HEADER HYDROLASE 15-DEC-09 3L2B TITLE CRYSTAL STRUCTURE OF THE CBS AND DRTGG DOMAINS OF THE REGULATORY TITLE 2 REGION OF CLOSTRIDIUM PERFRINGENS PYROPHOSPHATASE COMPLEXED WITH TITLE 3 ACTIVATOR, DIADENOSINE TETRAPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE MANGANASE-DEPENDENT INORGANIC PYROPHOSPHATASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: REGULATORY REGION (UNP RESIDUES 66-306); COMPND 5 EC: 3.6.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PERFRINGENS; SOURCE 3 ORGANISM_TAXID: 195102; SOURCE 4 STRAIN: STR. 13; SOURCE 5 GENE: CPE2055; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS CLOSTRIDIUM PERFRINGENS, FAMILY II, INORGANIC, PYROPHOSPHATASE, CBS KEYWDS 2 DOMAIN, BATEMAN DOMAIN, AP4A, DIADENOSINE POLYPHOSPHATE, DRTGG, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.TUOMINEN,A.SALMINEN,E.OKSANEN,J.JAMSEN,O.HEIKKILA,L.LEHTIO, AUTHOR 2 N.N.MAGRETOVA,A.GOLDMAN,A.A.BAYKOV,R.LAHTI REVDAT 2 01-NOV-23 3L2B 1 REMARK SEQADV REVDAT 1 21-APR-10 3L2B 0 JRNL AUTH H.TUOMINEN,A.SALMINEN,E.OKSANEN,J.JAMSEN,O.HEIKKILA, JRNL AUTH 2 L.LEHTIO,N.N.MAGRETOVA,A.GOLDMAN,A.A.BAYKOV,R.LAHTI JRNL TITL CRYSTAL STRUCTURES OF THE CBS AND DRTGG DOMAINS OF THE JRNL TITL 2 REGULATORY REGION OF CLOSTRIDIUMPERFRINGENS PYROPHOSPHATASE JRNL TITL 3 COMPLEXED WITH THE INHIBITOR, AMP, AND ACTIVATOR, JRNL TITL 4 DIADENOSINE TETRAPHOSPHATE. JRNL REF J.MOL.BIOL. 2010 JRNL REFN ESSN 1089-8638 JRNL PMID 20303981 JRNL DOI 10.1016/J.JMB.2010.03.019 REMARK 2 REMARK 2 RESOLUTION. 2.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0078 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) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 23255 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) : 0.209 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1298 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) : 2.27 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1130 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE SET COUNT : 58 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3551 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 55.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.48000 REMARK 3 B22 (A**2) : -1.22000 REMARK 3 B33 (A**2) : -3.26000 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): 0.322 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.241 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.180 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.299 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3672 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2371 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5000 ; 1.341 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5899 ; 1.219 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 465 ; 5.995 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 145 ;39.399 ;26.483 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 676 ;14.524 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;20.855 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 616 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3971 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 613 ; 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): 2319 ; 0.716 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 926 ; 0.133 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3784 ; 1.347 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1353 ; 2.042 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1214 ; 3.193 ; 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 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 65 A 297 REMARK 3 ORIGIN FOR THE GROUP (A): 16.9520 2.7460 -7.6510 REMARK 3 T TENSOR REMARK 3 T11: 0.0842 T22: 0.1861 REMARK 3 T33: 0.0435 T12: -0.0573 REMARK 3 T13: 0.0161 T23: -0.0149 REMARK 3 L TENSOR REMARK 3 L11: 0.7379 L22: 4.1186 REMARK 3 L33: 0.5833 L12: 1.6853 REMARK 3 L13: -0.1359 L23: -0.6983 REMARK 3 S TENSOR REMARK 3 S11: -0.0939 S12: 0.0279 S13: 0.0301 REMARK 3 S21: -0.1608 S22: 0.1483 S23: 0.0151 REMARK 3 S31: 0.0592 S32: 0.0927 S33: -0.0543 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 67 B 296 REMARK 3 ORIGIN FOR THE GROUP (A): 17.6010 2.1920 17.1970 REMARK 3 T TENSOR REMARK 3 T11: 0.1102 T22: 0.1715 REMARK 3 T33: 0.0397 T12: -0.0258 REMARK 3 T13: -0.0005 T23: 0.0298 REMARK 3 L TENSOR REMARK 3 L11: 0.4934 L22: 3.9210 REMARK 3 L33: 1.6346 L12: 1.3829 REMARK 3 L13: 0.0962 L23: -0.0016 REMARK 3 S TENSOR REMARK 3 S11: 0.1700 S12: 0.0334 S13: -0.0775 REMARK 3 S21: 0.2370 S22: -0.1278 S23: -0.0636 REMARK 3 S31: -0.1010 S32: 0.1883 S33: -0.0421 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 U VALUES: WITH TLS ADDED REMARK 4 REMARK 4 3L2B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056743. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979260 REMARK 200 MONOCHROMATOR : SILICON REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM Q315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE, XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24554 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.270 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : 0.05300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.37400 REMARK 200 R SYM FOR SHELL (I) : 0.37400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600 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: 3L31 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 4000, 100MM TRIS/HCL PH 8.5, REMARK 280 200MM LISO4, 0.25MM AP4A, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 31.92350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.16700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.88200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.16700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.92350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.88200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL 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 GLY A 62 REMARK 465 SER A 63 REMARK 465 HIS A 64 REMARK 465 HIS A 298 REMARK 465 LEU A 299 REMARK 465 ILE A 300 REMARK 465 SER A 301 REMARK 465 THR A 302 REMARK 465 HIS A 303 REMARK 465 LYS A 304 REMARK 465 LYS A 305 REMARK 465 LYS A 306 REMARK 465 GLY B 62 REMARK 465 SER B 63 REMARK 465 HIS B 64 REMARK 465 MET B 65 REMARK 465 VAL B 66 REMARK 465 PHE B 297 REMARK 465 HIS B 298 REMARK 465 LEU B 299 REMARK 465 ILE B 300 REMARK 465 SER B 301 REMARK 465 THR B 302 REMARK 465 HIS B 303 REMARK 465 LYS B 304 REMARK 465 LYS B 305 REMARK 465 LYS B 306 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 159 CG CD CE NZ REMARK 470 LYS B 270 NZ 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 TYR A 124 CE2 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 TYR A 124 CZ TYR A 124 CE2 0.182 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 TYR A 124 CG - CD2 - CE2 ANGL. DEV. = 6.5 DEGREES REMARK 500 TYR A 124 CZ - CE2 - CD2 ANGL. DEV. = -15.1 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 ARG A 277 28.69 46.52 REMARK 500 ILE B 127 124.33 -32.91 REMARK 500 ASN B 131 37.12 -98.26 REMARK 500 ARG B 277 3.27 83.43 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 B4P A 1 DBREF 3L2B A 66 306 UNP Q8XIQ9 Q8XIQ9_CLOPE 66 306 DBREF 3L2B B 66 306 UNP Q8XIQ9 Q8XIQ9_CLOPE 66 306 SEQADV 3L2B GLY A 62 UNP Q8XIQ9 EXPRESSION TAG SEQADV 3L2B SER A 63 UNP Q8XIQ9 EXPRESSION TAG SEQADV 3L2B HIS A 64 UNP Q8XIQ9 EXPRESSION TAG SEQADV 3L2B MET A 65 UNP Q8XIQ9 EXPRESSION TAG SEQADV 3L2B GLY B 62 UNP Q8XIQ9 EXPRESSION TAG SEQADV 3L2B SER B 63 UNP Q8XIQ9 EXPRESSION TAG SEQADV 3L2B HIS B 64 UNP Q8XIQ9 EXPRESSION TAG SEQADV 3L2B MET B 65 UNP Q8XIQ9 EXPRESSION TAG SEQRES 1 A 245 GLY SER HIS MET VAL LYS LEU LYS VAL GLU ASP LEU GLU SEQRES 2 A 245 MET ASP LYS ILE ALA PRO LEU ALA PRO GLU VAL SER LEU SEQRES 3 A 245 LYS MET ALA TRP ASN ILE MET ARG ASP LYS ASN LEU LYS SEQRES 4 A 245 SER ILE PRO VAL ALA ASP GLY ASN ASN HIS LEU LEU GLY SEQRES 5 A 245 MET LEU SER THR SER ASN ILE THR ALA THR TYR MET ASP SEQRES 6 A 245 ILE TRP ASP SER ASN ILE LEU ALA LYS SER ALA THR SER SEQRES 7 A 245 LEU ASP ASN ILE LEU ASP THR LEU SER ALA GLU ALA GLN SEQRES 8 A 245 ASN ILE ASN GLU GLU ARG LYS VAL PHE PRO GLY LYS VAL SEQRES 9 A 245 VAL VAL ALA ALA MET GLN ALA GLU SER LEU LYS GLU PHE SEQRES 10 A 245 ILE SER GLU GLY ASP ILE ALA ILE ALA GLY ASP ARG ALA SEQRES 11 A 245 GLU ILE GLN ALA GLU LEU ILE GLU LEU LYS VAL SER LEU SEQRES 12 A 245 LEU ILE VAL THR GLY GLY HIS THR PRO SER LYS GLU ILE SEQRES 13 A 245 ILE GLU LEU ALA LYS LYS ASN ASN ILE THR VAL ILE THR SEQRES 14 A 245 THR PRO HIS ASP SER PHE THR ALA SER ARG LEU ILE VAL SEQRES 15 A 245 GLN SER LEU PRO VAL ASP TYR VAL MET THR LYS ASP ASN SEQRES 16 A 245 LEU VAL ALA VAL SER THR ASP ASP LEU VAL GLU ASP VAL SEQRES 17 A 245 LYS VAL THR MET SER GLU THR ARG TYR SER ASN TYR PRO SEQRES 18 A 245 VAL ILE ASP GLU ASN ASN LYS VAL VAL GLY SER ILE ALA SEQRES 19 A 245 ARG PHE HIS LEU ILE SER THR HIS LYS LYS LYS SEQRES 1 B 245 GLY SER HIS MET VAL LYS LEU LYS VAL GLU ASP LEU GLU SEQRES 2 B 245 MET ASP LYS ILE ALA PRO LEU ALA PRO GLU VAL SER LEU SEQRES 3 B 245 LYS MET ALA TRP ASN ILE MET ARG ASP LYS ASN LEU LYS SEQRES 4 B 245 SER ILE PRO VAL ALA ASP GLY ASN ASN HIS LEU LEU GLY SEQRES 5 B 245 MET LEU SER THR SER ASN ILE THR ALA THR TYR MET ASP SEQRES 6 B 245 ILE TRP ASP SER ASN ILE LEU ALA LYS SER ALA THR SER SEQRES 7 B 245 LEU ASP ASN ILE LEU ASP THR LEU SER ALA GLU ALA GLN SEQRES 8 B 245 ASN ILE ASN GLU GLU ARG LYS VAL PHE PRO GLY LYS VAL SEQRES 9 B 245 VAL VAL ALA ALA MET GLN ALA GLU SER LEU LYS GLU PHE SEQRES 10 B 245 ILE SER GLU GLY ASP ILE ALA ILE ALA GLY ASP ARG ALA SEQRES 11 B 245 GLU ILE GLN ALA GLU LEU ILE GLU LEU LYS VAL SER LEU SEQRES 12 B 245 LEU ILE VAL THR GLY GLY HIS THR PRO SER LYS GLU ILE SEQRES 13 B 245 ILE GLU LEU ALA LYS LYS ASN ASN ILE THR VAL ILE THR SEQRES 14 B 245 THR PRO HIS ASP SER PHE THR ALA SER ARG LEU ILE VAL SEQRES 15 B 245 GLN SER LEU PRO VAL ASP TYR VAL MET THR LYS ASP ASN SEQRES 16 B 245 LEU VAL ALA VAL SER THR ASP ASP LEU VAL GLU ASP VAL SEQRES 17 B 245 LYS VAL THR MET SER GLU THR ARG TYR SER ASN TYR PRO SEQRES 18 B 245 VAL ILE ASP GLU ASN ASN LYS VAL VAL GLY SER ILE ALA SEQRES 19 B 245 ARG PHE HIS LEU ILE SER THR HIS LYS LYS LYS HET B4P A 1 53 HETNAM B4P BIS(ADENOSINE)-5'-TETRAPHOSPHATE FORMUL 3 B4P C20 H28 N10 O19 P4 FORMUL 4 HOH *74(H2 O) HELIX 1 1 LYS A 69 LEU A 73 5 5 HELIX 2 2 SER A 86 LYS A 97 1 12 HELIX 3 3 THR A 117 ASP A 126 1 10 HELIX 4 4 ASN A 131 SER A 136 1 6 HELIX 5 5 SER A 139 LEU A 147 1 9 HELIX 6 6 GLN A 171 PHE A 178 5 8 HELIX 7 7 ARG A 190 LEU A 200 1 11 HELIX 8 8 SER A 214 ASN A 225 1 12 HELIX 9 9 ASP A 234 ILE A 242 1 9 HELIX 10 10 VAL A 243 LEU A 246 5 4 HELIX 11 11 PRO A 247 MET A 252 1 6 HELIX 12 12 LEU A 265 ARG A 277 1 13 HELIX 13 13 LYS B 69 LEU B 73 5 5 HELIX 14 14 SER B 86 ASN B 98 1 13 HELIX 15 15 THR B 117 ASP B 126 1 10 HELIX 16 16 ASN B 131 SER B 136 1 6 HELIX 17 17 SER B 139 LEU B 147 1 9 HELIX 18 18 GLN B 171 PHE B 178 5 8 HELIX 19 19 ARG B 190 LEU B 200 1 11 HELIX 20 20 SER B 214 ASN B 225 1 12 HELIX 21 21 ASP B 234 VAL B 243 1 10 HELIX 22 22 GLN B 244 LEU B 246 5 3 HELIX 23 23 PRO B 247 MET B 252 1 6 HELIX 24 24 LEU B 265 ARG B 277 1 13 SHEET 1 A 2 SER A 101 ALA A 105 0 SHEET 2 A 2 LEU A 111 SER A 116 -1 O LEU A 112 N VAL A 104 SHEET 1 B 5 GLU A 150 ASN A 153 0 SHEET 2 B 5 THR A 227 THR A 230 -1 O VAL A 228 N GLN A 152 SHEET 3 B 5 LEU A 204 VAL A 207 1 N VAL A 207 O ILE A 229 SHEET 4 B 5 ILE A 184 ALA A 187 1 N ALA A 187 O ILE A 206 SHEET 5 B 5 VAL A 165 VAL A 167 1 N VAL A 166 O ILE A 186 SHEET 1 C 3 VAL A 260 SER A 261 0 SHEET 2 C 3 ASN A 280 ILE A 284 1 O ILE A 284 N VAL A 260 SHEET 3 C 3 VAL A 290 ALA A 295 -1 O VAL A 291 N VAL A 283 SHEET 1 D 2 SER B 101 ALA B 105 0 SHEET 2 D 2 LEU B 111 SER B 116 -1 O LEU B 112 N VAL B 104 SHEET 1 E 5 GLU B 150 ASN B 153 0 SHEET 2 E 5 THR B 227 THR B 230 -1 O VAL B 228 N GLN B 152 SHEET 3 E 5 LEU B 204 VAL B 207 1 N VAL B 207 O ILE B 229 SHEET 4 E 5 ILE B 184 ALA B 187 1 N ALA B 185 O ILE B 206 SHEET 5 E 5 VAL B 165 VAL B 167 1 N VAL B 166 O ILE B 186 SHEET 1 F 3 VAL B 260 SER B 261 0 SHEET 2 F 3 ASN B 280 ILE B 284 1 O PRO B 282 N VAL B 260 SHEET 3 F 3 VAL B 290 ALA B 295 -1 O VAL B 291 N VAL B 283 SITE 1 AC1 24 HOH A 20 HOH A 25 HOH A 31 LYS A 100 SITE 2 AC1 24 MET A 114 SER A 116 SER A 118 ASN A 256 SITE 3 AC1 24 LEU A 257 VAL A 258 TYR A 278 SER A 279 SITE 4 AC1 24 ASN A 280 TYR A 281 HOH A 316 LYS B 100 SITE 5 AC1 24 SER B 116 SER B 118 LEU B 257 VAL B 258 SITE 6 AC1 24 TYR B 278 SER B 279 ASN B 280 HOH B 315 CRYST1 63.847 71.764 116.334 90.00 90.00 90.00 P 21 21 21 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 0.015662 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013935 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008596 0.00000