 REFN ESSN 2073-4352 REMARK 1 DOI 10.3390/CRYST12111637 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) : 55.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 13652 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.670 REMARK 3 FREE R VALUE TEST SET COUNT : 911 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 55.7800 - 3.2500 0.97 1894 135 0.2265 0.2208 REMARK 3 2 3.2500 - 2.5800 1.00 1853 131 0.1861 0.1982 REMARK 3 3 2.5800 - 2.2500 1.00 1806 131 0.1841 0.1992 REMARK 3 4 2.2500 - 2.0500 1.00 1817 129 0.2186 0.2330 REMARK 3 5 2.0500 - 1.9000 1.00 1776 128 0.2260 0.2830 REMARK 3 6 1.9000 - 1.7900 1.00 1801 129 0.2806 0.3540 REMARK 3 7 1.7900 - 1.7000 1.00 1794 128 0.3001 0.3784 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.78 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 8H8U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1300033019. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 299.5 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) : 0.8009 REMARK 200 MONOCHROMATOR : MO/B4C MULTILAYER, 1.2 % BW REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14189 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 80.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 551.7 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.1300 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) : 1.76 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 REMARK 200 STARTING MODEL: 7WUC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA-ACETATE, NACL, PEG 8000, SMALL REMARK 280 TUBES, TEMPERATURE 298.5K 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 19.02500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.44000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.44000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.53750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.44000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.44000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.51250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.44000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.44000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.53750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.44000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.44000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.51250 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 19.02500 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: 140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6510 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 332 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 351 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 385 LIES ON A SPECIAL POSITION. 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 O HOH A 327 O HOH A 364 1.82 REMARK 500 NZ LYS A 114 O HOH A 301 2.02 REMARK 500 O HOH A 331 O HOH A 380 2.11 REMARK 500 NH1 ARG A 63 O HOH A 302 2.12 REMARK 500 O HOH A 365 O HOH A 382 2.12 REMARK 500 OD1 ASN A 121 O HOH A 303 2.14 REMARK 500 O HOH A 356 O HOH A 381 2.16 REMARK 500 O HOH A 333 O HOH A 375 2.17 REMARK 500 NE ARG A 130 O HOH A 304 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 389 O HOH A 389 8665 1.54 REMARK 500 O HOH A 376 O HOH A 384 8665 1.83 REMARK 500 O HOH A 361 O HOH A 372 3664 2.15 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 203 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 78 O REMARK 620 2 CYS A 82 O 88.2 REMARK 620 3 SER A 90 OG 88.3 166.2 REMARK 620 4 ARG A 91 O 91.8 96.0 97.5 REMARK 620 N 1 2 3 DBREF 8H8U A 19 147 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 CL A 201 1 HET CL A 202 1 HET NA A 203 1 HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION FORMUL 2 CL 2(CL 1-) FORMUL 4 NA NA 1+ FORMUL 5 HOH *89(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 2.04 SSBOND 3 CYS A 82 CYS A 98 1555 1555 2.03 SSBOND 4 CYS A 94 CYS A 112 1555 1555 2.05 LINK O SER A 78 NA NA A 203 1555 1555 2.34 LINK O CYS A 82 NA NA A 203 1555 1555 2.34 LINK OG SER A 90 NA NA A 203 1555 1555 2.52 LINK O ARG A 91 NA NA A 203 1555 1555 2.58 CRYST1 78.880 78.880 38.050 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 0.012677 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012677 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026281 0.00000