HEADER TOXIN 01-OCT-24 9GY5 TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN FROM THE BONT-LIKE TOXIN TITLE 2 COMPLEX PG1 OF PAENICLOSTRIDIUM GHONII COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATALYTIC DOMAIN FROM THE BONT-LIKE TOXIN COMPLEX PG1 OF COMPND 3 PAENICLOSTRIDIUM GHONII; COMPND 4 CHAIN: A; COMPND 5 EC: 3.4.24.69; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: RECOMBINANT PROTEIN WITH FIRST TWO RESIDUES FROM COMPND 8 EXPRESSION VECTOR. DISORDERED REGIONS NOT INCLUDED IN THE STRUCTURE COMPND 9 (ONE LOOP AND C-TER). NOTE PROTEIN IS NOT IN UNIPROT YET - SEE NCBI COMPND 10 ENTRY WP_250673407 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARACLOSTRIDIUM GHONII; SOURCE 3 ORGANISM_TAXID: 29358; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NEUROTOXIN, METALLOPROTEASE, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR G.MASUYER,P.STENMARK REVDAT 2 26-NOV-25 9GY5 1 JRNL REVDAT 1 15-OCT-25 9GY5 0 JRNL AUTH P.G.LEE,L.YIN,X.WEI,J.SHI,G.MASUYER,T.G.WENTZ,P.CHEN,Y.XU, JRNL AUTH 2 J.LIANG,H.ZHANG,S.PERSSON KOSENINA,B.LOBB,M.MANSFIELD, JRNL AUTH 3 S.S.GILL,S.PELLETT,P.STENMARK,A.C.DOXEY,M.DONG JRNL TITL IDENTIFICATION AND CHARACTERIZATION OF BOTULINUM JRNL TITL 2 NEUROTOXIN-LIKE TWO-COMPONENT TOXINS IN PAENICLOSTRIDIUM JRNL TITL 3 GHONII. JRNL REF SCI ADV V. 11 X6145 2025 JRNL REFN ESSN 2375-2548 JRNL PMID 41223264 JRNL DOI 10.1126/SCIADV.ADX6145 REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 48264 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.035 REMARK 3 FREE R VALUE TEST SET COUNT : 2430 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3312 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.4410 REMARK 3 BIN FREE R VALUE SET COUNT : 157 REMARK 3 BIN FREE R VALUE : 0.4270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2881 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 166 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.94700 REMARK 3 B22 (A**2) : 0.94700 REMARK 3 B33 (A**2) : -3.07200 REMARK 3 B12 (A**2) : 0.47400 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): 0.123 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.138 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.298 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2959 ; 0.003 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2842 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3998 ; 1.109 ; 1.832 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6569 ; 0.397 ; 1.776 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 360 ; 6.052 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 9 ; 9.330 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 544 ;11.404 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 461 ; 0.052 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3355 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 631 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 614 ; 0.204 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 38 ; 0.143 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1464 ; 0.173 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 167 ; 0.152 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.012 ; 0.200 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): 1447 ; 2.374 ; 4.247 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1446 ; 2.372 ; 4.247 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1804 ; 3.844 ; 7.621 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1805 ; 3.844 ; 7.625 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1512 ; 2.733 ; 4.635 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1513 ; 2.733 ; 4.636 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2194 ; 4.490 ; 8.383 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2195 ; 4.489 ; 8.384 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 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 0 A 1009 REMARK 3 ORIGIN FOR THE GROUP (A): 23.2248 55.6710 22.0369 REMARK 3 T TENSOR REMARK 3 T11: 0.1795 T22: 0.1384 REMARK 3 T33: 0.0224 T12: 0.1074 REMARK 3 T13: -0.0067 T23: 0.0270 REMARK 3 L TENSOR REMARK 3 L11: 0.3347 L22: 0.3681 REMARK 3 L33: 0.9792 L12: 0.0093 REMARK 3 L13: -0.4262 L23: 0.1721 REMARK 3 S TENSOR REMARK 3 S11: 0.0141 S12: 0.0280 S13: 0.0290 REMARK 3 S21: -0.1101 S22: -0.0572 S23: 0.0498 REMARK 3 S31: -0.1449 S32: -0.0064 S33: 0.0431 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9GY5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1292142152. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JAN-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48514 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 61.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 37.90 REMARK 200 R MERGE (I) : 0.15600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 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) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 39.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.300 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 (%): 55.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.0 5% V/V TACSIMATE TM REMARK 280 PH 7.0 10% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 5,000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 91.51067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 183.02133 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 91.51067 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 183.02133 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 91.51067 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 183.02133 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 91.51067 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 183.02133 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 TOTAL BURIED SURFACE AREA: 1240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -85.0 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 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 616 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 GLY A -1 REMARK 465 GLU A 54 REMARK 465 GLY A 55 REMARK 465 GLY A 56 REMARK 465 ILE A 57 REMARK 465 THR A 58 REMARK 465 SER A 59 REMARK 465 LYS A 60 REMARK 465 LYS A 61 REMARK 465 GLU A 62 REMARK 465 LYS A 63 REMARK 465 ALA A 64 REMARK 465 HIS A 65 REMARK 465 VAL A 66 REMARK 465 ASP A 67 REMARK 465 LYS A 68 REMARK 465 LYS A 69 REMARK 465 LYS A 378 REMARK 465 MET A 379 REMARK 465 ARG A 380 REMARK 465 ARG A 381 REMARK 465 ARG A 382 REMARK 465 ALA A 383 REMARK 465 LEU A 384 REMARK 465 ARG A 385 REMARK 465 ASN A 386 REMARK 465 PHE A 387 REMARK 465 LYS A 388 REMARK 465 CYS A 389 REMARK 465 THR A 390 REMARK 465 ILE A 391 REMARK 465 GLN A 392 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 O VAL A 222 OG SER A 234 2.19 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 OE1 GLU A 253 OE1 GLU A 253 8675 2.08 REMARK 500 REMARK 500 REMARK: NULL 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 137 CG - CD - NE ANGL. DEV. = -13.6 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 GLN A 18 -85.75 -111.72 REMARK 500 THR A 52 -118.37 -115.38 REMARK 500 LEU A 227 47.43 -97.19 REMARK 500 LYS A 228 -54.89 -167.38 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 137 0.12 SIDE CHAIN 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 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 202 NE2 REMARK 620 2 HIS A 206 NE2 104.6 REMARK 620 3 GLU A 241 OE1 135.5 89.5 REMARK 620 4 GLU A 241 OE2 84.8 118.6 52.1 REMARK 620 5 ACT A 406 O 85.8 99.0 134.1 142.5 REMARK 620 6 ACT A 406 OXT 127.1 121.7 72.9 93.5 64.3 REMARK 620 N 1 2 3 4 5 DBREF 9GY5 A -1 392 PDB 9GY5 9GY5 -1 392 SEQRES 1 A 394 GLY HIS MET ILE PRO ILE ASN ILE LYS ASP PHE ASN TYR SEQRES 2 A 394 SER ASP PRO VAL ASN ASN GLN ASP ILE ILE LEU VAL LYS SEQRES 3 A 394 ASN GLU LYS GLY SER PHE ASP LYS GLY PHE PHE VAL ALA SEQRES 4 A 394 ASP LYS ILE LEU LEU VAL PRO ALA ARG TYR GLY ASN ILE SEQRES 5 A 394 SER THR ASP GLU GLY GLY ILE THR SER LYS LYS GLU LYS SEQRES 6 A 394 ALA HIS VAL ASP LYS LYS ILE TYR LEU GLU THR ASP SER SEQRES 7 A 394 GLU LYS ASN GLU TYR LEU LYS ASN MET THR THR LEU LEU SEQRES 8 A 394 LYS ARG MET ASN SER TYR SER THR GLY ASN LYS LEU LEU SEQRES 9 A 394 ASN LEU ILE ILE LYS GLY GLU PRO ILE TYR SER LYS ASP SEQRES 10 A 394 LEU GLN GLY LYS PHE ILE GLU GLN THR PRO SER ARG TYR SEQRES 11 A 394 LEU ASP THR ASN THR GLY LYS ARG ARG VAL ASN VAL MET SEQRES 12 A 394 ILE THR GLY PRO GLY SER ASN VAL LEU THR LYS LYS CYS SEQRES 13 A 394 THR HIS ASN GLY MET GLY LEU GLU ASN ASP PRO ASN GLY SEQRES 14 A 394 LYS HIS SER ASN GLY THR GLY ILE LEU SER THR ILE GLU SEQRES 15 A 394 PHE SER PRO ASN TYR LEU ILE ALA TYR ASN LYS CYS VAL SEQRES 16 A 394 ALA ASP PRO VAL LEU THR LEU PHE HIS GLU LEU VAL HIS SEQRES 17 A 394 SER MET HIS ASN LEU TYR GLY ILE ALA PHE PRO ASP ASN SEQRES 18 A 394 VAL LYS VAL PRO TYR ASN ALA LEU LYS ASP LYS ASN LEU SEQRES 19 A 394 VAL SER GLY GLU GLU ALA LEU SER GLU ILE LEU THR PHE SEQRES 20 A 394 GLY GLY LYS ASP LEU THR THR GLU HIS LEU GLU THR LEU SEQRES 21 A 394 TRP LYS LYS LEU ALA GLU THR VAL ILE ILE VAL LYS ASP SEQRES 22 A 394 PHE VAL LYS THR ASP THR GLN ALA LYS ASP VAL PHE LEU SEQRES 23 A 394 ASN ASN LEU ARG PHE LEU SER LYS ASN GLU ASN ILE LYS SEQRES 24 A 394 ILE ASP THR ILE GLU ASP ILE VAL ASN GLY THR LEU LYS SEQRES 25 A 394 ILE LYS ASN ASN ILE SER ASN LEU THR GLU CYS GLU PHE SEQRES 26 A 394 CYS LYS GLU ILE GLY ASP VAL ARG ILE ARG THR ARG TYR SEQRES 27 A 394 ALA VAL HIS SER GLU ASP VAL THR PRO VAL GLU VAL VAL SEQRES 28 A 394 ASP PHE LYS ASN ASN TYR LYS LEU ASN SER GLY PHE LEU SEQRES 29 A 394 GLU GLY GLN ASP ILE SER LYS LYS TYR PHE ILE THR ASN SEQRES 30 A 394 PRO PRO LYS MET ARG ARG ARG ALA LEU ARG ASN PHE LYS SEQRES 31 A 394 CYS THR ILE GLN HET ZN A 401 1 HET SO4 A 402 5 HET SO4 A 403 5 HET SO4 A 404 5 HET SO4 A 405 5 HET ACT A 406 4 HET GOL A 407 6 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN ZN 2+ FORMUL 3 SO4 4(O4 S 2-) FORMUL 7 ACT C2 H3 O2 1- FORMUL 8 GOL C3 H8 O3 FORMUL 9 HOH *166(H2 O) HELIX 1 AA1 THR A 74 SER A 94 1 21 HELIX 2 AA2 TYR A 95 GLY A 108 1 14 HELIX 3 AA3 ASP A 195 TYR A 212 1 18 HELIX 4 AA4 LEU A 239 GLY A 246 1 8 HELIX 5 AA5 GLY A 247 LEU A 250 5 4 HELIX 6 AA6 THR A 251 LYS A 274 1 24 HELIX 7 AA7 ASP A 276 LYS A 292 1 17 HELIX 8 AA8 THR A 300 SER A 316 1 17 HELIX 9 AA9 THR A 319 GLY A 328 1 10 HELIX 10 AB1 ASP A 350 ASN A 354 1 5 SHEET 1 AA1 6 ILE A 20 LYS A 24 0 SHEET 2 AA1 6 PHE A 30 ALA A 37 -1 O ASP A 31 N VAL A 23 SHEET 3 AA1 6 ILE A 40 VAL A 43 -1 O LEU A 42 N PHE A 34 SHEET 4 AA1 6 VAL A 140 THR A 143 1 O ILE A 142 N LEU A 41 SHEET 5 AA1 6 SER A 177 GLU A 180 1 O ILE A 179 N MET A 141 SHEET 6 AA1 6 LYS A 153 THR A 155 -1 N THR A 155 O THR A 178 SHEET 1 AA2 2 SER A 113 LYS A 114 0 SHEET 2 AA2 2 PHE A 120 ILE A 121 -1 O ILE A 121 N SER A 113 SHEET 1 AA3 2 TYR A 128 THR A 131 0 SHEET 2 AA3 2 GLY A 134 ARG A 137 -1 O ARG A 136 N LEU A 129 SHEET 1 AA4 4 CYS A 192 VAL A 193 0 SHEET 2 AA4 4 TYR A 185 TYR A 189 -1 N TYR A 189 O CYS A 192 SHEET 3 AA4 4 VAL A 343 VAL A 348 -1 O VAL A 346 N LEU A 186 SHEET 4 AA4 4 PHE A 372 THR A 374 -1 O ILE A 373 N GLU A 347 SHEET 1 AA5 2 ASN A 219 LYS A 221 0 SHEET 2 AA5 2 GLU A 236 ALA A 238 -1 O GLU A 237 N VAL A 220 SHEET 1 AA6 2 TYR A 355 LYS A 356 0 SHEET 2 AA6 2 GLY A 360 PHE A 361 -1 O GLY A 360 N LYS A 356 LINK NE2 HIS A 202 ZN ZN A 401 1555 1555 2.05 LINK NE2 HIS A 206 ZN ZN A 401 1555 1555 2.05 LINK OE1 GLU A 241 ZN ZN A 401 1555 1555 2.38 LINK OE2 GLU A 241 ZN ZN A 401 1555 1555 2.62 LINK ZN ZN A 401 O ACT A 406 1555 1555 2.05 LINK ZN ZN A 401 OXT ACT A 406 1555 1555 2.03 CRYST1 79.217 79.217 274.532 90.00 90.00 120.00 P 64 2 2 12 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 0.012624 0.007288 0.000000 0.00000 SCALE2 0.000000 0.014576 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003643 0.00000 CONECT 1476 2883 CONECT 1510 2883 CONECT 1780 2883 CONECT 1781 2883 CONECT 2883 1476 1510 1780 1781 CONECT 2883 2905 2906 CONECT 2884 2885 2886 2887 2888 CONECT 2885 2884 CONECT 2886 2884 CONECT 2887 2884 CONECT 2888 2884 CONECT 2889 2890 2891 2892 2893 CONECT 2890 2889 CONECT 2891 2889 CONECT 2892 2889 CONECT 2893 2889 CONECT 2894 2895 2896 2897 2898 CONECT 2895 2894 CONECT 2896 2894 CONECT 2897 2894 CONECT 2898 2894 CONECT 2899 2900 2901 2902 2903 CONECT 2900 2899 CONECT 2901 2899 CONECT 2902 2899 CONECT 2903 2899 CONECT 2904 2905 2906 2907 CONECT 2905 2883 2904 CONECT 2906 2883 2904 CONECT 2907 2904 CONECT 2908 2909 2910 CONECT 2909 2908 CONECT 2910 2908 2911 2912 CONECT 2911 2910 CONECT 2912 2910 2913 CONECT 2913 2912 MASTER 437 0 7 10 18 0 0 6 3078 1 36 31 END