HEADER HYDROLASE 12-DEC-16 5U7W TITLE CRYSTAL STRUCTURE OF A NUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE TITLE 2 (NTPDASE) FROM THE LEGUME TRIFOLIUM REPENS IN COMPLEX WITH ADENINE TITLE 3 AND PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: APYRASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 39-455; COMPND 5 EC: 3.6.1.5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRIFOLIUM REPENS; SOURCE 3 ORGANISM_COMMON: CREEPING WHITE CLOVER; SOURCE 4 ORGANISM_TAXID: 3899; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS APYRASE, NTPDASE, RNASE-H FOLD, MIXED 5 STRAND BETA-SHEET, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.H.CUMMING,E.L.SUMMERS,T.OULAVALLICKAL,N.ROBERTS,V.L.ARCUS REVDAT 5 04-OCT-23 5U7W 1 REMARK REVDAT 4 02-AUG-17 5U7W 1 JRNL REVDAT 3 14-JUN-17 5U7W 1 JRNL REVDAT 2 07-JUN-17 5U7W 1 JRNL REVDAT 1 31-MAY-17 5U7W 0 JRNL AUTH E.L.SUMMERS,M.H.CUMMING,T.OULAVALLICKAL,N.J.ROBERTS, JRNL AUTH 2 V.L.ARCUS JRNL TITL STRUCTURES AND KINETICS FOR PLANT NUCLEOSIDE TRIPHOSPHATE JRNL TITL 2 DIPHOSPHOHYDROLASES SUPPORT A DOMAIN MOTION CATALYTIC JRNL TITL 3 MECHANISM. JRNL REF PROTEIN SCI. V. 26 1627 2017 JRNL REFN ESSN 1469-896X JRNL PMID 28543850 JRNL DOI 10.1002/PRO.3199 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 35652 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1887 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) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1750 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.31 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3084 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 392 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 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): 0.134 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.129 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.086 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.269 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3204 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3011 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4365 ; 2.046 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6930 ; 0.931 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 413 ; 6.712 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 136 ;35.146 ;25.147 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 510 ;14.355 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;18.980 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 485 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3678 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 716 ; 0.001 ; 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): 1628 ; 1.790 ; 1.740 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1627 ; 1.782 ; 1.739 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2033 ; 2.626 ; 2.601 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2034 ; 2.625 ; 2.603 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1576 ; 2.595 ; 2.019 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1569 ; 2.547 ; 2.001 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2315 ; 3.825 ; 2.890 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4200 ; 5.865 ;15.903 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4201 ; 5.865 ;15.907 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 4 A 125 REMARK 3 ORIGIN FOR THE GROUP (A): 3.9915 -8.3690 23.3033 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: -0.0000 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 : A 126 A 411 REMARK 3 ORIGIN FOR THE GROUP (A): -12.6675 6.8426 8.3232 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: -0.0000 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5U7W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1000225464. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44133 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 71.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.72500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.700 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: 5U7P REMARK 200 REMARK 200 REMARK: LARGE THICK PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM DIHYDROGEN REMARK 280 ORTHOPHOSPHATE, 15% PEG 3350, PH 8.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 26.40550 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 THR A 3 REMARK 465 VAL A 181 REMARK 465 THR A 182 REMARK 465 ASP A 183 REMARK 465 GLY A 184 REMARK 465 ARG A 413 REMARK 465 LEU A 414 REMARK 465 MET A 415 REMARK 465 TYR A 416 REMARK 465 PHE A 417 REMARK 465 VAL A 418 REMARK 465 VAL A 419 REMARK 465 GLU A 420 REMARK 465 HIS A 421 REMARK 465 HIS A 422 REMARK 465 HIS A 423 REMARK 465 HIS A 424 REMARK 465 HIS A 425 REMARK 465 HIS A 426 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 GLN A 27 CG CD OE1 NE2 REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 GLU A 75 CD OE1 OE2 REMARK 470 LYS A 80 CG CD CE NZ REMARK 470 ALA A 89 CA CB REMARK 470 LEU A 93 CG CD1 CD2 REMARK 470 ASP A 95 CG OD1 OD2 REMARK 470 ARG A 176 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 180 CG CD CE NZ REMARK 470 LYS A 190 CD CE NZ REMARK 470 ASP A 312 OD1 OD2 REMARK 470 ASN A 314 CB CG OD1 ND2 REMARK 470 LYS A 410 CG CD CE NZ 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 HOH A 800 O HOH A 927 1.88 REMARK 500 O1 PO4 A 502 O HOH A 601 1.92 REMARK 500 O HOH A 605 O HOH A 891 1.93 REMARK 500 O HOH A 612 O HOH A 949 1.98 REMARK 500 O GLU A 412 O HOH A 602 2.00 REMARK 500 OD1 ASP A 257 O HOH A 603 2.06 REMARK 500 OG SER A 205 O HOH A 604 2.06 REMARK 500 O HOH A 918 O HOH A 969 2.06 REMARK 500 O HOH A 726 O HOH A 960 2.08 REMARK 500 OG1 THR A 115 O HOH A 605 2.09 REMARK 500 O HOH A 899 O HOH A 984 2.14 REMARK 500 O HOH A 819 O HOH A 903 2.15 REMARK 500 OE2 GLU A 386 O HOH A 606 2.16 REMARK 500 O HOH A 885 O HOH A 933 2.18 REMARK 500 OG SER A 79 O HOH A 607 2.18 REMARK 500 O HOH A 638 O HOH A 647 2.18 REMARK 500 O HOH A 909 O HOH A 937 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 O HOH A 877 O HOH A 894 2546 1.64 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 ASP A 26 CB - CG - OD1 ANGL. DEV. = 9.5 DEGREES REMARK 500 ARG A 107 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 307 CB - CG - OD2 ANGL. DEV. = -6.1 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 HIS A 223 -114.08 47.16 REMARK 500 TYR A 275 -162.22 -124.20 REMARK 500 THR A 279 -76.32 -82.17 REMARK 500 SER A 299 -118.96 55.05 REMARK 500 GLN A 388 -122.85 47.60 REMARK 500 LYS A 410 -72.21 91.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 127 GLY A 128 131.28 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 ADE A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5U7X RELATED DB: PDB REMARK 900 RELATED ID: 5U7V RELATED DB: PDB REMARK 900 RELATED ID: 5U7P RELATED DB: PDB DBREF 5U7W A 2 418 UNP B9U139 B9U139_TRIRP 39 455 SEQADV 5U7W MET A 1 UNP B9U139 INITIATING METHIONINE SEQADV 5U7W VAL A 419 UNP B9U139 EXPRESSION TAG SEQADV 5U7W GLU A 420 UNP B9U139 EXPRESSION TAG SEQADV 5U7W HIS A 421 UNP B9U139 EXPRESSION TAG SEQADV 5U7W HIS A 422 UNP B9U139 EXPRESSION TAG SEQADV 5U7W HIS A 423 UNP B9U139 EXPRESSION TAG SEQADV 5U7W HIS A 424 UNP B9U139 EXPRESSION TAG SEQADV 5U7W HIS A 425 UNP B9U139 EXPRESSION TAG SEQADV 5U7W HIS A 426 UNP B9U139 EXPRESSION TAG SEQRES 1 A 426 MET GLY THR ILE THR SER TYR ALA VAL VAL PHE ASP ALA SEQRES 2 A 426 GLY SER THR GLY SER ARG VAL HIS VAL TYR HIS PHE ASP SEQRES 3 A 426 GLN ASN LEU ASP LEU LEU HIS ILE GLY LYS ASP VAL GLU SEQRES 4 A 426 PHE TYR ASN LYS ILE GLN PRO GLY LEU SER ALA TYR ALA SEQRES 5 A 426 ASP ASN PRO GLU GLN ALA ALA LYS SER LEU ILE PRO LEU SEQRES 6 A 426 LEU GLU GLN ALA GLU ASN VAL VAL PRO GLU ASP PHE HIS SEQRES 7 A 426 SER LYS THR PRO ILE ARG LEU GLY ALA THR ALA GLY LEU SEQRES 8 A 426 ARG LEU LEU ASP GLY ASP ALA SER GLU ARG ILE LEU GLN SEQRES 9 A 426 ALA VAL ARG ASP MET LEU ASN ASN LYS SER THR PHE ASN SEQRES 10 A 426 VAL GLN PRO ASP ALA VAL SER ILE ILE ASP GLY THR GLN SEQRES 11 A 426 GLU GLY SER TYR LEU TRP VAL THR ILE ASN TYR VAL LEU SEQRES 12 A 426 GLY ASN LEU GLY LYS ARG PHE THR ASN THR VAL GLY VAL SEQRES 13 A 426 ILE ASP LEU GLY GLY GLY SER VAL GLN MET ALA TYR ALA SEQRES 14 A 426 VAL SER LYS LYS THR ALA ARG ASN ALA PRO LYS VAL THR SEQRES 15 A 426 ASP GLY GLU ASP PRO TYR ILE LYS LYS ILE VAL LEU LYS SEQRES 16 A 426 GLY LYS PRO TYR ASP LEU TYR VAL HIS SER TYR LEU HIS SEQRES 17 A 426 PHE GLY ARG GLU ALA SER ARG ALA GLU ILE LEU LYS VAL SEQRES 18 A 426 THR HIS GLY SER ALA SER PRO CYS ILE LEU ALA GLY PHE SEQRES 19 A 426 ASP GLY ILE TYR THR TYR SER GLY GLU GLU PHE LYS ALA SEQRES 20 A 426 SER ALA PRO THR SER GLY ALA ASN PHE ASP LYS CYS LYS SEQRES 21 A 426 LYS ILE ILE GLN LYS ALA LEU LYS LEU ASP TYR PRO CYS SEQRES 22 A 426 PRO TYR GLN ASN CYS THR PHE GLY GLY ILE TRP ASN GLY SEQRES 23 A 426 GLY GLY GLY SER GLY GLN LYS LYS LEU PHE ALA ALA SER SEQRES 24 A 426 SER PHE PHE TYR LEU PRO GLN ASP VAL GLY MET VAL ASP SEQRES 25 A 426 PRO ASN LYS SER ASN LEU LYS LEU ARG PRO VAL ASP LEU SEQRES 26 A 426 GLU ASN LYS ALA LYS ILE VAL CYS THR LEU ASN VAL GLU SEQRES 27 A 426 ASP VAL LYS SER ALA TYR PRO LEU LEU GLU LYS PHE ASN SEQRES 28 A 426 ILE VAL PRO TYR ALA CYS MET ASP LEU ILE TYR GLN TYR SEQRES 29 A 426 GLU LEU LEU VAL ASP GLY PHE GLY LEU ASP PRO LEU GLN SEQRES 30 A 426 GLU ILE THR ALA GLY GLU LYS ILE GLU TYR GLN GLU ALA SEQRES 31 A 426 LEU VAL ASP ALA ALA TRP ALA LEU GLY ASN ALA VAL GLU SEQRES 32 A 426 ALA VAL LEU LEU LEU PRO LYS PHE GLU ARG LEU MET TYR SEQRES 33 A 426 PHE VAL VAL GLU HIS HIS HIS HIS HIS HIS HET ADE A 501 10 HET PO4 A 502 5 HET PO4 A 503 5 HETNAM ADE ADENINE HETNAM PO4 PHOSPHATE ION FORMUL 2 ADE C5 H5 N5 FORMUL 3 PO4 2(O4 P 3-) FORMUL 5 HOH *392(H2 O) HELIX 1 AA1 GLY A 47 ALA A 52 5 6 HELIX 2 AA2 ASN A 54 SER A 61 1 8 HELIX 3 AA3 LEU A 62 VAL A 73 1 12 HELIX 4 AA4 PRO A 74 THR A 81 5 8 HELIX 5 AA5 GLY A 90 LEU A 94 5 5 HELIX 6 AA6 ASP A 97 SER A 114 1 18 HELIX 7 AA7 ASP A 127 LEU A 143 1 17 HELIX 8 AA8 ARG A 149 THR A 153 5 5 HELIX 9 AA9 SER A 171 ASN A 177 1 7 HELIX 10 AB1 GLY A 210 VAL A 221 1 12 HELIX 11 AB2 ASN A 255 LYS A 268 1 14 HELIX 12 AB3 GLY A 289 LYS A 293 5 5 HELIX 13 AB4 SER A 300 VAL A 308 1 9 HELIX 14 AB5 ARG A 321 CYS A 333 1 13 HELIX 15 AB6 ASN A 336 TYR A 344 1 9 HELIX 16 AB7 TYR A 344 PHE A 350 1 7 HELIX 17 AB8 ILE A 352 PRO A 354 5 3 HELIX 18 AB9 TYR A 355 VAL A 368 1 14 HELIX 19 AC1 TRP A 396 LEU A 407 1 12 SHEET 1 AA1 5 PHE A 40 ILE A 44 0 SHEET 2 AA1 5 SER A 18 PHE A 25 -1 N VAL A 20 O ASN A 42 SHEET 3 AA1 5 SER A 6 ALA A 13 -1 N SER A 6 O PHE A 25 SHEET 4 AA1 5 ILE A 83 ALA A 87 1 O ARG A 84 N PHE A 11 SHEET 5 AA1 5 VAL A 123 ILE A 125 1 O SER A 124 N LEU A 85 SHEET 1 AA2 7 ILE A 189 LEU A 194 0 SHEET 2 AA2 7 LYS A 197 LEU A 207 -1 O LEU A 201 N LYS A 190 SHEET 3 AA2 7 SER A 163 VAL A 170 -1 N VAL A 164 O TYR A 206 SHEET 4 AA2 7 GLY A 155 LEU A 159 -1 N VAL A 156 O ALA A 167 SHEET 5 AA2 7 LEU A 295 SER A 299 1 O ALA A 298 N ILE A 157 SHEET 6 AA2 7 ILE A 379 GLY A 382 1 O THR A 380 N ALA A 297 SHEET 7 AA2 7 ASN A 317 LEU A 320 -1 N LEU A 320 O ILE A 379 SHEET 1 AA3 2 ASP A 235 TYR A 240 0 SHEET 2 AA3 2 GLU A 243 SER A 248 -1 O ALA A 247 N GLY A 236 SHEET 1 AA4 2 LYS A 384 TYR A 387 0 SHEET 2 AA4 2 ALA A 390 ASP A 393 -1 O VAL A 392 N ILE A 385 SSBOND 1 CYS A 229 CYS A 259 1555 1555 2.07 SSBOND 2 CYS A 273 CYS A 278 1555 1555 2.05 SSBOND 3 CYS A 333 CYS A 357 1555 1555 2.01 CISPEP 1 GLN A 45 PRO A 46 0 1.19 SITE 1 AC1 4 TYR A 303 GLN A 306 ASP A 307 PHE A 350 SITE 1 AC2 8 GLY A 161 GLY A 162 SER A 163 HOH A 601 SITE 2 AC2 8 HOH A 623 HOH A 638 HOH A 647 HOH A 649 SITE 1 AC3 4 GLY A 14 SER A 15 THR A 16 ARG A 19 CRYST1 53.910 52.811 72.180 90.00 94.96 90.00 P 1 21 1 2 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 0.018549 0.000000 0.001610 0.00000 SCALE2 0.000000 0.018936 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013906 0.00000