HEADER ANTIMICROBIAL PROTEIN 29-AUG-25 9WIW TITLE CRYSTAL STRUCTURE OF A ESCHERICHIA PHAGE UPEC07 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDORIBONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THE SEQUENCE OF ORGANISM ESCHERICHIA PHAGE T4 IS NOT COMPND 6 AVAILABLE DURING THE BIOCURATION, REPLACED BY A0A8T8L841 TEMPORARILY. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE T4; SOURCE 3 ORGANISM_TAXID: 2681598; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HELIX, DIMER, SPONGE PROTEIN, ANTI TYPEIV THOERIS, ANTIMICROBIAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,Y.FENG,L.L.WEI REVDAT 1 04-MAR-26 9WIW 0 JRNL AUTH H.WANG,Y.FENG,L.L.WEI JRNL TITL CRYSTAL STRUCTURE OF A ESCHERICHIA PHAGE UPEC07 PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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) : 2.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 3979 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 399 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 41.6400 - 3.7000 1.00 1251 140 0.2206 0.2621 REMARK 3 2 3.7000 - 2.9400 1.00 1169 131 0.2215 0.2293 REMARK 3 3 2.9400 - 2.5600 1.00 1160 128 0.2741 0.3618 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) : 0.362 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.511 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.13 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 : 0.002 602 REMARK 3 ANGLE : 0.299 804 REMARK 3 CHIRALITY : 0.030 82 REMARK 3 PLANARITY : 0.001 107 REMARK 3 DIHEDRAL : 6.880 77 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 9WIW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 02-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1300063161. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4014 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.560 REMARK 200 RESOLUTION RANGE LOW (A) : 41.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 44.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 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 : 4.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M AMMONIUM SULFATE 1.0 M LITHIUM REMARK 280 SULFATE 0.1 M SODIUM CITRATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 27.26950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.23550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.23550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 40.90425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.23550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.23550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 13.63475 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.23550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.23550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 40.90425 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.23550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.23550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 13.63475 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 27.26950 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 1 REMARK 465 ALA A 2 REMARK 465 GLN A 3 REMARK 465 ILE A 4 REMARK 465 ASN A 5 REMARK 465 SER A 6 REMARK 465 GLY A 7 REMARK 465 PHE A 8 REMARK 465 GLY A 9 REMARK 465 TYR A 10 REMARK 465 GLU A 11 REMARK 465 LEU A 12 REMARK 465 SER A 13 REMARK 465 THR A 14 REMARK 465 ALA A 15 REMARK 465 SER A 16 REMARK 465 HIS A 17 REMARK 465 ARG A 18 REMARK 465 ARG A 19 REMARK 465 ILE A 20 REMARK 465 SER A 21 REMARK 465 ASP A 22 REMARK 465 SER A 23 REMARK 465 ASN A 24 REMARK 465 PRO A 25 REMARK 465 PHE A 26 REMARK 465 GLY A 27 REMARK 465 PHE A 28 REMARK 465 THR A 29 REMARK 465 SER A 30 REMARK 465 LYS A 31 REMARK 465 PRO A 32 REMARK 465 LEU A 102 REMARK 465 GLU A 103 REMARK 465 HIS A 104 REMARK 465 HIS A 105 REMARK 465 HIS A 106 REMARK 465 HIS A 107 REMARK 465 HIS A 108 REMARK 465 HIS A 109 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 O3 SO4 A 201 O HOH A 301 1.91 REMARK 500 O HOH A 305 O HOH A 308 2.11 REMARK 500 OH TYR A 55 O HOH A 302 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 O HOH A 310 O HOH A 311 4445 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 311 DISTANCE = 6.21 ANGSTROMS DBREF1 9WIW A 1 101 UNP A0A8T8L841_9CAUD DBREF2 9WIW A A0A8T8L841 1 101 SEQADV 9WIW LEU A 102 UNP A0A8T8L84 EXPRESSION TAG SEQADV 9WIW GLU A 103 UNP A0A8T8L84 EXPRESSION TAG SEQADV 9WIW HIS A 104 UNP A0A8T8L84 EXPRESSION TAG SEQADV 9WIW HIS A 105 UNP A0A8T8L84 EXPRESSION TAG SEQADV 9WIW HIS A 106 UNP A0A8T8L84 EXPRESSION TAG SEQADV 9WIW HIS A 107 UNP A0A8T8L84 EXPRESSION TAG SEQADV 9WIW HIS A 108 UNP A0A8T8L84 EXPRESSION TAG SEQADV 9WIW HIS A 109 UNP A0A8T8L84 EXPRESSION TAG SEQRES 1 A 109 MET ALA GLN ILE ASN SER GLY PHE GLY TYR GLU LEU SER SEQRES 2 A 109 THR ALA SER HIS ARG ARG ILE SER ASP SER ASN PRO PHE SEQRES 3 A 109 GLY PHE THR SER LYS PRO LYS LYS ILE GLN GLY LEU ASP SEQRES 4 A 109 ASP PHE GLN GLU VAL ILE ARG GLN ALA PHE GLN ASP TYR SEQRES 5 A 109 ALA ARG TYR LEU LYS GLU ASP LYS GLU ASP CYS LEU GLU SEQRES 6 A 109 GLU ASP GLU ILE GLU TYR TYR GLU GLN ARG LEU GLU GLN SEQRES 7 A 109 ILE LYS ASN LEU HIS ALA VAL ARG ASP GLU VAL ALA LYS SEQRES 8 A 109 ALA MET ASN LYS LEU ILE SER PHE LYS GLU LEU GLU HIS SEQRES 9 A 109 HIS HIS HIS HIS HIS HET SO4 A 201 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *11(H2 O) HELIX 1 AA1 GLY A 37 GLU A 66 1 30 HELIX 2 AA2 GLU A 68 ASN A 94 1 27 CRYST1 64.471 64.471 54.539 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 0.015511 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015511 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018336 0.00000 CONECT 592 593 594 595 596 CONECT 593 592 CONECT 594 592 CONECT 595 592 CONECT 596 592 MASTER 305 0 1 2 0 0 0 6 606 1 5 9 END