HEADER HYDROLASE 11-JAN-24 8RNX TITLE HEN EGG WHITE LYSOZYME SOAKED WITH [HISQ][TRANS-RUCL4(DMSO)(ISQ)] 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: GALLUS GALLUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9031 KEYWDS LYSOZYME, RUTHENIUM, COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.OSZAJCA,M.FLEJSZAR,A.SZURA,P.DROZDZ,M.BRINDELL,K.KURPIEWSKA REVDAT 2 01-MAY-24 8RNX 1 JRNL REVDAT 1 24-JAN-24 8RNX 0 JRNL AUTH M.OSZAJCA,M.FLEJSZAR,A.SZURA,P.DROZDZ,M.BRINDELL, JRNL AUTH 2 K.KURPIEWSKA JRNL TITL EXPLORING THE COORDINATION CHEMISTRY OF RUTHENIUM COMPLEXES JRNL TITL 2 WITH LYSOZYMES: STRUCTURAL AND IN-SOLUTION STUDIES. JRNL REF FRONT CHEM V. 12 71637 2024 JRNL REFN ESSN 2296-2646 JRNL PMID 38638879 JRNL DOI 10.3389/FCHEM.2024.1371637 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.870 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 32398 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.380 REMARK 3 FREE R VALUE TEST SET COUNT : 2053 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 4.0100 - 3.0800 0.99 3964 137 0.1663 0.1918 REMARK 3 2 3.0800 - 2.4400 0.97 3877 136 0.2194 0.2563 REMARK 3 3 2.4400 - 2.1400 0.97 3879 136 0.2136 0.2395 REMARK 3 4 2.1400 - 1.9400 0.98 3929 137 0.2137 0.2192 REMARK 3 5 1.9400 - 1.8000 0.99 3969 143 0.2187 0.2362 REMARK 3 6 1.8000 - 1.7000 0.99 3983 137 0.2348 0.2465 REMARK 3 7 1.7000 - 1.6100 1.00 3949 139 0.2365 0.2455 REMARK 3 8 1.6100 - 1.5400 1.00 4005 136 0.2646 0.2946 REMARK 3 9 1.5400 - 1.4800 1.00 3987 143 0.2927 0.3642 REMARK 3 10 1.4800 - 1.4300 1.00 3986 145 0.3239 0.4020 REMARK 3 11 1.4300 - 1.3900 1.00 3990 140 0.3546 0.3589 REMARK 3 12 1.3900 - 1.3500 1.00 4012 141 0.3615 0.4193 REMARK 3 13 1.3500 - 1.3100 1.00 3985 141 0.4286 0.4560 REMARK 3 14 1.3100 - 1.2800 1.00 3972 133 0.4672 0.4783 REMARK 3 15 1.2800 - 1.2500 0.80 3221 109 0.5235 0.5575 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.130 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 : 0.006 NULL REMARK 3 ANGLE : 0.873 NULL REMARK 3 CHIRALITY : 0.082 154 REMARK 3 PLANARITY : 0.014 194 REMARK 3 DIHEDRAL : 13.417 400 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 8RNX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1292135803. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 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 : 32398 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 39.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.02300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.20800 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8M NACL, 0.05M SODIUM ACETATE, PH REMARK 280 4.5, VAPOR DIFFUSION, HANGING DROP, 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 18.50100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.49650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.49650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.75150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.49650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.49650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.25050 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.49650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.49650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.75150 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.49650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.49650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.25050 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 18.50100 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: 890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 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 356 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 393 LIES ON A SPECIAL POSITION. 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 128 0.09 SIDE CHAIN 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 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 60 O REMARK 620 2 CYS A 64 O 89.3 REMARK 620 3 SER A 72 OG 87.7 167.5 REMARK 620 4 ARG A 73 O 93.2 91.3 101.0 REMARK 620 5 HOH A 334 O 99.9 87.5 81.1 166.8 REMARK 620 6 HOH A 348 O 173.2 96.9 85.7 89.5 77.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 RU A 207 RU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 101 OD2 REMARK 620 2 HOH A 368 O 84.2 REMARK 620 3 HOH A 377 O 92.1 86.5 REMARK 620 4 HOH A 392 O 167.8 106.8 83.4 REMARK 620 N 1 2 3 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 HOH A 341 O REMARK 620 2 HOH A 379 O 150.4 REMARK 620 3 HOH A 381 O 128.0 80.2 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5LVG RELATED DB: PDB REMARK 900 RELATED ID: 5LVH RELATED DB: PDB REMARK 900 RELATED ID: 5LVI RELATED DB: PDB REMARK 900 RELATED ID: 5LVJ RELATED DB: PDB DBREF 8RNX 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 EDO A 201 4 HET NA A 202 1 HET NA A 203 1 HET CL A 204 1 HET CL A 205 1 HET CL A 206 1 HET RU A 207 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM RU RUTHENIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 NA 2(NA 1+) FORMUL 5 CL 3(CL 1-) FORMUL 8 RU RU 3+ FORMUL 9 HOH *93(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 2.03 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.04 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.02 LINK O SER A 60 NA NA A 202 1555 1555 2.37 LINK O CYS A 64 NA NA A 202 1555 1555 2.43 LINK OG SER A 72 NA NA A 202 1555 1555 2.53 LINK O ARG A 73 NA NA A 202 1555 1555 2.44 LINK OD2 ASP A 101 RU RU A 207 1555 1555 2.34 LINK NA NA A 202 O HOH A 334 1555 1555 2.45 LINK NA NA A 202 O HOH A 348 1555 1555 2.41 LINK NA NA A 203 O HOH A 341 1555 1555 2.32 LINK NA NA A 203 O HOH A 379 1555 1555 2.37 LINK NA NA A 203 O HOH A 381 1555 1555 2.89 LINK RU RU A 207 O HOH A 368 1555 1555 2.26 LINK RU RU A 207 O HOH A 377 1555 1555 2.06 LINK RU RU A 207 O HOH A 392 1555 1555 2.30 CRYST1 78.993 78.993 37.002 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 0.012659 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012659 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027026 0.00000