PDB Short entry for 3BX4 HEADER TOXIN 11-JAN-08 3BX4 TITLE CRYSTAL STRUCTURE OF THE SNAKE VENOM TOXIN AGGRETIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AGGRETIN ALPHA CHAIN; COMPND 3 CHAIN: A, C; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: AGGRETIN BETA CHAIN; COMPND 6 CHAIN: B, D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AGKISTRODON RHODOSTOMA; SOURCE 3 ORGANISM_COMMON: MALAYAN PIT VIPER; SOURCE 4 SECRETION: VENOM; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: AGKISTRODON RHODOSTOMA; SOURCE 7 ORGANISM_COMMON: MALAYAN PIT VIPER; SOURCE 8 SECRETION: VENOM KEYWDS TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR E.HOOLEY,E.PAPAGRIGORIOU,A.NAVDAEV,A.PANDEY,J.M.CLEMETSON, AUTHOR 2 K.J.CLEMETSON,J.EMSLEY REVDAT 4 30-AUG-23 3BX4 1 REMARK REVDAT 3 13-JUL-11 3BX4 1 VERSN REVDAT 2 24-FEB-09 3BX4 1 VERSN REVDAT 1 26-AUG-08 3BX4 0 JRNL AUTH E.HOOLEY,E.PAPAGRIGORIOU,A.NAVDAEV,A.V.PANDEY,J.M.CLEMETSON, JRNL AUTH 2 K.J.CLEMETSON,J.EMSLEY JRNL TITL THE CRYSTAL STRUCTURE OF THE PLATELET ACTIVATOR AGGRETIN JRNL TITL 2 REVEALS A NOVEL (ALPHABETA)2 DIMERIC STRUCTURE. JRNL REF BIOCHEMISTRY V. 47 7831 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18597489 JRNL DOI 10.1021/BI800528T REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 73565 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3853 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5312 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 270 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4189 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 324 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.00000 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): 0.100 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.101 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.070 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.121 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4320 ; 0.020 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5873 ; 1.876 ; 1.908 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 511 ; 6.428 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 225 ;32.643 ;24.844 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 675 ;14.680 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;18.582 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 568 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3363 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1932 ; 0.214 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2872 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 282 ; 0.179 ; 0.200 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): 55 ; 0.217 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.195 ; 0.200 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): 2587 ; 1.337 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4052 ; 2.173 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2056 ; 2.929 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1818 ; 4.251 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A C REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 6 A 134 5 REMARK 3 1 C 6 C 134 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 513 ; 0.24 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 516 ; 0.64 ; 5.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 513 ; 2.59 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 516 ; 3.05 ; 10.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : B D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 B 4 B 121 4 REMARK 3 1 D 4 D 121 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 B (A): 947 ; 0.44 ; 0.50 REMARK 3 MEDIUM THERMAL 2 B (A**2): 947 ; 2.87 ; 2.00 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3BX4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000046065. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : SILICON CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77418 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 14.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 <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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1FVU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4M AMMONIUM SULPHATE, 25MM AMMONIUM REMARK 280 ACETATE, 2% ISOPROPANOL, PH 5.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 32.15900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.65250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.15900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.65250 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11710 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 GLY A 1 REMARK 465 LEU A 2 REMARK 465 GLU A 3 REMARK 465 TYR A 136 REMARK 465 MET B -22 REMARK 465 GLY B -21 REMARK 465 ARG B -20 REMARK 465 PHE B -19 REMARK 465 ILE B -18 REMARK 465 PHE B -17 REMARK 465 VAL B -16 REMARK 465 SER B -15 REMARK 465 PHE B -14 REMARK 465 GLY B -13 REMARK 465 LEU B -12 REMARK 465 LEU B -11 REMARK 465 VAL B -10 REMARK 465 VAL B -9 REMARK 465 PHE B -8 REMARK 465 LEU B -7 REMARK 465 SER B -6 REMARK 465 LEU B -5 REMARK 465 SER B -4 REMARK 465 GLY B -3 REMARK 465 THR B -2 REMARK 465 GLY B -1 REMARK 465 ALA B 0 REMARK 465 ASP B 1 REMARK 465 GLY C 1 REMARK 465 LEU C 2 REMARK 465 MET D -22 REMARK 465 GLY D -21 REMARK 465 ARG D -20 REMARK 465 PHE D -19 REMARK 465 ILE D -18 REMARK 465 PHE D -17 REMARK 465 VAL D -16 REMARK 465 SER D -15 REMARK 465 PHE D -14 REMARK 465 GLY D -13 REMARK 465 LEU D -12 REMARK 465 LEU D -11 REMARK 465 VAL D -10 REMARK 465 VAL D -9 REMARK 465 PHE D -8 REMARK 465 LEU D -7 REMARK 465 SER D -6 REMARK 465 LEU D -5 REMARK 465 SER D -4 REMARK 465 GLY D -3 REMARK 465 THR D -2 REMARK 465 GLY D -1 REMARK 465 ALA D 0 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 14 CG CD OE1 NE2 REMARK 480 GLU A 22 CD OE1 OE2 REMARK 480 GLU A 46 OE1 OE2 REMARK 480 LYS A 79 CG CD CE NZ REMARK 480 LYS A 117 CD CE NZ REMARK 480 LYS B 35 CE NZ REMARK 480 ARG B 84 CG CD NE CZ NH1 NH2 REMARK 480 GLU C 3 CB CG CD OE1 OE2 REMARK 480 LYS C 79 CD CE NZ REMARK 480 TYR C 136 CG CD1 CD2 CE1 CE2 CZ OH REMARK 480 ASP D 1 CB CG OD1 OD2 REMARK 480 LYS D 31 CE NZ REMARK 480 GLU D 46 CG CD OE1 OE2 REMARK 480 ARG D 56 CG CD NE CZ NH1 NH2 REMARK 480 LYS D 60 CB CG CD CE NZ REMARK 480 ARG D 84 CD NE CZ NH1 NH2 REMARK 480 GLU D 92 CD OE1 OE2 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 CE LYS A 79 OE1 GLN C 77 1.65 REMARK 500 OE1 GLU C 28 O HOH C 205 1.93 REMARK 500 OG SER C 59 O HOH C 239 1.97 REMARK 500 N CYS B 2 O HOH B 202 2.00 REMARK 500 OE1 GLU C 28 O HOH C 192 2.03 REMARK 500 NZ LYS A 79 CD GLN C 77 2.05 REMARK 500 O HOH A 189 O HOH C 140 2.05 REMARK 500 NZ LYS A 79 OE1 GLN C 77 2.15 REMARK 500 NZ LYS D 31 O HOH D 153 2.17 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 NH1 ARG B 100 OE2 GLU C 22 2655 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 22 CG GLU A 22 CD -0.119 REMARK 500 LYS A 79 CB LYS A 79 CG -0.258 REMARK 500 GLU C 3 CA GLU C 3 CB -0.701 REMARK 500 GLU D 46 CB GLU D 46 CG -0.127 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 GLU A 46 CG - CD - OE1 ANGL. DEV. = -13.7 DEGREES REMARK 500 LEU A 133 CA - CB - CG ANGL. DEV. = 13.9 DEGREES REMARK 500 LEU A 133 CB - CG - CD2 ANGL. DEV. = -12.1 DEGREES REMARK 500 LYS B 35 CG - CD - CE ANGL. DEV. = 19.3 DEGREES REMARK 500 LYS B 35 CD - CE - NZ ANGL. DEV. = 22.4 DEGREES REMARK 500 GLU C 3 CB - CA - C ANGL. DEV. = 38.0 DEGREES REMARK 500 GLU C 3 N - CA - CB ANGL. DEV. = -11.3 DEGREES REMARK 500 GLU C 3 CA - CB - CG ANGL. DEV. = 17.6 DEGREES REMARK 500 ASP C 27 CB - CG - OD1 ANGL. DEV. = 6.8 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 13 56.42 39.52 REMARK 500 GLN A 14 -1.24 80.93 REMARK 500 GLU A 37 -130.88 54.47 REMARK 500 SER A 94 -72.36 -125.14 REMARK 500 ALA A 128 170.04 -58.44 REMARK 500 LYS B 60 -133.30 65.06 REMARK 500 ASP B 89 40.37 -144.35 REMARK 500 ASP C 4 122.67 72.73 REMARK 500 ASP C 13 -130.32 47.03 REMARK 500 GLU C 37 -129.47 52.21 REMARK 500 SER C 94 -79.85 -124.05 REMARK 500 LYS C 104 45.92 -106.07 REMARK 500 ARG C 116 -65.25 -120.83 REMARK 500 GLU D 10 59.80 33.07 REMARK 500 GLU D 19 109.15 -53.71 REMARK 500 LYS D 60 -127.02 59.18 REMARK 500 ASN D 86 -61.12 -97.09 REMARK 500 ASP D 89 57.13 -147.16 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 GLU A 46 0.14 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 124 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 124 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 137 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 137 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 125 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 125 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 126 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 127 DBREF 3BX4 A 1 136 UNP Q9I841 Q9I841_AGKRH 1 136 DBREF 3BX4 B -22 123 UNP Q9I840 Q9I840_AGKRH 1 146 DBREF 3BX4 C 1 136 UNP Q9I841 Q9I841_AGKRH 1 136 DBREF 3BX4 D -22 123 UNP Q9I840 Q9I840_AGKRH 1 146 SEQRES 1 A 136 GLY LEU GLU ASP CYS ASP PHE GLY TRP SER PRO TYR ASP SEQRES 2 A 136 GLN HIS CYS TYR GLN ALA PHE ASN GLU GLN LYS THR TRP SEQRES 3 A 136 ASP GLU ALA GLU LYS PHE CYS ARG ALA GLN GLU ASN GLY SEQRES 4 A 136 ALA HIS LEU ALA SER ILE GLU SER ASN GLY GLU ALA ASP SEQRES 5 A 136 PHE VAL SER TRP LEU ILE SER GLN LYS ASP GLU LEU ALA SEQRES 6 A 136 ASP GLU ASP TYR VAL TRP ILE GLY LEU ARG ALA GLN ASN SEQRES 7 A 136 LYS GLU GLN GLN CYS SER SER GLU TRP SER ASP GLY SER SEQRES 8 A 136 SER VAL SER TYR GLU ASN LEU ILE ASP LEU HIS THR LYS SEQRES 9 A 136 LYS CYS GLY ALA LEU GLU LYS LEU THR GLY PHE ARG LYS SEQRES 10 A 136 TRP VAL ASN TYR TYR CYS GLU GLN MET HIS ALA PHE VAL SEQRES 11 A 136 CYS LYS LEU LEU PRO TYR SEQRES 1 B 146 MET GLY ARG PHE ILE PHE VAL SER PHE GLY LEU LEU VAL SEQRES 2 B 146 VAL PHE LEU SER LEU SER GLY THR GLY ALA ASP CYS PRO SEQRES 3 B 146 SER GLY TRP SER SER TYR GLU GLY HIS CYS TYR LYS PRO SEQRES 4 B 146 PHE ASN GLU PRO LYS ASN TRP ALA ASP ALA GLU ARG PHE SEQRES 5 B 146 CYS LYS LEU GLN PRO LYS HIS SER HIS LEU VAL SER PHE SEQRES 6 B 146 GLN SER ALA GLU GLU ALA ASP PHE VAL VAL LYS LEU THR SEQRES 7 B 146 ARG PRO ARG LEU LYS ALA ASN LEU VAL TRP MET GLY LEU SEQRES 8 B 146 SER ASN ILE TRP HIS GLY CYS ASN TRP GLN TRP SER ASP SEQRES 9 B 146 GLY ALA ARG LEU ASN TYR LYS ASP TRP GLN GLU GLN SER SEQRES 10 B 146 GLU CYS LEU ALA PHE ARG GLY VAL HIS THR GLU TRP LEU SEQRES 11 B 146 ASN MET ASP CYS SER SER THR CYS SER PHE VAL CYS LYS SEQRES 12 B 146 PHE LYS ALA SEQRES 1 C 136 GLY LEU GLU ASP CYS ASP PHE GLY TRP SER PRO TYR ASP SEQRES 2 C 136 GLN HIS CYS TYR GLN ALA PHE ASN GLU GLN LYS THR TRP SEQRES 3 C 136 ASP GLU ALA GLU LYS PHE CYS ARG ALA GLN GLU ASN GLY SEQRES 4 C 136 ALA HIS LEU ALA SER ILE GLU SER ASN GLY GLU ALA ASP SEQRES 5 C 136 PHE VAL SER TRP LEU ILE SER GLN LYS ASP GLU LEU ALA SEQRES 6 C 136 ASP GLU ASP TYR VAL TRP ILE GLY LEU ARG ALA GLN ASN SEQRES 7 C 136 LYS GLU GLN GLN CYS SER SER GLU TRP SER ASP GLY SER SEQRES 8 C 136 SER VAL SER TYR GLU ASN LEU ILE ASP LEU HIS THR LYS SEQRES 9 C 136 LYS CYS GLY ALA LEU GLU LYS LEU THR GLY PHE ARG LYS SEQRES 10 C 136 TRP VAL ASN TYR TYR CYS GLU GLN MET HIS ALA PHE VAL SEQRES 11 C 136 CYS LYS LEU LEU PRO TYR SEQRES 1 D 146 MET GLY ARG PHE ILE PHE VAL SER PHE GLY LEU LEU VAL SEQRES 2 D 146 VAL PHE LEU SER LEU SER GLY THR GLY ALA ASP CYS PRO SEQRES 3 D 146 SER GLY TRP SER SER TYR GLU GLY HIS CYS TYR LYS PRO SEQRES 4 D 146 PHE ASN GLU PRO LYS ASN TRP ALA ASP ALA GLU ARG PHE SEQRES 5 D 146 CYS LYS LEU GLN PRO LYS HIS SER HIS LEU VAL SER PHE SEQRES 6 D 146 GLN SER ALA GLU GLU ALA ASP PHE VAL VAL LYS LEU THR SEQRES 7 D 146 ARG PRO ARG LEU LYS ALA ASN LEU VAL TRP MET GLY LEU SEQRES 8 D 146 SER ASN ILE TRP HIS GLY CYS ASN TRP GLN TRP SER ASP SEQRES 9 D 146 GLY ALA ARG LEU ASN TYR LYS ASP TRP GLN GLU GLN SER SEQRES 10 D 146 GLU CYS LEU ALA PHE ARG GLY VAL HIS THR GLU TRP LEU SEQRES 11 D 146 ASN MET ASP CYS SER SER THR CYS SER PHE VAL CYS LYS SEQRES 12 D 146 PHE LYS ALA HET SO4 A 137 5 HET SO4 A 138 5 HET SO4 B 124 5 HET SO4 B 125 5 HET SO4 C 137 5 HET SO4 C 138 5 HET SO4 D 124 5 HET SO4 D 125 5 HET SO4 D 126 5 HET GOL D 127 6 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 SO4 9(O4 S 2-) FORMUL 14 GOL C3 H8 O3 FORMUL 15 HOH *324(H2 O) HELIX 1 1 THR A 25 ALA A 35 1 11 HELIX 2 2 SER A 47 GLN A 60 1 14 HELIX 3 3 LYS A 61 ALA A 65 5 5 HELIX 4 4 LEU A 112 GLY A 114 5 3 HELIX 5 5 ASN B 22 GLN B 33 1 12 HELIX 6 6 SER B 44 ARG B 56 1 13 HELIX 7 7 THR C 25 ALA C 35 1 11 HELIX 8 8 SER C 47 GLN C 60 1 14 HELIX 9 9 LYS C 61 ALA C 65 5 5 HELIX 10 10 LEU C 112 GLY C 114 5 3 HELIX 11 11 ASN D 22 LEU D 32 1 11 HELIX 12 12 SER D 44 LYS D 60 1 17 SHEET 1 A 6 SER A 10 TYR A 12 0 SHEET 2 A 6 HIS A 15 LYS A 24 -1 O TYR A 17 N SER A 10 SHEET 3 A 6 HIS A 127 LEU A 133 -1 O PHE A 129 N PHE A 20 SHEET 4 A 6 TYR A 69 ALA A 76 1 N TRP A 71 O ALA A 128 SHEET 5 A 6 CYS A 106 GLU A 110 -1 O LEU A 109 N VAL A 70 SHEET 6 A 6 TRP A 118 TYR A 121 -1 O TYR A 121 N CYS A 106 SHEET 1 B 4 HIS A 41 LEU A 42 0 SHEET 2 B 4 HIS A 127 LEU A 133 -1 O LYS A 132 N HIS A 41 SHEET 3 B 4 TYR A 69 ALA A 76 1 N TRP A 71 O ALA A 128 SHEET 4 B 4 TRP B 77 TRP B 79 -1 O GLN B 78 N ARG A 75 SHEET 1 C 4 SER B 7 TYR B 9 0 SHEET 2 C 4 HIS B 12 LYS B 21 -1 O TYR B 14 N SER B 7 SHEET 3 C 4 CYS B 115 LYS B 122 -1 O PHE B 121 N CYS B 13 SHEET 4 C 4 HIS B 38 LEU B 39 -1 N HIS B 38 O LYS B 120 SHEET 1 D 6 SER B 7 TYR B 9 0 SHEET 2 D 6 HIS B 12 LYS B 21 -1 O TYR B 14 N SER B 7 SHEET 3 D 6 CYS B 115 LYS B 122 -1 O PHE B 121 N CYS B 13 SHEET 4 D 6 LEU B 63 TRP B 65 1 N TRP B 65 O SER B 116 SHEET 5 D 6 GLU B 95 ARG B 100 -1 O PHE B 99 N VAL B 64 SHEET 6 D 6 TRP B 106 ASP B 110 -1 O MET B 109 N CYS B 96 SHEET 1 E 6 SER C 10 TYR C 12 0 SHEET 2 E 6 HIS C 15 LYS C 24 -1 O TYR C 17 N SER C 10 SHEET 3 E 6 HIS C 127 LEU C 133 -1 O LEU C 133 N CYS C 16 SHEET 4 E 6 TYR C 69 ALA C 76 1 N TRP C 71 O ALA C 128 SHEET 5 E 6 CYS C 106 GLU C 110 -1 O GLY C 107 N LEU C 74 SHEET 6 E 6 TRP C 118 TYR C 121 -1 O TYR C 121 N CYS C 106 SHEET 1 F 4 HIS C 41 LEU C 42 0 SHEET 2 F 4 HIS C 127 LEU C 133 -1 O LYS C 132 N HIS C 41 SHEET 3 F 4 TYR C 69 ALA C 76 1 N TRP C 71 O ALA C 128 SHEET 4 F 4 TRP D 77 TRP D 79 -1 O GLN D 78 N ARG C 75 SHEET 1 G 4 SER D 7 TYR D 9 0 SHEET 2 G 4 HIS D 12 LYS D 21 -1 O TYR D 14 N SER D 7 SHEET 3 G 4 CYS D 115 LYS D 122 -1 O PHE D 121 N CYS D 13 SHEET 4 G 4 HIS D 38 LEU D 39 -1 N HIS D 38 O LYS D 120 SHEET 1 H 6 SER D 7 TYR D 9 0 SHEET 2 H 6 HIS D 12 LYS D 21 -1 O TYR D 14 N SER D 7 SHEET 3 H 6 CYS D 115 LYS D 122 -1 O PHE D 121 N CYS D 13 SHEET 4 H 6 LEU D 63 SER D 69 1 N TRP D 65 O SER D 116 SHEET 5 H 6 GLU D 95 ARG D 100 -1 O PHE D 99 N VAL D 64 SHEET 6 H 6 HIS D 103 ASP D 110 -1 O MET D 109 N CYS D 96 SSBOND 1 CYS A 5 CYS A 16 1555 1555 2.46 SSBOND 2 CYS A 33 CYS A 131 1555 1555 2.04 SSBOND 3 CYS A 83 CYS B 75 1555 1555 2.04 SSBOND 4 CYS A 106 CYS A 123 1555 1555 2.02 SSBOND 5 CYS B 2 CYS B 13 1555 1555 2.08 SSBOND 6 CYS B 30 CYS B 119 1555 1555 2.03 SSBOND 7 CYS B 96 CYS B 111 1555 1555 2.05 SSBOND 8 CYS C 5 CYS C 16 1555 1555 2.14 SSBOND 9 CYS C 33 CYS C 131 1555 1555 2.05 SSBOND 10 CYS C 83 CYS D 75 1555 1555 2.06 SSBOND 11 CYS C 106 CYS C 123 1555 1555 2.07 SSBOND 12 CYS D 2 CYS D 13 1555 1555 2.09 SSBOND 13 CYS D 30 CYS D 119 1555 1555 2.06 SSBOND 14 CYS D 96 CYS D 111 1555 1555 2.08 SITE 1 AC1 5 HIS D 73 GLY D 74 CYS D 75 ASN D 76 SITE 2 AC1 5 TRP D 77 SITE 1 AC2 4 GLY B 74 CYS B 75 ASN B 76 TRP B 77 SITE 1 AC3 3 TYR A 12 GLY A 49 LYS D 15 SITE 1 AC4 2 PHE C 7 GLY C 8 SITE 1 AC5 3 ARG A 75 GLN A 81 LYS A 105 SITE 1 AC6 7 GLY B 5 LYS B 15 TYR C 12 ASP C 13 SITE 2 AC6 7 SER C 47 GLY C 49 GLU C 50 SITE 1 AC7 4 PHE D 17 ASN D 18 GLU D 19 ARG D 58 SITE 1 AC8 2 ASN D 70 HIS D 73 SITE 1 AC9 4 ARG C 75 GLN C 81 THR C 103 LYS C 105 SITE 1 BC1 3 TRP D 72 HIS D 73 TRP D 77 CRYST1 64.318 91.305 118.916 90.00 90.00 90.00 P 21 21 2 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 0.015548 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010952 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008409 0.00000