HEADER HYDROLASE 26-JUN-24 9FUE TITLE SERIAL MICROSECONDS CRYSTALLOGRAPHY AT ID29 USING FIXED-TARGET (SI TITLE 2 CHIP): LYSOZYME - WITH LIGAND GLCNAC 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 SERIAL CRYSTALLOGRAPHY, SERIAL MICROSECOND CRYSTALLOGRAPHY, ROOM KEYWDS 2 TEMPERATURE, ID29, ESRF-EBS, FIXED-TARGET, LYSOZYME, GLCNAC, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.ORLANS,S.L.ROSE,S.BASU,D.DE SANCTIS REVDAT 1 22-JAN-25 9FUE 0 JRNL AUTH J.ORLANS,S.L.ROSE,G.FERGUSON,M.OSCARSSON,A.HOMS PURON, JRNL AUTH 2 A.BETEVA,S.DEBIONNE,P.THEVENEAU,N.COQUELLE,J.KIEFFER, JRNL AUTH 3 P.BUSCA,J.SINOIR,V.ARMIJO,M.LOPEZ MARRERO,F.FELISAZ,G.PAPP, JRNL AUTH 4 H.GONZALEZ,H.CASEROTTO,F.DOBIAS,J.GIGMES,G.LEBON,S.BASU, JRNL AUTH 5 D.DE SANCTIS JRNL TITL ADVANCING MACROMOLECULAR STRUCTURE DETERMINATION WITH JRNL TITL 2 MICROSECOND X-RAY PULSES AT A 4TH GENERATION SYNCHROTRON. JRNL REF COMMUN CHEM V. 8 6 2025 JRNL REFN ESSN 2399-3669 JRNL PMID 39775172 JRNL DOI 10.1038/S42004-024-01404-Y REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21_5207 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 7822 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 783 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 55.5500 - 3.7300 1.00 1260 141 0.1718 0.2220 REMARK 3 2 3.7200 - 2.9600 1.00 1192 132 0.1842 0.2371 REMARK 3 3 2.9600 - 2.5800 1.00 1161 129 0.2507 0.3053 REMARK 3 4 2.5800 - 2.3500 1.00 1150 128 0.2681 0.3485 REMARK 3 5 2.3500 - 2.1800 1.00 1146 127 0.2938 0.3881 REMARK 3 6 2.1800 - 2.0500 0.98 1130 126 0.3296 0.3960 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) : 0.345 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.212 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.84 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 : 0.002 1021 REMARK 3 ANGLE : 0.483 1388 REMARK 3 CHIRALITY : 0.042 150 REMARK 3 PLANARITY : 0.003 181 REMARK 3 DIHEDRAL : 14.190 374 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 9FUE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1292139734. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-24 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.072 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI JUNGFRAU 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7877 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 78.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 123.0 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 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 <I/SIGMA(I)> 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M SODIUM ACETATE PH 3.0, 20% (W/V) REMARK 280 NACL, 5% (W/V) PEG 6000, BATCH MODE, 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 18.89500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.28000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.28000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.34250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.28000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.28000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.44750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.28000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.28000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.34250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.28000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.28000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.44750 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 18.89500 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: 1130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 329 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 333 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 31 CG CD CE NZ REMARK 470 ARG A 79 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 115 CG CD CE NZ REMARK 470 ARG A 143 CG CD NE CZ NH1 NH2 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 TRP A 80 -39.63 -132.84 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 78 O REMARK 620 2 CYS A 82 O 76.2 REMARK 620 3 SER A 90 OG 92.0 159.8 REMARK 620 4 ARG A 91 O 92.1 88.3 108.8 REMARK 620 5 HOH A 313 O 95.2 87.9 76.7 170.6 REMARK 620 6 HOH A 331 O 175.7 99.6 91.9 88.3 83.9 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9FTU RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 9FTS RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 9FTV RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 9FTX RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 9FTY RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 9FU1 RELATED DB: PDB REMARK 900 SAME CITATION REMARK 900 RELATED ID: 9FUD RELATED DB: PDB REMARK 900 SAME CITATION - APO FORM OF THIS STRUCTURE DBREF 9FUE 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 NA A 201 1 HET CL A 202 1 HET CL A 203 1 HET CL A 204 1 HET CL A 205 1 HET NDG A 206 15 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM NDG 2-ACETAMIDO-2-DEOXY-ALPHA-D-GLUCOPYRANOSE HETSYN NDG N-ACETYL-ALPHA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 NDG ALPHA-D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2- HETSYN 3 NDG ACETAMIDO-2-DEOXY-GLUCOSE; 2-(ACETYLAMINO)-2-DEOXY-A- HETSYN 4 NDG D-GLUCOPYRANOSE FORMUL 2 NA NA 1+ FORMUL 3 CL 4(CL 1-) FORMUL 7 NDG C8 H15 N O6 FORMUL 8 HOH *41(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 VAL A 117 1 12 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 ILE A 142 5 6 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 2.03 SSBOND 2 CYS A 48 CYS A 133 1555 1555 2.03 SSBOND 3 CYS A 82 CYS A 98 1555 1555 2.03 SSBOND 4 CYS A 94 CYS A 112 1555 1555 2.03 LINK O SER A 78 NA NA A 201 1555 1555 2.34 LINK O CYS A 82 NA NA A 201 1555 1555 2.41 LINK OG SER A 90 NA NA A 201 1555 1555 2.57 LINK O ARG A 91 NA NA A 201 1555 1555 2.51 LINK NA NA A 201 O HOH A 313 1555 1555 2.56 LINK NA NA A 201 O HOH A 331 1555 1555 2.69 CRYST1 78.560 78.560 37.790 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 0.012729 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012729 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026462 0.00000