HEADER TRANSFERASE 06-APR-25 9UDH TITLE BACTERIOPHAGE LYTIC TRANSGLYCOSIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYTIC TRANSGLYCOSIDASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA VARIICOLA; SOURCE 3 ORGANISM_TAXID: 244366; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LYTIC TRANSGLYCOSIDASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.CHOI REVDAT 1 08-APR-26 9UDH 0 JRNL AUTH J.CHOI JRNL TITL CRYSTAL STRUCTURE OF NOVEL LYTIC GLYGOSIDAS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.85 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 17715 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1772 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 30.2900 - 4.3500 1.00 1328 148 0.2084 0.2086 REMARK 3 2 4.3400 - 3.4500 1.00 1266 141 0.1675 0.1911 REMARK 3 3 3.4500 - 3.0200 1.00 1245 138 0.1849 0.2231 REMARK 3 4 3.0200 - 2.7400 1.00 1247 139 0.2034 0.1992 REMARK 3 5 2.7400 - 2.5500 1.00 1226 136 0.1903 0.2575 REMARK 3 6 2.5400 - 2.3900 1.00 1241 138 0.1859 0.1969 REMARK 3 7 2.3900 - 2.2700 1.00 1224 135 0.1865 0.1924 REMARK 3 8 2.2700 - 2.1800 0.99 1216 136 0.1845 0.2086 REMARK 3 9 2.1800 - 2.0900 0.99 1213 134 0.1985 0.2276 REMARK 3 10 2.0900 - 2.0200 0.99 1208 134 0.2179 0.2589 REMARK 3 11 2.0200 - 1.9600 0.98 1191 133 0.2123 0.2525 REMARK 3 12 1.9600 - 1.9000 0.97 1186 132 0.2328 0.2564 REMARK 3 13 1.9000 - 1.8500 0.93 1152 128 0.2691 0.2868 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) : 0.155 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.218 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.88 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 : 0.007 1249 REMARK 3 ANGLE : 0.901 1678 REMARK 3 CHIRALITY : 0.051 184 REMARK 3 PLANARITY : 0.007 214 REMARK 3 DIHEDRAL : 16.562 471 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 9UDH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-APR-25. REMARK 100 THE DEPOSITION ID IS D_1300058272. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-24 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18434 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 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: PHENIX REMARK 200 STARTING MODEL: ALPHAFOLD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, MAGNESIUM FORMATE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 33.86950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.86950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.86350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.79150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.86350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.79150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.86950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.86350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.79150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 33.86950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.86350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.79150 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 301 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 327 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 331 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 335 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 339 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 TYR A 127 REMARK 465 ASN A 128 REMARK 465 ASP A 129 REMARK 465 ASN A 130 REMARK 465 LYS A 131 REMARK 465 GLY A 132 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 OH TYR A 92 O HOH A 201 1.87 REMARK 500 N ALA A 52 O HOH A 202 1.89 REMARK 500 O HOH A 325 O HOH A 330 1.95 REMARK 500 O HOH A 280 O HOH A 306 2.08 REMARK 500 C SER A 51 O HOH A 202 2.14 REMARK 500 O HOH A 273 O HOH A 305 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 OD2 ASP A 116 NZ LYS A 137 4555 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 97 -51.95 -127.93 REMARK 500 CYS A 108 82.39 -164.44 REMARK 500 ALA A 125 79.52 49.26 REMARK 500 REMARK 500 REMARK: NULL DBREF 9UDH A 1 164 PDB 9UDH 9UDH 1 164 SEQRES 1 A 164 MET ALA TRP GLY ALA LYS VAL SER LYS GLU PHE LYS LEU SEQRES 2 A 164 LYS VAL ILE GLU VAL CYS GLU ARG LEU GLU ILE ASN PRO SEQRES 3 A 164 ASP TYR LEU MET SER CYS MET ALA PHE GLU THR GLY GLU SEQRES 4 A 164 THR PHE SER PRO SER VAL ARG ASN PRO ASN GLY SER ALA SEQRES 5 A 164 THR GLY LEU ILE GLN PHE MET SER ASN THR ALA ARG SER SEQRES 6 A 164 LEU GLY THR THR THR ASN GLU LEU ALA ASP MET THR SER SEQRES 7 A 164 VAL GLU GLN MET ASP TYR VAL GLU LYS TYR PHE LYS PRO SEQRES 8 A 164 TYR ALA GLY LYS ILE LYS THR ILE GLU ASP VAL TYR MET SEQRES 9 A 164 VAL ILE PHE CYS PRO ARG ALA VAL GLY LYS PRO ASP SER SEQRES 10 A 164 TYR ILE LEU ALA ASP ALA GLY ALA ALA TYR ASN ASP ASN SEQRES 11 A 164 LYS GLY ALA ASP LEU ASN LYS ASP ASN ALA ILE THR LYS SEQRES 12 A 164 TYR GLU ALA GLY PHE LYS VAL ARG GLU LYS LEU LYS LEU SEQRES 13 A 164 GLY MET LYS GLU GLY TYR ARG GLY FORMUL 2 HOH *139(H2 O) HELIX 1 AA1 TRP A 3 VAL A 7 5 5 HELIX 2 AA2 SER A 8 GLU A 23 1 16 HELIX 3 AA3 ASN A 25 GLY A 38 1 14 HELIX 4 AA4 SER A 60 LEU A 66 1 7 HELIX 5 AA5 THR A 69 ASP A 75 1 7 HELIX 6 AA6 THR A 77 LYS A 90 1 14 HELIX 7 AA7 PRO A 91 ALA A 93 5 3 HELIX 8 AA8 THR A 98 CYS A 108 1 11 HELIX 9 AA9 PRO A 109 VAL A 112 5 4 HELIX 10 AB1 LYS A 143 GLY A 147 1 5 HELIX 11 AB2 GLY A 147 MET A 158 1 12 SHEET 1 AA1 2 ALA A 52 THR A 53 0 SHEET 2 AA1 2 PHE A 58 MET A 59 -1 O PHE A 58 N THR A 53 SHEET 1 AA2 2 ILE A 119 ALA A 121 0 SHEET 2 AA2 2 ILE A 141 THR A 142 -1 O ILE A 141 N LEU A 120 CRYST1 67.727 89.583 67.739 90.00 90.00 90.00 C 2 2 21 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 0.014765 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011163 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014763 0.00000 MASTER 299 0 0 11 4 0 0 6 1367 1 0 13 END