HEADER ANTIFUNGAL PROTEIN 30-JUL-21 7ROA TITLE CRYSTAL STRUCTURE OF ENTV136 FROM ENTEROCOCCUS FAECALIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENTV; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS OG1RF; SOURCE 3 ORGANISM_COMMON: STREPTOCOCCUS FAECALIS; SOURCE 4 ORGANISM_TAXID: 474186; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: -GOLD; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS ALL ALPHA PROTEIN, ANTIFUNGAL, STRUCTURAL GENOMICS, CSGID, CENTER FOR KEYWDS 2 STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, NIAID, NATIONAL KEYWDS 3 INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES, ANTIFUNGAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.J.STOGIOS,E.EVDOKIMOVA,Y.KIM,D.GARSIN,A.SAVCHENKO,A.JOACHIMIAK, AUTHOR 2 K.J.F.SATCHELL,CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES AUTHOR 3 (CSGID),CENTER FOR STRUCTURAL BIOLOGY OF INFECTIOUS DISEASES (CSBID) REVDAT 3 25-JAN-23 7ROA 1 AUTHOR REVDAT 2 23-NOV-22 7ROA 1 JRNL REVDAT 1 12-OCT-22 7ROA 0 JRNL AUTH M.R.CRUZ,S.CRISTY,S.GUHA,G.B.DE CESARE,E.EVDOKIMOVA, JRNL AUTH 2 H.SANCHEZ,D.BOREK,P.MIRAMON,J.YANO,P.L.FIDEL JR., JRNL AUTH 3 A.SAVCHENKO,D.R.ANDES,P.J.STOGIOS,M.C.LORENZ,D.A.GARSIN JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF ENTV REVEALS A 12 JRNL TITL 2 AMINO ACID FRAGMENT PROTECTIVE AGAINST FUNGAL INFECTIONS. JRNL REF NAT COMMUN V. 13 6047 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 36229448 JRNL DOI 10.1038/S41467-022-33613-1 REMARK 2 REMARK 2 RESOLUTION. 1.82 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.6 REMARK 3 NUMBER OF REFLECTIONS : 8823 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.560 REMARK 3 FREE R VALUE TEST SET COUNT : 685 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 31.1900 - 3.1000 0.94 3159 163 0.1582 0.1949 REMARK 3 2 3.1000 - 2.4600 0.96 3191 149 0.1790 0.2404 REMARK 3 3 2.4600 - 2.1500 0.91 3083 120 0.1906 0.2236 REMARK 3 4 2.1500 - 1.9600 0.84 2735 176 0.1876 0.2323 REMARK 3 5 1.9600 - 1.8200 0.63 2161 77 0.2049 0.2688 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) : 0.135 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.316 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.95 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 : 0.006 914 REMARK 3 ANGLE : 0.858 1232 REMARK 3 CHIRALITY : 0.048 144 REMARK 3 PLANARITY : 0.006 158 REMARK 3 DIHEDRAL : 21.195 333 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 58 THROUGH 75 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.4585 18.6738 -14.8318 REMARK 3 T TENSOR REMARK 3 T11: 0.1451 T22: 0.1188 REMARK 3 T33: 0.1363 T12: 0.0338 REMARK 3 T13: -0.0147 T23: 0.0150 REMARK 3 L TENSOR REMARK 3 L11: 6.6491 L22: 4.5041 REMARK 3 L33: 4.2234 L12: 3.6949 REMARK 3 L13: 3.2834 L23: 4.2279 REMARK 3 S TENSOR REMARK 3 S11: -0.0581 S12: 0.0382 S13: 0.5220 REMARK 3 S21: -0.4869 S22: 0.1705 S23: -0.2691 REMARK 3 S31: -0.5185 S32: 0.1181 S33: 0.0387 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 76 THROUGH 104 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.9644 5.1934 -18.8338 REMARK 3 T TENSOR REMARK 3 T11: 0.0684 T22: 0.1352 REMARK 3 T33: 0.1298 T12: 0.0073 REMARK 3 T13: 0.0109 T23: -0.0589 REMARK 3 L TENSOR REMARK 3 L11: 4.1807 L22: 3.5687 REMARK 3 L33: 2.6358 L12: -0.5413 REMARK 3 L13: -0.0893 L23: -0.9505 REMARK 3 S TENSOR REMARK 3 S11: -0.1289 S12: 0.2218 S13: -0.1219 REMARK 3 S21: -0.4477 S22: 0.0516 S23: -0.4491 REMARK 3 S31: 0.2316 S32: -0.1696 S33: -0.0037 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 105 THROUGH 139 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.2928 1.4725 -5.5340 REMARK 3 T TENSOR REMARK 3 T11: 0.2015 T22: 0.0421 REMARK 3 T33: 0.1282 T12: 0.0023 REMARK 3 T13: 0.0382 T23: 0.0276 REMARK 3 L TENSOR REMARK 3 L11: 6.2865 L22: 4.8886 REMARK 3 L33: 4.0310 L12: -1.4045 REMARK 3 L13: -3.1750 L23: -1.6434 REMARK 3 S TENSOR REMARK 3 S11: -0.1435 S12: 0.1133 S13: -0.3425 REMARK 3 S21: 0.3884 S22: 0.0266 S23: 0.1766 REMARK 3 S31: 0.3580 S32: -0.1615 S33: 0.1292 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 140 THROUGH 168 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.1022 15.2186 -7.3665 REMARK 3 T TENSOR REMARK 3 T11: 0.1174 T22: 0.1132 REMARK 3 T33: 0.0928 T12: 0.0484 REMARK 3 T13: 0.0233 T23: -0.0746 REMARK 3 L TENSOR REMARK 3 L11: 3.3239 L22: 5.2206 REMARK 3 L33: 5.2931 L12: 0.6141 REMARK 3 L13: 0.1648 L23: -0.4233 REMARK 3 S TENSOR REMARK 3 S11: 0.0233 S12: 0.2753 S13: 0.1000 REMARK 3 S21: 0.4415 S22: -0.0577 S23: 0.3353 REMARK 3 S31: 0.0454 S32: -0.3284 S33: 0.0226 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 169 THROUGH 189 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.8501 7.4741 -10.3876 REMARK 3 T TENSOR REMARK 3 T11: 0.0507 T22: 0.0362 REMARK 3 T33: 0.0718 T12: 0.0257 REMARK 3 T13: -0.0222 T23: -0.0086 REMARK 3 L TENSOR REMARK 3 L11: 5.5777 L22: 4.2515 REMARK 3 L33: 6.0540 L12: -0.6013 REMARK 3 L13: -1.0043 L23: -0.6409 REMARK 3 S TENSOR REMARK 3 S11: -0.0731 S12: -0.1765 S13: -0.1431 REMARK 3 S21: 0.4076 S22: -0.0040 S23: -0.2834 REMARK 3 S31: 0.2938 S32: -0.0088 S33: 0.0096 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 7ROA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1000258434. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8895 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 98.6 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 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 : 6.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE, MLPHARE, DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8 AND 28% (W/V) PEG4K, REMARK 280 CRYOPROTECTANT PARATONE-N OIL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 31.19700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.03200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 31.19700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.03200 REMARK 290 SMTRY3 4 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 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 249 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 257 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 267 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 SER A 56 REMARK 465 ASP A 57 REMARK 465 ALA A 111 REMARK 465 SER A 112 REMARK 465 THR A 113 REMARK 465 VAL A 114 REMARK 465 VAL A 115 REMARK 465 GLN A 116 REMARK 465 ALA A 117 REMARK 465 ARG A 118 REMARK 465 PHE A 119 REMARK 465 ASN A 120 REMARK 465 TRP A 121 REMARK 465 ASN A 122 REMARK 465 ALA A 123 REMARK 465 LEU A 124 REMARK 465 GLY A 125 REMARK 465 LEU A 190 REMARK 465 SER A 191 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: IDP96499 RELATED DB: TARGETTRACK DBREF1 7ROA A 56 191 UNP A0A1G1SCE7_ENTFL DBREF2 7ROA A A0A1G1SCE7 35 170 SEQRES 1 A 136 SER ASP GLN LEU GLU ASP SER GLU VAL GLU ALA VAL ALA SEQRES 2 A 136 LYS GLY LEU GLU GLU MSE TYR ALA ASN GLY VAL THR GLU SEQRES 3 A 136 ASP ASN PHE LYS ASN TYR VAL LYS ASN ASN PHE ALA GLN SEQRES 4 A 136 GLN GLU ILE SER SER VAL GLU GLU GLU LEU ASN VAL ASN SEQRES 5 A 136 ILE SER ASP ALA SER THR VAL VAL GLN ALA ARG PHE ASN SEQRES 6 A 136 TRP ASN ALA LEU GLY SER CYS VAL ALA ASN LYS ILE LYS SEQRES 7 A 136 ASP GLU PHE PHE ALA MSE ILE SER ILE SER ALA ILE VAL SEQRES 8 A 136 LYS ALA ALA GLN LYS LYS ALA TRP LYS GLU LEU ALA VAL SEQRES 9 A 136 THR VAL LEU ARG PHE ALA LYS ALA ASN GLY LEU LYS THR SEQRES 10 A 136 ASN ALA ILE ILE VAL ALA GLY GLN LEU ALA LEU TRP ALA SEQRES 11 A 136 VAL GLN CYS GLY LEU SER MODRES 7ROA MSE A 74 MET MODIFIED RESIDUE MODRES 7ROA MSE A 139 MET MODIFIED RESIDUE HET MSE A 74 8 HET MSE A 139 13 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *84(H2 O) HELIX 1 AA1 GLU A 60 TYR A 75 1 16 HELIX 2 AA2 THR A 80 PHE A 92 1 13 HELIX 3 AA3 ALA A 93 ASN A 105 1 13 HELIX 4 AA4 ASN A 130 ILE A 140 1 11 HELIX 5 AA5 SER A 141 LYS A 151 1 11 HELIX 6 AA6 ALA A 153 ASN A 168 1 16 HELIX 7 AA7 ASN A 173 GLY A 189 1 17 LINK C GLU A 73 N MSE A 74 1555 1555 1.34 LINK C MSE A 74 N TYR A 75 1555 1555 1.33 LINK C ALA A 138 N MSE A 139 1555 1555 1.34 LINK C MSE A 139 N ILE A 140 1555 1555 1.33 CRYST1 62.394 32.064 49.992 90.00 90.86 90.00 C 1 2 1 4 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 0.016027 0.000000 0.000241 0.00000 SCALE2 0.000000 0.031188 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020005 0.00000