HEADER TOXIN/IMMUNE SYSTEM 28-MAR-24 8YVJ TITLE CRYSTAL STRUCTURE OF THE C. DIFFICILE TOXIN A CROPS DOMAIN FRAGMENT TITLE 2 2592-2710 BOUND TO H5.2 NANOBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: H5.2 NANOBODY (VHH); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TOXIN A; COMPND 7 CHAIN: B; 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 EXPRESSION_SYSTEM_VECTOR_TYPE: PMAL-C5X; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: CLOSTRIDIOIDES DIFFICILE 342; SOURCE 10 ORGANISM_TAXID: 1151306; SOURCE 11 STRAIN: VPI10463; SOURCE 12 GENE: TCDA, TOXA; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PMAL-C5X 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 8YVJ 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. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 25128 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) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1304 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1592 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.1590 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.2150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1883 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 351 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.11000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.101 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.054 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.532 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1965 ; 0.011 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2657 ; 2.040 ; 1.788 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 249 ; 6.852 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 9 ; 9.175 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 307 ;11.689 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 273 ; 0.145 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1547 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 990 ; 1.196 ; 0.834 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1235 ; 1.926 ; 1.488 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 975 ; 2.189 ; 1.027 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3196 ; 4.977 ;15.970 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 8YVJ 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_1300046404. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-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) : 1.5418 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 : 26488 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 21.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 54.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.10700 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: MORDA REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM PHOSPHATE DIBASIC, PH REMARK 280 8.0, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 288K 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 16.07800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.70250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.86950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.70250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.07800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.86950 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 HIS B 2590 REMARK 465 MET B 2591 REMARK 465 GLY B 2592 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 41 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 41 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG B2641 NE - CZ - NH2 ANGL. DEV. = -4.5 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 ASP A 58 -54.42 -139.91 REMARK 500 ALA A 78 16.26 -140.83 REMARK 500 TYR B2642 102.13 -164.10 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 A 103 0.08 SIDE CHAIN 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 495 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH B2956 DISTANCE = 6.28 ANGSTROMS DBREF 8YVJ A 1 129 PDB 8YVJ 8YVJ 1 129 DBREF 8YVJ B 2592 2710 UNP P16154 TCDA_CLODI 2592 2710 SEQADV 8YVJ HIS B 2590 UNP P16154 EXPRESSION TAG SEQADV 8YVJ MET B 2591 UNP P16154 EXPRESSION TAG SEQRES 1 A 129 HIS MET ALA GLN VAL THR LEU LYS GLU SER GLY GLY GLY SEQRES 2 A 129 SER VAL GLN ALA GLY GLY SER LEU ARG LEU SER CYS ALA SEQRES 3 A 129 GLY PRO ARG HIS ILE PRO GLY SER VAL CYS MET GLY TRP SEQRES 4 A 129 TYR ARG GLN VAL PRO GLY LYS GLU ARG GLU GLY VAL ALA SEQRES 5 A 129 LEU ILE LEU ILE GLY ASP GLY HIS THR ASN TYR ALA ASP SEQRES 6 A 129 SER VAL LYS GLY ARG PHE THR ILE SER GLN ASP SER ALA SEQRES 7 A 129 ALA ASN THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO SEQRES 8 A 129 GLU ASP THR ALA VAL TYR TYR CYS ALA ALA ALA ARG GLY SEQRES 9 A 129 LEU SER ASP TRP THR CYS SER PHE GLU SER GLY VAL ASN SEQRES 10 A 129 SER TRP GLY GLN GLY THR GLN VAL THR VAL SER SER SEQRES 1 B 121 HIS MET GLY ALA ASN GLY TYR LYS THR ILE ASP ASN LYS SEQRES 2 B 121 ASN PHE TYR PHE ARG ASN GLY LEU PRO GLN ILE GLY VAL SEQRES 3 B 121 PHE LYS GLY SER ASN GLY PHE GLU TYR PHE ALA PRO ALA SEQRES 4 B 121 ASN THR ASP ALA ASN ASN ILE GLU GLY GLN ALA ILE ARG SEQRES 5 B 121 TYR GLN ASN ARG PHE LEU HIS LEU LEU GLY LYS ILE TYR SEQRES 6 B 121 TYR PHE GLY ASN ASN SER LYS ALA VAL THR GLY TRP GLN SEQRES 7 B 121 THR ILE ASN GLY LYS VAL TYR TYR PHE MET PRO ASP THR SEQRES 8 B 121 ALA MET ALA ALA ALA GLY GLY LEU PHE GLU ILE ASP GLY SEQRES 9 B 121 VAL ILE TYR PHE PHE GLY VAL ASP GLY VAL LYS ALA PRO SEQRES 10 B 121 GLY ILE TYR GLY HET EDO A 201 4 HET PO4 A 202 5 HETNAM EDO 1,2-ETHANEDIOL HETNAM PO4 PHOSPHATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO C2 H6 O2 FORMUL 4 PO4 O4 P 3- FORMUL 5 HOH *351(H2 O) HELIX 1 AA1 LYS A 90 THR A 94 5 5 SHEET 1 AA1 4 LYS A 8 GLY A 11 0 SHEET 2 AA1 4 LEU A 21 ALA A 26 -1 O ALA A 26 N LYS A 8 SHEET 3 AA1 4 THR A 81 MET A 86 -1 O MET A 86 N LEU A 21 SHEET 4 AA1 4 PHE A 71 GLN A 75 -1 N THR A 72 O GLN A 85 SHEET 1 AA2 6 GLY A 13 GLN A 16 0 SHEET 2 AA2 6 THR A 123 SER A 128 1 O THR A 126 N GLY A 13 SHEET 3 AA2 6 ALA A 95 ARG A 103 -1 N TYR A 97 O THR A 123 SHEET 4 AA2 6 VAL A 35 GLN A 42 -1 N CYS A 36 O ALA A 102 SHEET 5 AA2 6 ARG A 48 LEU A 55 -1 O GLU A 49 N ARG A 41 SHEET 6 AA2 6 THR A 61 TYR A 63 -1 O ASN A 62 N LEU A 53 SHEET 1 AA3 4 GLY A 13 GLN A 16 0 SHEET 2 AA3 4 THR A 123 SER A 128 1 O THR A 126 N GLY A 13 SHEET 3 AA3 4 ALA A 95 ARG A 103 -1 N TYR A 97 O THR A 123 SHEET 4 AA3 4 SER A 118 TRP A 119 -1 O SER A 118 N ALA A 101 SHEET 1 AA4 3 HIS A 30 PRO A 32 0 SHEET 2 AA4 3 GLY B2665 ILE B2669 -1 O THR B2668 N ILE A 31 SHEET 3 AA4 3 LYS B2672 PHE B2676 -1 O PHE B2676 N GLY B2665 SHEET 1 AA5 3 GLY B2595 ILE B2599 0 SHEET 2 AA5 3 LYS B2602 ARG B2607 -1 O PHE B2606 N GLY B2595 SHEET 3 AA5 3 LEU B2610 PRO B2611 -1 O LEU B2610 N ARG B2607 SHEET 1 AA6 2 GLY B2614 GLY B2618 0 SHEET 2 AA6 2 GLY B2621 PHE B2625 -1 O PHE B2625 N GLY B2614 SHEET 1 AA7 2 ARG B2645 LEU B2649 0 SHEET 2 AA7 2 LYS B2652 PHE B2656 -1 O PHE B2656 N ARG B2645 SHEET 1 AA8 2 GLY B2687 ILE B2691 0 SHEET 2 AA8 2 VAL B2694 PHE B2698 -1 O VAL B2694 N ILE B2691 SSBOND 1 CYS A 25 CYS A 99 1555 1555 2.05 SSBOND 2 CYS A 36 CYS A 110 1555 1555 2.04 CRYST1 32.156 71.739 93.405 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 0.031098 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013939 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010706 0.00000