HEADER HYDROLASE 23-MAY-25 9OS0 TITLE MICROED STRUCTURE OF LYSOZYME COMPLEXED WITH N,N',N"- TITLE 2 TRIACETYLCHITOTRIOSE FROM COCKTAIL-SOAKED CRYSTALS 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031 KEYWDS ENZYME, COMPLEX, MICROED, COCKTAIL, HYDROLASE EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR N.W.VLAHAKIS,C.W.FLOWERS,J.A.RODRIGUEZ REVDAT 2 13-AUG-25 9OS0 1 JRNL REVDAT 1 18-JUN-25 9OS0 0 JRNL AUTH N.W.VLAHAKIS,C.W.FLOWERS,M.LIU,M.P.AGDANOWSKI,S.JOHNSON, JRNL AUTH 2 J.A.SUMMERS,L.M.C.JACOBS,C.KEYSER,P.RUSSELL,S.L.ROSE, JRNL AUTH 3 J.ORLANS,N.ADHAMI,Y.CHEN,M.R.SAWAYA,S.BASU,D.DE SANCTIS, JRNL AUTH 4 Y.CHEN,S.WAKATSUKI,H.M.NELSON,J.A.LOO,Y.TANG,J.A.RODRIGUEZ JRNL TITL COMBINING MICROED AND NATIVE MASS SPECTROMETRY FOR JRNL TITL 2 STRUCTURAL DISCOVERY OF ENZYME-SMALL MOLECULE COMPLEXES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 122 80122 2025 JRNL REFN ESSN 1091-6490 JRNL PMID 40720654 JRNL DOI 10.1073/PNAS.2503780122 REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.8 REMARK 3 NUMBER OF REFLECTIONS : 4003 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 402 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 54.2100 - 3.4600 0.83 1250 140 0.1683 0.2187 REMARK 3 2 3.4600 - 2.7500 0.84 1183 132 0.2325 0.2945 REMARK 3 3 2.7500 - 2.4000 0.84 1168 130 0.2624 0.2973 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.610 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 : 0.010 1068 REMARK 3 ANGLE : 1.397 1449 REMARK 3 CHIRALITY : 0.076 160 REMARK 3 PLANARITY : 0.011 184 REMARK 3 DIHEDRAL : 18.564 187 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 9OS0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1000296216. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : NULL REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : TFS TALOS F200C REMARK 240 DETECTOR TYPE : DIRECT ELECTRON APOLLO (4K X REMARK 240 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 240 RESOLUTION RANGE HIGH (A) : NULL REMARK 240 RESOLUTION RANGE LOW (A) : NULL REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : NULL REMARK 240 DATA REDUNDANCY : NULL REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :NULL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :NULL REMARK 240 COMPLETENESS FOR SHELL (%) : NULL REMARK 240 DATA REDUNDANCY IN SHELL : NULL REMARK 240 R MERGE FOR SHELL (I) : NULL REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 240 SOFTWARE USED : PHASER REMARK 240 STARTING MODEL : NULL 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 19.11000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.33000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.33000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.66500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.33000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.33000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.55500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.33000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.33000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.66500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.33000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.33000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.55500 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 19.11000 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, E 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS A 13 OXT LEU A 129 8554 2.08 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 ASN A 65 OD1 REMARK 620 2 SER A 72 OG 128.1 REMARK 620 3 ARG A 73 O 154.2 77.6 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9ORZ RELATED DB: PDB REMARK 900 MICROED STRUCTURE OF THE SAME PROTEIN IN APO-FORM REMARK 900 RELATED ID: 9ORX RELATED DB: PDB REMARK 900 XRD STRUCTURE OF THE SAME PROTEIN-LIGAND COMPLEX DBREF 9OS0 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 NAG E 1 15 HET NAG E 2 14 HET NAG E 3 14 HET NA A 201 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG 3(C8 H15 N O6) FORMUL 3 NA NA 1+ FORMUL 4 HOH *4(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 SER A 81 LEU A 84 5 4 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 SHEET 1 AA2 2 CYS A 64 ASN A 65 0 SHEET 2 AA2 2 ILE A 78 PRO A 79 1 O ILE A 78 N ASN A 65 SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.05 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.06 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.02 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.04 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.40 LINK O4 NAG E 2 C1 NAG E 3 1555 1555 1.41 LINK OD1 ASN A 65 NA NA A 201 1555 1555 3.14 LINK OG SER A 72 NA NA A 201 1555 1555 2.04 LINK O ARG A 73 NA NA A 201 1555 1555 3.13 CRYST1 76.660 76.660 38.220 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 0.013045 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013045 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026164 0.00000 CONECT 48 983 CONECT 238 891 CONECT 513 630 CONECT 520 1048 CONECT 568 1048 CONECT 572 1048 CONECT 601 726 CONECT 630 513 CONECT 726 601 CONECT 891 238 CONECT 983 48 CONECT 1005 1006 1014 1017 CONECT 1006 1005 1007 1013 CONECT 1007 1006 1008 1015 CONECT 1008 1007 1009 1016 CONECT 1009 1008 1010 1017 CONECT 1010 1009 1018 CONECT 1011 1012 1013 1019 CONECT 1012 1011 CONECT 1013 1006 1011 CONECT 1014 1005 CONECT 1015 1007 CONECT 1016 1008 1020 CONECT 1017 1005 1009 CONECT 1018 1010 CONECT 1019 1011 CONECT 1020 1016 1021 1031 CONECT 1021 1020 1022 1028 CONECT 1022 1021 1023 1029 CONECT 1023 1022 1024 1030 CONECT 1024 1023 1025 1031 CONECT 1025 1024 1032 CONECT 1026 1027 1028 1033 CONECT 1027 1026 CONECT 1028 1021 1026 CONECT 1029 1022 CONECT 1030 1023 1034 CONECT 1031 1020 1024 CONECT 1032 1025 CONECT 1033 1026 CONECT 1034 1030 1035 1045 CONECT 1035 1034 1036 1042 CONECT 1036 1035 1037 1043 CONECT 1037 1036 1038 1044 CONECT 1038 1037 1039 1045 CONECT 1039 1038 1046 CONECT 1040 1041 1042 1047 CONECT 1041 1040 CONECT 1042 1035 1040 CONECT 1043 1036 CONECT 1044 1037 CONECT 1045 1034 1038 CONECT 1046 1039 CONECT 1047 1040 CONECT 1048 520 568 572 MASTER 217 0 4 8 5 0 0 6 1049 1 55 10 END