HEADER HYDROLASE 18-MAY-22 8CW1 TITLE 20US TEMPERATURE-JUMP (DARK1) XFEL STRUCTURE OF LYSOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LYZOZYME; COMPND 5 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C,ALLERGEN GAL D IV; COMPND 6 EC: 3.2.1.17; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 4 ORGANISM_COMMON: CHICKEN; SOURCE 5 ORGANISM_TAXID: 9031 KEYWDS LYSOZYME, TEMPERATURE-JUMP, DARK1, 20US, XFEL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.M.WOLFF,M.C.THOMPSON,J.S.FRASER,E.NANGO REVDAT 6 16-OCT-24 8CW1 1 REMARK REVDAT 5 15-NOV-23 8CW1 1 JRNL REVDAT 4 18-OCT-23 8CW1 1 REMARK REVDAT 3 04-OCT-23 8CW1 1 JRNL REVDAT 2 16-AUG-23 8CW1 1 JRNL REVDAT 1 22-JUN-22 8CW1 0 JRNL AUTH A.M.WOLFF,E.NANGO,I.D.YOUNG,A.S.BREWSTER,M.KUBO,T.NOMURA, JRNL AUTH 2 M.SUGAHARA,S.OWADA,B.A.BARAD,K.ITO,A.BHOWMICK,S.CARBAJO, JRNL AUTH 3 T.HINO,J.M.HOLTON,D.IM,L.J.O'RIORDAN,T.TANAKA,R.TANAKA, JRNL AUTH 4 R.G.SIERRA,F.YUMOTO,K.TONO,S.IWATA,N.K.SAUTER,J.S.FRASER, JRNL AUTH 5 M.C.THOMPSON JRNL TITL MAPPING PROTEIN DYNAMICS AT HIGH SPATIAL RESOLUTION WITH JRNL TITL 2 TEMPERATURE-JUMP X-RAY CRYSTALLOGRAPHY. JRNL REF NAT.CHEM. V. 15 1549 2023 JRNL REFN ESSN 1755-4349 JRNL PMID 37723259 JRNL DOI 10.1038/S41557-023-01329-4 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.M.WOLFF,E.NANGO,I.D.YOUNG,A.S.BREWSTER,M.KUBO,T.NOMURA, REMARK 1 AUTH 2 M.SUGAHARA,S.OWADA,B.A.BARAD,K.ITO,A.BHOWMICK,S.CARBAJO, REMARK 1 AUTH 3 T.HINO,J.M.HOLTON,D.IM,L.J.O'RIORDAN,T.TANAKA,R.TANAKA, REMARK 1 AUTH 4 R.G.SIERRA,F.YUMOTO,K.TONO,S.IWATA,N.K.SAUTER,J.S.FRASER, REMARK 1 AUTH 5 M.C.THOMPSON REMARK 1 TITL MAPPING PROTEIN DYNAMICS AT HIGH-RESOLUTION WITH REMARK 1 TITL 2 TEMPERATURE-JUMP X-RAY CRYSTALLOGRAPHY REMARK 1 REF BIORXIV 2022 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2022.06.10.495662 REMARK 2 REMARK 2 RESOLUTION. 1.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.720 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 17626 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 896 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 28.0900 - 2.8500 1.00 2959 152 0.1539 0.1516 REMARK 3 2 2.8500 - 2.2600 1.00 2800 145 0.1320 0.1750 REMARK 3 3 2.2600 - 1.9800 1.00 2762 159 0.1241 0.1479 REMARK 3 4 1.9800 - 1.8000 1.00 2727 161 0.1355 0.1680 REMARK 3 5 1.8000 - 1.6700 1.00 2742 139 0.1700 0.2097 REMARK 3 6 1.6700 - 1.5700 1.00 2740 140 0.2118 0.2555 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) : 0.134 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.754 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.09 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 : 0.005 1135 REMARK 3 ANGLE : 0.766 1546 REMARK 3 CHIRALITY : 0.044 158 REMARK 3 PLANARITY : 0.007 210 REMARK 3 DIHEDRAL : 13.214 423 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 8CW1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000265534. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 291 REMARK 200 PH : 3.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : BL3 REMARK 200 X-RAY GENERATOR MODEL : SACLA BEAMLINE BL3 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.24 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MPCCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CCTBX.XFEL REMARK 200 DATA SCALING SOFTWARE : CXI.MERGE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2144941 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 28.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 121.8 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 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: 1IEE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LYSOZYME [20 MG/ML DISSOLVED IN 0.1 M REMARK 280 SODIUM ACETATE AT PH 3.0] MIXED WITH PRECIPITANT [28% (W/V) NACL, REMARK 280 8% (W/V) PEG6000 AND 0.1 M SODIUM ACETATE AT PH 3.0] IN A 1:1 REMARK 280 RATIO, BATCH MODE, TEMPERATURE 291K 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 19.09900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.72150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.72150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.64850 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.72150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.72150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.54950 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.72150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.72150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.64850 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.72150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.72150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.54950 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 19.09900 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 357 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 366 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 HH21 ARG A 14 O HOH A 301 1.51 REMARK 500 O HOH A 387 O HOH A 391 1.84 REMARK 500 O HOH A 375 O HOH A 383 2.13 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 89.3 REMARK 620 3 SER A 72 OG 90.1 165.2 REMARK 620 4 ARG A 73 O 94.8 92.9 101.9 REMARK 620 5 HOH A 354 O 100.1 87.7 77.8 165.1 REMARK 620 6 HOH A 359 O 172.4 97.8 82.4 87.6 77.6 REMARK 620 N 1 2 3 4 5 DBREF 8CW1 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 1 HET ACT A 202 7 HET ACT 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 HETNAM NA SODIUM ION HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION FORMUL 2 NA NA 1+ FORMUL 3 ACT 2(C2 H3 O2 1-) FORMUL 5 CL 5(CL 1-) FORMUL 10 HOH *94(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 2.03 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.03 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.03 LINK O SER A 60 NA NA A 201 1555 1555 2.32 LINK O CYS A 64 NA NA A 201 1555 1555 2.42 LINK OG SER A 72 NA NA A 201 1555 1555 2.50 LINK O ARG A 73 NA NA A 201 1555 1555 2.52 LINK NA NA A 201 O HOH A 354 1555 1555 2.50 LINK NA NA A 201 O HOH A 359 1555 1555 2.49 CRYST1 79.443 79.443 38.198 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 0.012588 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012588 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026179 0.00000