HEADER HYDROLASE 16-OCT-24 9H3E TITLE HEN EGG WHITE LYSOZYME CRYSTALLIZATION AND STRUCTURE DETERMINATION AT TITLE 2 ROOM TEMPERATURE IN THE CRYSTALCHIP 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 LYSOZYME, MICROFLUIDICS, ROOM TEMPERATURE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.PACHL,L.COUDRAY,R.VINCENT,C.SAUTER REVDAT 2 16-APR-25 9H3E 1 JRNL REVDAT 1 04-DEC-24 9H3E 0 JRNL AUTH P.PACHL,L.COUDRAY,R.VINCENT,L.NILLES,H.SCHEER, JRNL AUTH 2 C.RITZENTHALER,A.FEJFAROVA,P.REZACOVA,S.ENGILBERGE,C.SAUTER JRNL TITL PROTEIN CRYSTALLIZATION AND STRUCTURE DETERMINATION AT ROOM JRNL TITL 2 TEMPERATURE IN THE CRYSTALCHIP. JRNL REF FEBS OPEN BIO V. 15 532 2025 JRNL REFN ESSN 2211-5463 JRNL PMID 39572886 JRNL DOI 10.1002/2211-5463.13932 REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 19912 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 996 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 35.4000 - 2.8700 1.00 2885 152 0.1418 0.1710 REMARK 3 2 2.8700 - 2.2800 1.00 2730 144 0.1471 0.1743 REMARK 3 3 2.2800 - 1.9900 1.00 2693 142 0.1078 0.1536 REMARK 3 4 1.9900 - 1.8100 1.00 2678 141 0.1134 0.1928 REMARK 3 5 1.8100 - 1.6800 1.00 2674 140 0.1362 0.1806 REMARK 3 6 1.6800 - 1.5800 0.99 2640 139 0.1576 0.2338 REMARK 3 7 1.5800 - 1.5000 0.98 2616 138 0.2060 0.2545 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) : 0.163 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.86 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 : 0.004 1028 REMARK 3 ANGLE : 0.713 1391 REMARK 3 CHIRALITY : 0.076 147 REMARK 3 PLANARITY : 0.004 181 REMARK 3 DIHEDRAL : 11.950 369 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 9H3E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1292142516. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-24 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM07 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37004 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 35.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 9.920 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.88 REMARK 200 R MERGE FOR SHELL (I) : 0.21980 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.940 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CRYSTALLIZED BY COUNTER REMARK 280 -DIFFUSION IN THE CRYSTALCHIP, STOCK SOLUTION 60 MG/ML IN 50 MM REMARK 280 NA ACETATE PH 4.5, RESERVOIR SOLUTION 2 M NACL, 50 MM NA ACETATE REMARK 280 PH 4.5, 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 19.07500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.58000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.58000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.61250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.58000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.58000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.53750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.58000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.58000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.61250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.58000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.58000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.53750 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 19.07500 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: 520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 331 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 349 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 391 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -17 REMARK 465 ARG A -16 REMARK 465 SER A -15 REMARK 465 LEU A -14 REMARK 465 LEU A -13 REMARK 465 ILE A -12 REMARK 465 LEU A -11 REMARK 465 VAL A -10 REMARK 465 LEU A -9 REMARK 465 CYS A -8 REMARK 465 PHE A -7 REMARK 465 LEU A -6 REMARK 465 PRO A -5 REMARK 465 LEU A -4 REMARK 465 ALA A -3 REMARK 465 ALA A -2 REMARK 465 LEU A -1 REMARK 465 GLY A 0 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 87.4 REMARK 620 3 SER A 72 OG 88.3 164.6 REMARK 620 4 ARG A 73 O 96.3 93.6 101.5 REMARK 620 5 HOH A 343 O 96.9 86.8 79.1 166.7 REMARK 620 6 HOH A 376 O 172.1 98.1 85.0 89.0 77.8 REMARK 620 N 1 2 3 4 5 DBREF 9H3E A -17 129 UNP P00698 LYSC_CHICK 1 147 SEQRES 1 A 147 MET ARG SER LEU LEU ILE LEU VAL LEU CYS PHE LEU PRO SEQRES 2 A 147 LEU ALA ALA LEU GLY LYS VAL PHE GLY ARG CYS GLU LEU SEQRES 3 A 147 ALA ALA ALA MET LYS ARG HIS GLY LEU ASP ASN TYR ARG SEQRES 4 A 147 GLY TYR SER LEU GLY ASN TRP VAL CYS ALA ALA LYS PHE SEQRES 5 A 147 GLU SER ASN PHE ASN THR GLN ALA THR ASN ARG ASN THR SEQRES 6 A 147 ASP GLY SER THR ASP TYR GLY ILE LEU GLN ILE ASN SER SEQRES 7 A 147 ARG TRP TRP CYS ASN ASP GLY ARG THR PRO GLY SER ARG SEQRES 8 A 147 ASN LEU CYS ASN ILE PRO CYS SER ALA LEU LEU SER SER SEQRES 9 A 147 ASP ILE THR ALA SER VAL ASN CYS ALA LYS LYS ILE VAL SEQRES 10 A 147 SER ASP GLY ASN GLY MET ASN ALA TRP VAL ALA TRP ARG SEQRES 11 A 147 ASN ARG CYS LYS GLY THR ASP VAL GLN ALA TRP ILE ARG SEQRES 12 A 147 GLY CYS ARG LEU HET NA A 201 1 HET CL A 202 1 HET CL A 203 1 HET CL A 204 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 2 NA NA 1+ FORMUL 3 CL 3(CL 1-) FORMUL 6 HOH *91(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 2.03 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.04 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 A NA A 201 1555 1555 2.34 LINK O CYS A 64 NA A NA A 201 1555 1555 2.40 LINK OG SER A 72 NA A NA A 201 1555 1555 2.50 LINK O ARG A 73 NA A NA A 201 1555 1555 2.46 LINK NA A NA A 201 O HOH A 343 1555 1555 2.52 LINK NA A NA A 201 O HOH A 376 1555 1555 2.47 CRYST1 79.160 79.160 38.150 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 0.012633 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012633 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026212 0.00000 CONECT 50 988 CONECT 240 896 CONECT 468 1010 CONECT 513 1010 CONECT 515 632 CONECT 570 1010 CONECT 574 1010 CONECT 603 728 CONECT 632 515 CONECT 728 603 CONECT 896 240 CONECT 988 50 CONECT 1010 468 513 570 574 CONECT 1010 1056 1089 CONECT 1056 1010 CONECT 1089 1010 MASTER 266 0 4 8 3 0 0 6 1096 1 16 12 END