HEADER HYDROLASE 12-FEB-21 7LPM TITLE X-RAY RADIATION DAMAGE SERIES ON LYSOZYME AT 277K, MULTI-CONFORMER TITLE 2 MODEL, CRYSTAL 2 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 RADIATION DAMAGE, CONFORMATIONAL HETEROGENEITY, ANTIMICROBIAL ENZYME, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.YABUKARSKI,T.DOUKOV,D.HERSCHLAG REVDAT 3 18-OCT-23 7LPM 1 REMARK REVDAT 2 17-AUG-22 7LPM 1 JRNL REVDAT 1 23-FEB-22 7LPM 0 JRNL AUTH F.YABUKARSKI,T.DOUKOV,D.A.MOKHTARI,S.DU,D.HERSCHLAG JRNL TITL EVALUATING THE IMPACT OF X-RAY DAMAGE ON CONFORMATIONAL JRNL TITL 2 HETEROGENEITY IN ROOM-TEMPERATURE (277 K) AND CRYO-COOLED JRNL TITL 3 PROTEIN CRYSTALS. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 78 945 2022 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 35916220 JRNL DOI 10.1107/S2059798322005939 REMARK 2 REMARK 2 RESOLUTION. 1.10 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 46100 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.137 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.158 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 2313 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 34.6200 - 2.8300 0.95 2693 146 0.1314 0.1479 REMARK 3 2 2.8300 - 2.2400 0.98 2620 142 0.1222 0.1420 REMARK 3 3 2.2400 - 1.9600 0.98 2570 147 0.1037 0.1373 REMARK 3 4 1.9600 - 1.7800 0.99 2602 134 0.1101 0.1338 REMARK 3 5 1.7800 - 1.6500 0.99 2588 138 0.1154 0.1485 REMARK 3 6 1.6500 - 1.5600 0.99 2604 133 0.1120 0.1298 REMARK 3 7 1.5600 - 1.4800 0.99 2553 152 0.1225 0.1505 REMARK 3 8 1.4800 - 1.4100 1.00 2579 141 0.1305 0.1584 REMARK 3 9 1.4100 - 1.3600 1.00 2572 151 0.1508 0.1668 REMARK 3 10 1.3600 - 1.3100 1.00 2586 120 0.1659 0.1888 REMARK 3 11 1.3100 - 1.2700 1.00 2585 137 0.1761 0.2171 REMARK 3 12 1.2700 - 1.2400 0.99 2541 145 0.2033 0.2511 REMARK 3 13 1.2400 - 1.2000 1.00 2562 129 0.2297 0.2320 REMARK 3 14 1.2000 - 1.1700 1.00 2548 140 0.2524 0.2642 REMARK 3 15 1.1700 - 1.1500 1.00 2576 113 0.2602 0.2821 REMARK 3 16 1.1500 - 1.1200 0.99 2550 131 0.2737 0.2874 REMARK 3 17 1.1200 - 1.1000 0.96 2458 114 0.3069 0.3133 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) : 0.108 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.917 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.72 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.14 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 : 0.006 3039 REMARK 3 ANGLE : 0.811 4100 REMARK 3 CHIRALITY : 0.068 429 REMARK 3 PLANARITY : 0.005 532 REMARK 3 DIHEDRAL : 12.793 1083 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 7LPM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1000254806. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.88557 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46250 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 38.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 8.40 REMARK 200 R MERGE FOR SHELL (I) : 2.94000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.700 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: 7LLP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LYSOZYME WAS DISSOLVED IN 0.1 M SODIUM REMARK 280 ACETATE PH 4.6 AT 100 MG/ML AND 5 MICROLITERS OF THIS PROTEIN REMARK 280 SOLUTION WAS MIXED WITH 5 MICROLITERS OF 0.1 M SODIUM ACETATE REMARK 280 AND 0.6 M SODIUM CHLORIDE SOLUTION PH 4.6. THE 10 MICROLITERS REMARK 280 DROP WAS EQUILIBRATED AGAINST 0.7 MILLILITERS OF 2.2 M AMMONIUM REMARK 280 SULFATE WELL SOLUTION., VAPOR DIFFUSION, HANGING 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 18.70900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.70450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.70450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.06350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.70450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.70450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.35450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.70450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.70450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.06350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.70450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.70450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.35450 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 18.70900 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 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 318 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 380 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 409 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 412 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 25 -36.39 -36.45 REMARK 500 ARG A 68 30.88 -158.76 REMARK 500 THR A 69 76.07 -111.43 REMARK 500 LEU A 83 3.21 -68.48 REMARK 500 ASN A 106 -8.50 -59.51 REMARK 500 CYS A 115 -33.43 -139.56 REMARK 500 LYS A 116 123.34 -38.91 REMARK 500 ARG A 125 123.35 -38.19 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 60 O REMARK 620 2 CYS A 64 O 86.9 REMARK 620 3 SER A 72 OG 81.5 159.1 REMARK 620 4 ARG A 73 O 108.8 99.0 101.1 REMARK 620 5 HOH A 345 O 79.8 79.5 81.3 171.2 REMARK 620 6 HOH A 389 O 156.4 105.5 80.2 89.4 82.7 REMARK 620 N 1 2 3 4 5 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 60 O REMARK 620 2 CYS A 64 O 71.3 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7LLP RELATED DB: PDB REMARK 900 RELATED ID: 7LN8 RELATED DB: PDB REMARK 900 RELATED ID: 7LN9 RELATED DB: PDB REMARK 900 RELATED ID: 7LOQ RELATED DB: PDB REMARK 900 RELATED ID: 7LOR RELATED DB: PDB REMARK 900 RELATED ID: 7LP6 RELATED DB: PDB REMARK 900 RELATED ID: 7LPL RELATED DB: PDB DBREF 7LPM 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 NA A 201 2 HET CL A 202 2 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 2 NA NA 1+ FORMUL 3 CL CL 1- FORMUL 4 HOH *112(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 CYS A 80 SER A 85 5 6 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 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 2.02 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.03 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.05 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.02 LINK O ASER A 60 NA A NA A 201 1555 1555 2.38 LINK O BSER A 60 NA B NA A 201 1555 1555 2.58 LINK O ACYS A 64 NA A NA A 201 1555 1555 2.85 LINK O BCYS A 64 NA B NA A 201 1555 1555 2.50 LINK OG ASER A 72 NA A NA A 201 1555 1555 2.52 LINK O AARG A 73 NA A NA A 201 1555 1555 2.44 LINK NA A NA A 201 O HOH A 345 1555 1555 2.52 LINK NA A NA A 201 O AHOH A 389 1555 1555 2.42 CRYST1 77.409 77.409 37.418 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 0.012918 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012918 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026725 0.00000