HEADER TOXIN/IMMUNE SYSTEM 28-MAR-24 8YVO TITLE CRYSTAL STRUCTURE OF THE C. DIFFICILE TOXIN A CROPS DOMAIN FRAGMENT TITLE 2 2639-2707 BOUND TO C4.2 NANOBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: C4.2 NANOBODY; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TOXIN A; COMPND 7 CHAIN: C, D; COMPND 8 EC: 3.4.22.-; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAMELUS DROMEDARIUS; SOURCE 3 ORGANISM_TAXID: 9838; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: CLOSTRIDIOIDES DIFFICILE; SOURCE 9 ORGANISM_TAXID: 1496; SOURCE 10 STRAIN: VPI10463; SOURCE 11 GENE: TCDA, TOXA; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 14 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS CROPS DOMAIN FRAGMENT, TOXIN A, COMPLEX WITH NANOBODY, CLOSTRIDIOIDES KEYWDS 2 DIFFICILE, TOXIN, TOXIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.N.SLUCHANKO,L.A.VARFOLOMEEVA,D.V.SHCHEBLYAKOV,Y.F.BELYI, AUTHOR 2 D.Y.LOGUNOV,A.L.GINTSBURG,V.O.POPOV,K.M.BOYKO REVDAT 1 18-DEC-24 8YVO 0 JRNL AUTH N.N.SLUCHANKO,I.V.SOKOLOVA,I.A.FAVORSKAYA,I.B.ESMAGAMBETOV, JRNL AUTH 2 A.I.TUKHVATULIN,I.A.ALEKSEEVA,A.S.UNGUR,L.A.VARFOLOMEEVA, JRNL AUTH 3 K.M.BOYKO,D.Y.LOGUNOV,A.L.GINTSBURG,V.O.POPOV, JRNL AUTH 4 D.V.SHCHEBLYAKOV,Y.F.BELYI JRNL TITL STRUCTURAL INSIGHT INTO RECOGNITION OF CLOSTRIDIOIDES JRNL TITL 2 DIFFICILE TOXIN A BY NOVEL NEUTRALIZING NANOBODIES TARGETING JRNL TITL 3 QTIN-LIKE MOTIFS WITHIN ITS RECEPTOR-BINDING DOMAIN. JRNL REF INT.J.BIOL.MACROMOL. V. 283 37910 2024 JRNL REFN ISSN 0141-8130 JRNL PMID 39577542 JRNL DOI 10.1016/J.IJBIOMAC.2024.137910 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 79.9 REMARK 3 NUMBER OF REFLECTIONS : 47501 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2501 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 0 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 0.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.0000 REMARK 3 BIN FREE R VALUE SET COUNT : 0 REMARK 3 BIN FREE R VALUE : 0.0000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3012 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.95000 REMARK 3 B22 (A**2) : 7.21000 REMARK 3 B33 (A**2) : -10.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.70000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.030 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.029 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.543 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.925 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3142 ; 0.012 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2900 ; 0.003 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4224 ; 2.001 ; 1.798 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6627 ; 0.788 ; 1.744 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 388 ; 8.074 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 21 ; 9.122 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 488 ;14.690 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 433 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3807 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 825 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1564 ; 2.820 ; 2.111 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1564 ; 2.819 ; 2.110 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1948 ; 3.994 ; 3.782 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1949 ; 3.994 ; 3.783 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1578 ; 3.186 ; 2.279 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1579 ; 3.185 ; 2.280 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2277 ; 4.486 ; 4.082 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3443 ; 6.281 ;20.870 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3378 ; 6.176 ;20.660 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.9141 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -H,-K,L REMARK 3 TWIN FRACTION : 0.0859 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 23 A 202 REMARK 3 ORIGIN FOR THE GROUP (A): 11.9597 -26.5040 14.6514 REMARK 3 T TENSOR REMARK 3 T11: 0.0790 T22: 0.0688 REMARK 3 T33: 0.0219 T12: 0.0008 REMARK 3 T13: 0.0093 T23: -0.0188 REMARK 3 L TENSOR REMARK 3 L11: 0.4597 L22: 0.2498 REMARK 3 L33: 1.4000 L12: -0.1072 REMARK 3 L13: 0.4577 L23: -0.0673 REMARK 3 S TENSOR REMARK 3 S11: 0.0137 S12: 0.0879 S13: -0.0447 REMARK 3 S21: 0.0542 S22: 0.0141 S23: -0.0361 REMARK 3 S31: 0.1104 S32: -0.0312 S33: -0.0278 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 23 B 201 REMARK 3 ORIGIN FOR THE GROUP (A): 14.2487 -17.5954 -16.8690 REMARK 3 T TENSOR REMARK 3 T11: 0.0793 T22: 0.0672 REMARK 3 T33: 0.0551 T12: 0.0034 REMARK 3 T13: 0.0576 T23: -0.0170 REMARK 3 L TENSOR REMARK 3 L11: 0.8176 L22: 0.1940 REMARK 3 L33: 1.3538 L12: 0.1829 REMARK 3 L13: -0.5951 L23: 0.1426 REMARK 3 S TENSOR REMARK 3 S11: 0.0160 S12: -0.0784 S13: 0.0536 REMARK 3 S21: -0.0436 S22: -0.0062 S23: -0.0174 REMARK 3 S31: -0.0764 S32: -0.0244 S33: -0.0097 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 2639 C 2802 REMARK 3 ORIGIN FOR THE GROUP (A): 22.0719 -23.8951 40.5614 REMARK 3 T TENSOR REMARK 3 T11: 0.1105 T22: 0.0043 REMARK 3 T33: 0.0353 T12: 0.0149 REMARK 3 T13: -0.0144 T23: -0.0024 REMARK 3 L TENSOR REMARK 3 L11: 0.4459 L22: 1.0399 REMARK 3 L33: 1.0609 L12: 0.3823 REMARK 3 L13: 0.2707 L23: -0.5609 REMARK 3 S TENSOR REMARK 3 S11: 0.0157 S12: 0.0278 S13: -0.0289 REMARK 3 S21: -0.0151 S22: 0.0444 S23: 0.0039 REMARK 3 S31: 0.0127 S32: -0.0096 S33: -0.0601 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 2639 D 2801 REMARK 3 ORIGIN FOR THE GROUP (A): 28.0170 -20.1345 -41.0667 REMARK 3 T TENSOR REMARK 3 T11: 0.1108 T22: 0.0156 REMARK 3 T33: 0.0714 T12: -0.0092 REMARK 3 T13: 0.0855 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 0.2636 L22: 0.8847 REMARK 3 L33: 0.7877 L12: 0.0101 REMARK 3 L13: -0.3816 L23: -0.3899 REMARK 3 S TENSOR REMARK 3 S11: 0.0182 S12: -0.0250 S13: 0.0284 REMARK 3 S21: -0.0053 S22: 0.0203 S23: 0.0254 REMARK 3 S31: 0.0129 S32: -0.0032 S33: -0.0386 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 8YVO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-APR-24. REMARK 100 THE DEPOSITION ID IS D_1300046462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU PHOTONJET-S REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50005 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.81200 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4M POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 50.51331 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.42500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 88.90926 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.51331 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.42500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 88.90926 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 APPLY THE FOLLOWING TO CHAINS: A, C 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 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 LYS A 2 REMARK 465 TYR A 3 REMARK 465 LEU A 4 REMARK 465 LEU A 5 REMARK 465 PRO A 6 REMARK 465 THR A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 9 REMARK 465 ALA A 10 REMARK 465 GLY A 11 REMARK 465 LEU A 12 REMARK 465 LEU A 13 REMARK 465 LEU A 14 REMARK 465 LEU A 15 REMARK 465 ALA A 16 REMARK 465 ALA A 17 REMARK 465 GLN A 18 REMARK 465 PRO A 19 REMARK 465 ALA A 20 REMARK 465 MET A 21 REMARK 465 ALA A 22 REMARK 465 ALA A 150 REMARK 465 ALA A 151 REMARK 465 GLU A 152 REMARK 465 GLN A 153 REMARK 465 LYS A 154 REMARK 465 LEU A 155 REMARK 465 ILE A 156 REMARK 465 SER A 157 REMARK 465 GLU A 158 REMARK 465 GLU A 159 REMARK 465 ASP A 160 REMARK 465 LEU A 161 REMARK 465 ASN A 162 REMARK 465 GLY A 163 REMARK 465 ALA A 164 REMARK 465 ALA A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 REMARK 465 HIS A 171 REMARK 465 GLY A 172 REMARK 465 SER A 173 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 TYR B 3 REMARK 465 LEU B 4 REMARK 465 LEU B 5 REMARK 465 PRO B 6 REMARK 465 THR B 7 REMARK 465 ALA B 8 REMARK 465 ALA B 9 REMARK 465 ALA B 10 REMARK 465 GLY B 11 REMARK 465 LEU B 12 REMARK 465 LEU B 13 REMARK 465 LEU B 14 REMARK 465 LEU B 15 REMARK 465 ALA B 16 REMARK 465 ALA B 17 REMARK 465 GLN B 18 REMARK 465 PRO B 19 REMARK 465 ALA B 20 REMARK 465 MET B 21 REMARK 465 ALA B 22 REMARK 465 ALA B 150 REMARK 465 ALA B 151 REMARK 465 GLU B 152 REMARK 465 GLN B 153 REMARK 465 LYS B 154 REMARK 465 LEU B 155 REMARK 465 ILE B 156 REMARK 465 SER B 157 REMARK 465 GLU B 158 REMARK 465 GLU B 159 REMARK 465 ASP B 160 REMARK 465 LEU B 161 REMARK 465 ASN B 162 REMARK 465 GLY B 163 REMARK 465 ALA B 164 REMARK 465 ALA B 165 REMARK 465 HIS B 166 REMARK 465 HIS B 167 REMARK 465 HIS B 168 REMARK 465 HIS B 169 REMARK 465 HIS B 170 REMARK 465 HIS B 171 REMARK 465 GLY B 172 REMARK 465 SER B 173 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 62 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 64 CA - CB - CG ANGL. DEV. = 13.3 DEGREES REMARK 500 ARG A 71 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 MET A 102 CG - SD - CE ANGL. DEV. = 10.1 DEGREES REMARK 500 GLU A 136 CG - CD - OE1 ANGL. DEV. = -12.9 DEGREES 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 ALA A 111 163.65 177.70 REMARK 500 ALA B 111 162.03 176.38 REMARK 500 TYR C2642 91.87 -166.46 REMARK 500 MET C2706 -75.56 25.55 REMARK 500 TYR D2642 96.47 -163.69 REMARK 500 MET D2706 12.09 -141.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 MET C 2706 GLY C 2707 -146.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG C2645 0.08 SIDE CHAIN REMARK 500 ARG D2645 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8YVO A 1 173 PDB 8YVO 8YVO 1 173 DBREF 8YVO B 1 173 PDB 8YVO 8YVO 1 173 DBREF 8YVO C 2639 2707 UNP P16154 TCDA_CLODI 2639 2707 DBREF 8YVO D 2639 2707 UNP P16154 TCDA_CLODI 2639 2707 SEQADV 8YVO MET C 2706 UNP P16154 PRO 2706 CONFLICT SEQADV 8YVO MET D 2706 UNP P16154 PRO 2706 CONFLICT SEQRES 1 A 173 MET LYS TYR LEU LEU PRO THR ALA ALA ALA GLY LEU LEU SEQRES 2 A 173 LEU LEU ALA ALA GLN PRO ALA MET ALA GLU VAL GLN LEU SEQRES 3 A 173 VAL GLU SER GLY GLY GLY SER VAL GLN ALA GLY GLY SER SEQRES 4 A 173 LEU ARG LEU SER CYS ALA ALA SER ALA PHE GLY ASN TYR SEQRES 5 A 173 MET GLY TRP PHE ARG GLN ALA PRO GLY LYS GLU ARG GLU SEQRES 6 A 173 GLY VAL ALA ALA ILE ARG THR GLY GLY GLY SER THR TYR SEQRES 7 A 173 TYR THR ASP SER VAL LYS GLY ARG PHE THR ILE SER GLN SEQRES 8 A 173 ASP LYS ALA LYS ASN THR VAL TYR LEU GLN MET ASN SER SEQRES 9 A 173 LEU LYS PRO GLU ASP THR ALA MET TYR VAL CYS ALA THR SEQRES 10 A 173 ALA GLY ASP ARG TRP HIS ALA THR ASP ALA PHE ILE LEU SEQRES 11 A 173 ARG ASP PHE VAL TYR GLU TYR TRP GLY GLN GLY THR GLN SEQRES 12 A 173 VAL THR VAL SER SER ALA ALA ALA GLU GLN LYS LEU ILE SEQRES 13 A 173 SER GLU GLU ASP LEU ASN GLY ALA ALA HIS HIS HIS HIS SEQRES 14 A 173 HIS HIS GLY SER SEQRES 1 B 173 MET LYS TYR LEU LEU PRO THR ALA ALA ALA GLY LEU LEU SEQRES 2 B 173 LEU LEU ALA ALA GLN PRO ALA MET ALA GLU VAL GLN LEU SEQRES 3 B 173 VAL GLU SER GLY GLY GLY SER VAL GLN ALA GLY GLY SER SEQRES 4 B 173 LEU ARG LEU SER CYS ALA ALA SER ALA PHE GLY ASN TYR SEQRES 5 B 173 MET GLY TRP PHE ARG GLN ALA PRO GLY LYS GLU ARG GLU SEQRES 6 B 173 GLY VAL ALA ALA ILE ARG THR GLY GLY GLY SER THR TYR SEQRES 7 B 173 TYR THR ASP SER VAL LYS GLY ARG PHE THR ILE SER GLN SEQRES 8 B 173 ASP LYS ALA LYS ASN THR VAL TYR LEU GLN MET ASN SER SEQRES 9 B 173 LEU LYS PRO GLU ASP THR ALA MET TYR VAL CYS ALA THR SEQRES 10 B 173 ALA GLY ASP ARG TRP HIS ALA THR ASP ALA PHE ILE LEU SEQRES 11 B 173 ARG ASP PHE VAL TYR GLU TYR TRP GLY GLN GLY THR GLN SEQRES 12 B 173 VAL THR VAL SER SER ALA ALA ALA GLU GLN LYS LEU ILE SEQRES 13 B 173 SER GLU GLU ASP LEU ASN GLY ALA ALA HIS HIS HIS HIS SEQRES 14 B 173 HIS HIS GLY SER SEQRES 1 C 69 ALA ILE ARG TYR GLN ASN ARG PHE LEU HIS LEU LEU GLY SEQRES 2 C 69 LYS ILE TYR TYR PHE GLY ASN ASN SER LYS ALA VAL THR SEQRES 3 C 69 GLY TRP GLN THR ILE ASN GLY LYS VAL TYR TYR PHE MET SEQRES 4 C 69 PRO ASP THR ALA MET ALA ALA ALA GLY GLY LEU PHE GLU SEQRES 5 C 69 ILE ASP GLY VAL ILE TYR PHE PHE GLY VAL ASP GLY VAL SEQRES 6 C 69 LYS ALA MET GLY SEQRES 1 D 69 ALA ILE ARG TYR GLN ASN ARG PHE LEU HIS LEU LEU GLY SEQRES 2 D 69 LYS ILE TYR TYR PHE GLY ASN ASN SER LYS ALA VAL THR SEQRES 3 D 69 GLY TRP GLN THR ILE ASN GLY LYS VAL TYR TYR PHE MET SEQRES 4 D 69 PRO ASP THR ALA MET ALA ALA ALA GLY GLY LEU PHE GLU SEQRES 5 D 69 ILE ASP GLY VAL ILE TYR PHE PHE GLY VAL ASP GLY VAL SEQRES 6 D 69 LYS ALA MET GLY HET EDO A 201 4 HET EDO A 202 4 HET EDO B 201 4 HET EDO B 202 4 HET EDO C2801 4 HET EDO C2802 4 HET EDO C2803 4 HET EDO D2801 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 EDO 8(C2 H6 O2) FORMUL 13 HOH *350(H2 O) HELIX 1 AA1 ASP A 81 LYS A 84 5 4 HELIX 2 AA2 LYS A 93 LYS A 95 5 3 HELIX 3 AA3 LYS A 106 THR A 110 5 5 HELIX 4 AA4 THR A 125 ILE A 129 5 5 HELIX 5 AA5 ARG A 131 TYR A 135 5 5 HELIX 6 AA6 ASP B 81 LYS B 84 5 4 HELIX 7 AA7 LYS B 93 LYS B 95 5 3 HELIX 8 AA8 LYS B 106 THR B 110 5 5 HELIX 9 AA9 THR B 125 ILE B 129 5 5 HELIX 10 AB1 ARG B 131 TYR B 135 5 5 SHEET 1 AA1 4 LEU A 26 SER A 29 0 SHEET 2 AA1 4 LEU A 40 ALA A 46 -1 O ALA A 45 N VAL A 27 SHEET 3 AA1 4 THR A 97 MET A 102 -1 O MET A 102 N LEU A 40 SHEET 4 AA1 4 PHE A 87 ASP A 92 -1 N ASP A 92 O THR A 97 SHEET 1 AA2 6 SER A 33 GLN A 35 0 SHEET 2 AA2 6 THR A 142 SER A 147 1 O SER A 147 N VAL A 34 SHEET 3 AA2 6 ALA A 111 THR A 117 -1 N TYR A 113 O THR A 142 SHEET 4 AA2 6 TYR A 52 GLN A 58 -1 N PHE A 56 O VAL A 114 SHEET 5 AA2 6 GLU A 65 ARG A 71 -1 O VAL A 67 N TRP A 55 SHEET 6 AA2 6 THR A 77 TYR A 79 -1 O TYR A 78 N ALA A 69 SHEET 1 AA3 4 SER A 33 GLN A 35 0 SHEET 2 AA3 4 THR A 142 SER A 147 1 O SER A 147 N VAL A 34 SHEET 3 AA3 4 ALA A 111 THR A 117 -1 N TYR A 113 O THR A 142 SHEET 4 AA3 4 TYR A 137 TRP A 138 -1 O TYR A 137 N THR A 117 SHEET 1 AA4 3 TRP A 122 HIS A 123 0 SHEET 2 AA4 3 GLY C2665 ILE C2669 1 O THR C2668 N HIS A 123 SHEET 3 AA4 3 LYS C2672 PHE C2676 -1 O LYS C2672 N ILE C2669 SHEET 1 AA5 4 LEU B 26 SER B 29 0 SHEET 2 AA5 4 LEU B 40 ALA B 46 -1 O ALA B 45 N VAL B 27 SHEET 3 AA5 4 THR B 97 MET B 102 -1 O MET B 102 N LEU B 40 SHEET 4 AA5 4 PHE B 87 ASP B 92 -1 N ASP B 92 O THR B 97 SHEET 1 AA6 6 GLY B 32 GLN B 35 0 SHEET 2 AA6 6 THR B 142 SER B 147 1 O SER B 147 N VAL B 34 SHEET 3 AA6 6 ALA B 111 THR B 117 -1 N TYR B 113 O THR B 142 SHEET 4 AA6 6 TYR B 52 GLN B 58 -1 N PHE B 56 O VAL B 114 SHEET 5 AA6 6 ARG B 64 ARG B 71 -1 O VAL B 67 N TRP B 55 SHEET 6 AA6 6 THR B 77 TYR B 79 -1 O TYR B 78 N ALA B 69 SHEET 1 AA7 4 GLY B 32 GLN B 35 0 SHEET 2 AA7 4 THR B 142 SER B 147 1 O SER B 147 N VAL B 34 SHEET 3 AA7 4 ALA B 111 THR B 117 -1 N TYR B 113 O THR B 142 SHEET 4 AA7 4 TYR B 137 TRP B 138 -1 O TYR B 137 N THR B 117 SHEET 1 AA8 3 TRP B 122 HIS B 123 0 SHEET 2 AA8 3 GLY D2665 ILE D2669 1 O THR D2668 N HIS B 123 SHEET 3 AA8 3 LYS D2672 PHE D2676 -1 O TYR D2674 N GLN D2667 SHEET 1 AA9 2 ARG C2645 LEU C2649 0 SHEET 2 AA9 2 LYS C2652 PHE C2656 -1 O PHE C2656 N ARG C2645 SHEET 1 AB1 2 GLY C2687 ILE C2691 0 SHEET 2 AB1 2 VAL C2694 PHE C2698 -1 O VAL C2694 N ILE C2691 SHEET 1 AB2 2 ARG D2645 LEU D2649 0 SHEET 2 AB2 2 LYS D2652 PHE D2656 -1 O PHE D2656 N ARG D2645 SHEET 1 AB3 2 GLY D2687 ILE D2691 0 SHEET 2 AB3 2 VAL D2694 PHE D2698 -1 O VAL D2694 N ILE D2691 SSBOND 1 CYS A 44 CYS A 115 1555 1555 2.05 SSBOND 2 CYS B 44 CYS B 115 1555 1555 2.03 CRYST1 113.804 42.850 178.277 90.00 94.11 90.00 I 1 2 1 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 0.008787 0.000000 0.000631 0.00000 SCALE2 0.000000 0.023337 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005624 0.00000