HEADER TOXIN 23-MAY-24 8ZMN TITLE CRYSTAL STRUCTURE OF ANTXR1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTHRAX TOXIN RECEPTOR 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: ANTXR1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TOXIN RECEPTOR, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHENG,J.HU,L.FU,R.CHEN REVDAT 2 16-OCT-24 8ZMN 1 REMARK REVDAT 1 26-JUN-24 8ZMN 0 JRNL AUTH H.ZHENG,R.CHEN JRNL TITL X-RAY STRUCTURE OF ANTHRAX TOXIN RECEPTOR 1 APO FROM RATTUS JRNL TITL 2 NORVEGICUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.14 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) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 3 NUMBER OF REFLECTIONS : 7795 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) : 0.210 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 366 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 36.6400 - 3.0900 0.91 2713 129 0.1827 0.2229 REMARK 3 2 3.0900 - 2.4500 0.89 2520 142 0.2443 0.3168 REMARK 3 3 2.4500 - 2.1400 0.78 2196 95 0.2601 0.3289 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) : 0.236 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.026 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.31 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 1527 REMARK 3 ANGLE : 0.748 2060 REMARK 3 CHIRALITY : 0.047 218 REMARK 3 PLANARITY : 0.008 269 REMARK 3 DIHEDRAL : 15.152 558 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 35 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.2174 5.8231 -12.6667 REMARK 3 T TENSOR REMARK 3 T11: 0.1581 T22: 0.1534 REMARK 3 T33: 0.1743 T12: 0.0154 REMARK 3 T13: 0.0439 T23: -0.0157 REMARK 3 L TENSOR REMARK 3 L11: 1.0183 L22: 2.7190 REMARK 3 L33: 2.2557 L12: -0.0432 REMARK 3 L13: 0.5703 L23: 0.2276 REMARK 3 S TENSOR REMARK 3 S11: -0.0139 S12: -0.0092 S13: -0.0229 REMARK 3 S21: 0.1128 S22: 0.0111 S23: 0.1437 REMARK 3 S31: -0.1098 S32: -0.1642 S33: -0.0007 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 118 THROUGH 134 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.2820 -1.0793 -23.1750 REMARK 3 T TENSOR REMARK 3 T11: 0.2504 T22: 0.2047 REMARK 3 T33: 0.1451 T12: -0.0634 REMARK 3 T13: 0.0174 T23: -0.0224 REMARK 3 L TENSOR REMARK 3 L11: 2.2690 L22: 1.8249 REMARK 3 L33: 0.9914 L12: -0.3385 REMARK 3 L13: 0.6966 L23: 0.8564 REMARK 3 S TENSOR REMARK 3 S11: -0.0794 S12: 0.2414 S13: 0.0487 REMARK 3 S21: -0.8289 S22: 0.0562 S23: 0.2890 REMARK 3 S31: 0.6995 S32: -0.0539 S33: 0.0782 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 135 THROUGH 201 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.6592 -1.4302 -10.7101 REMARK 3 T TENSOR REMARK 3 T11: 0.1831 T22: 0.2111 REMARK 3 T33: 0.2010 T12: 0.0045 REMARK 3 T13: -0.0036 T23: -0.0098 REMARK 3 L TENSOR REMARK 3 L11: 1.8963 L22: 2.8528 REMARK 3 L33: 2.2265 L12: -0.2276 REMARK 3 L13: -0.7790 L23: 1.2260 REMARK 3 S TENSOR REMARK 3 S11: -0.0076 S12: -0.0031 S13: 0.0258 REMARK 3 S21: 0.3439 S22: 0.1747 S23: -0.1890 REMARK 3 S31: 0.2127 S32: 0.2853 S33: -0.1431 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 202 THROUGH 218 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.4159 15.3095 -9.0395 REMARK 3 T TENSOR REMARK 3 T11: 0.2721 T22: 0.2429 REMARK 3 T33: 0.4220 T12: 0.0324 REMARK 3 T13: -0.1121 T23: -0.0987 REMARK 3 L TENSOR REMARK 3 L11: 3.9520 L22: 5.5050 REMARK 3 L33: 3.2663 L12: 1.0795 REMARK 3 L13: 0.5913 L23: -0.9242 REMARK 3 S TENSOR REMARK 3 S11: -0.0187 S12: -1.0878 S13: -0.0861 REMARK 3 S21: 0.3184 S22: -0.2232 S23: -1.2676 REMARK 3 S31: 0.4680 S32: 0.6746 S33: -0.0432 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 8ZMN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 24-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1300048137. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL10U2 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 EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7809 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.140 REMARK 200 RESOLUTION RANGE LOW (A) : 36.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : 0.15370 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 1.00700 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 (%): 32.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 0.1 M BIS-TRIS REMARK 280 PH 6.5, 28% W/V POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.25800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.29650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.61200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.29650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.25800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.61200 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 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 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 OG1 THR A 116 O HOH A 401 2.08 REMARK 500 O HOH A 405 O HOH A 430 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 ILE A 72 -63.09 70.70 REMARK 500 GLN A 75 74.38 -119.04 REMARK 500 SER A 84 -96.39 -145.95 REMARK 500 LYS A 179 -146.50 65.88 REMARK 500 ASP A 180 58.68 -93.39 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 301 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 48 OD2 REMARK 620 2 SER A 50 OG 81.3 REMARK 620 3 SER A 52 OG 133.3 75.7 REMARK 620 4 THR A 116 OG1 109.6 64.0 96.0 REMARK 620 5 ASP A 148 OD1 75.5 138.7 96.1 156.6 REMARK 620 6 ASP A 148 OD2 99.5 109.2 53.1 148.0 44.2 REMARK 620 7 HOH A 401 O 144.4 66.6 54.3 42.8 139.5 105.2 REMARK 620 N 1 2 3 4 5 6 DBREF 8ZMN A 35 218 UNP Q0PMD2 ANTR1_RAT 35 218 SEQADV 8ZMN ALA A 175 UNP Q0PMD2 CYS 175 ENGINEERED MUTATION SEQRES 1 A 184 PRO ALA CYS TYR GLY GLY PHE ASP LEU TYR PHE ILE LEU SEQRES 2 A 184 ASP LYS SER GLY SER VAL LEU HIS HIS TRP ASN GLU ILE SEQRES 3 A 184 TYR TYR PHE VAL GLU GLN LEU ALA HIS ARG PHE ILE SER SEQRES 4 A 184 PRO GLN LEU ARG MET SER PHE ILE VAL PHE SER THR ARG SEQRES 5 A 184 GLY THR THR LEU MET LYS LEU THR GLU ASP ARG GLU GLN SEQRES 6 A 184 ILE ARG GLN GLY LEU GLU GLU LEU GLN LYS VAL LEU PRO SEQRES 7 A 184 GLY GLY ASP THR TYR MET HIS GLU GLY PHE GLU ARG ALA SEQRES 8 A 184 SER GLU GLN ILE TYR TYR GLU ASN SER GLN GLY TYR ARG SEQRES 9 A 184 THR ALA SER VAL ILE ILE ALA LEU THR ASP GLY GLU LEU SEQRES 10 A 184 HIS GLU ASP LEU PHE PHE TYR SER GLU ARG GLU ALA ASN SEQRES 11 A 184 ARG SER ARG ASP LEU GLY ALA ILE VAL TYR ALA VAL GLY SEQRES 12 A 184 VAL LYS ASP PHE ASN GLU THR GLN LEU ALA ARG ILE ALA SEQRES 13 A 184 ASP SER LYS ASP HIS VAL PHE PRO VAL ASN ASP GLY PHE SEQRES 14 A 184 GLN ALA LEU GLN GLY ILE ILE HIS SER ILE LEU LYS LYS SEQRES 15 A 184 SER CYS HET NA A 301 1 HETNAM NA SODIUM ION FORMUL 2 NA NA 1+ FORMUL 3 HOH *34(H2 O) HELIX 1 AA1 SER A 50 HIS A 55 5 6 HELIX 2 AA2 HIS A 56 HIS A 69 1 14 HELIX 3 AA3 ASP A 96 LYS A 109 1 14 HELIX 4 AA4 TYR A 117 GLN A 135 1 19 HELIX 5 AA5 HIS A 152 LEU A 169 1 18 HELIX 6 AA6 ASN A 182 ALA A 190 1 9 HELIX 7 AA7 SER A 192 ASP A 194 5 3 HELIX 8 AA8 ASP A 201 LYS A 216 1 16 SHEET 1 AA1 6 GLY A 87 THR A 94 0 SHEET 2 AA1 6 LEU A 76 PHE A 83 -1 N VAL A 82 O THR A 88 SHEET 3 AA1 6 PHE A 41 ASP A 48 1 N LEU A 47 O ILE A 81 SHEET 4 AA1 6 ALA A 140 THR A 147 1 O ILE A 144 N TYR A 44 SHEET 5 AA1 6 ILE A 172 GLY A 177 1 O VAL A 176 N ALA A 145 SHEET 6 AA1 6 VAL A 196 PRO A 198 1 O PHE A 197 N ALA A 175 SSBOND 1 CYS A 37 CYS A 218 1555 1555 2.04 LINK OD2 ASP A 48 NA NA A 301 1555 1555 2.82 LINK OG SER A 50 NA NA A 301 1555 1555 2.69 LINK OG SER A 52 NA NA A 301 1555 1555 2.56 LINK OG1 THR A 116 NA NA A 301 1555 1555 3.07 LINK OD1 ASP A 148 NA NA A 301 1555 1555 2.63 LINK OD2 ASP A 148 NA NA A 301 1555 1555 3.08 LINK NA NA A 301 O HOH A 401 1555 1555 2.27 CRYST1 38.516 39.224 102.593 90.00 90.00 90.00 P 21 21 21 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 0.025963 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025495 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009747 0.00000