HEADER HYDROLASE 06-FEB-12 4DL8 TITLE CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI DUTPASE WITH DUMP, PLANAR TITLE 2 [ALF3-OPO3] TRANSITION STATE ANALOGUE, MG2+, AND NA+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYURIDINE TRIPHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEOXYURIDINE TRIPHOSPHATE NUCLEOTIDOHYDROLASE; COMPND 5 EC: 3.6.1.23; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 3 ORGANISM_TAXID: 5691; SOURCE 4 STRAIN: 427; SOURCE 5 GENE: TB927.7.5160; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-YSBLLIC KEYWDS ALL ALPHA NTP PYROPHOSPHOHYDROLASE, ALL ALPHA NTP PYROPHOSPHATASE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.R.HEMSWORTH,D.GONZALEZ-PACANOWSKA,K.S.WILSON REVDAT 5 13-SEP-23 4DL8 1 REMARK SEQADV LINK REVDAT 4 15-NOV-17 4DL8 1 REMARK REVDAT 3 06-NOV-13 4DL8 1 JRNL REVDAT 2 18-SEP-13 4DL8 1 JRNL REVDAT 1 07-AUG-13 4DL8 0 JRNL AUTH G.R.HEMSWORTH,D.GONZALEZ-PACANOWSKA,K.S.WILSON JRNL TITL ON THE CATALYTIC MECHANISM OF DIMERIC DUTPASES. JRNL REF BIOCHEM.J. V. 456 81 2013 JRNL REFN ISSN 0264-6021 JRNL PMID 24001052 JRNL DOI 10.1042/BJ20130796 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 28.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 33293 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1661 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) : 2237 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1764 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 166 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.50000 REMARK 3 B22 (A**2) : 0.50000 REMARK 3 B33 (A**2) : -1.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.083 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.055 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.681 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1836 ; 0.016 ; 0.027 REMARK 3 BOND LENGTHS OTHERS (A): 1184 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2493 ; 1.416 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2893 ; 0.944 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 222 ; 5.106 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 84 ;37.527 ;24.881 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 297 ;11.825 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;13.339 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 279 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2022 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 360 ; 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): 1114 ;20.910 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 452 ; 0.606 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1785 ;18.155 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 722 ;21.286 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 708 ;17.605 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4DL8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070469. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.917 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.16, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33398 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.698 REMARK 200 RESOLUTION RANGE LOW (A) : 28.203 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 15.70 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : 0.07800 REMARK 200 FOR THE DATA SET : 23.5000 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) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 15.70 REMARK 200 R MERGE FOR SHELL (I) : 0.92300 REMARK 200 R SYM FOR SHELL (I) : 0.92300 REMARK 200 FOR SHELL : 0.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: REFINED 4DKB REMARK 200 SOFTWARE USED: REFMAC 5.5.0109 REMARK 200 STARTING MODEL: PDB ENTRY 4DKB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM SULFATE, 0.1 M BIS-TRIS REMARK 280 PROPANE, PH 6.5, 20% W/V PEG3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 61.87950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.29500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.29500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 92.81925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.29500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.29500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.93975 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.29500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.29500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 92.81925 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.29500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.29500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.93975 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 61.87950 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: 5830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -106.0 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 61.87950 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 -2 REMARK 465 PRO A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 ASN A 3 REMARK 465 ALA A 4 REMARK 465 ARG A 5 REMARK 465 ARG A 6 REMARK 465 SER A 96 REMARK 465 GLY A 97 REMARK 465 ALA A 98 REMARK 465 VAL A 99 REMARK 465 HIS A 100 REMARK 465 LYS A 101 REMARK 465 ALA A 102 REMARK 465 GLU A 103 REMARK 465 ALA A 104 REMARK 465 GLY A 105 REMARK 465 SER A 106 REMARK 465 ASN A 107 REMARK 465 GLY A 108 REMARK 465 GLU A 109 REMARK 465 SER A 110 REMARK 465 GLY A 111 REMARK 465 LYS A 112 REMARK 465 HIS A 113 REMARK 465 TRP A 114 REMARK 465 CYS A 115 REMARK 465 TYR A 116 REMARK 465 PHE A 117 REMARK 465 ASP A 118 REMARK 465 GLN A 119 REMARK 465 PRO A 120 REMARK 465 ARG A 121 REMARK 465 ALA A 122 REMARK 465 LEU A 123 REMARK 465 PRO A 124 REMARK 465 ALA A 125 REMARK 465 ALA A 126 REMARK 465 GLY A 127 REMARK 465 GLY A 128 REMARK 465 ALA A 129 REMARK 465 GLU A 130 REMARK 465 TYR A 131 REMARK 465 VAL A 132 REMARK 465 ALA A 133 REMARK 465 CYS A 134 REMARK 465 VAL A 135 REMARK 465 GLU A 136 REMARK 465 THR A 137 REMARK 465 PRO A 138 REMARK 465 GLY A 139 REMARK 465 SER A 140 REMARK 465 SER A 141 REMARK 465 LEU A 142 REMARK 465 SER A 143 REMARK 465 ALA A 144 REMARK 465 PRO A 145 REMARK 465 VAL A 146 REMARK 465 SER A 147 REMARK 465 ALA A 148 REMARK 465 ASP A 149 REMARK 465 GLU A 150 REMARK 465 CYS A 151 REMARK 465 ASP A 152 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 30 CG CD CE NZ REMARK 470 ASN A 95 CG OD1 ND2 REMARK 470 ASP A 155 CG OD1 OD2 REMARK 470 PHE A 156 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 176 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 275 CG CD CE NZ REMARK 470 GLU A 276 CG CD OE1 OE2 REMARK 470 LYS A 286 CG CD CE NZ 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 ASN A 63 68.21 32.34 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 MG A 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 48 OE2 REMARK 620 2 GLU A 51 OE2 89.7 REMARK 620 3 UMP A 301 OP2 95.7 173.1 REMARK 620 4 PO4 A 303 O2 169.9 86.9 87.1 REMARK 620 5 HOH A 437 O 86.3 83.4 92.6 83.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 305 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 48 OE1 REMARK 620 2 GLU A 51 OE1 87.4 REMARK 620 3 GLU A 76 OE1 93.8 80.4 REMARK 620 4 ASP A 79 OD2 94.3 173.2 92.9 REMARK 620 5 HOH A 401 O 162.4 85.4 100.8 94.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 306 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 51 OE1 REMARK 620 2 GLU A 76 OE2 80.4 REMARK 620 3 PO4 A 303 O1 72.3 148.3 REMARK 620 4 HOH A 401 O 75.2 97.5 60.4 REMARK 620 5 HOH A 402 O 97.0 90.8 108.1 167.4 REMARK 620 6 HOH A 403 O 158.3 79.6 123.6 99.0 91.7 REMARK 620 7 HOH A 485 O 127.3 152.2 56.5 89.1 87.9 72.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AF3 A 302 AL REMARK 620 N RES CSSEQI ATOM REMARK 620 1 UMP A 301 OP1 REMARK 620 2 AF3 A 302 F1 85.6 REMARK 620 3 AF3 A 302 F2 93.5 86.4 REMARK 620 4 AF3 A 302 F3 91.3 95.2 175.0 REMARK 620 5 PO4 A 303 O1 94.1 175.4 89.0 89.3 REMARK 620 6 HOH A 401 O 171.3 91.6 94.6 80.7 89.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UMP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AF3 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DK2 RELATED DB: PDB REMARK 900 RELATED ID: 4DK4 RELATED DB: PDB REMARK 900 RELATED ID: 4DKB RELATED DB: PDB REMARK 900 RELATED ID: 4DLC RELATED DB: PDB DBREF 4DL8 A 1 287 UNP Q57ZH3 Q57ZH3_TRYB2 1 287 SEQADV 4DL8 GLY A -2 UNP Q57ZH3 EXPRESSION TAG SEQADV 4DL8 PRO A -1 UNP Q57ZH3 EXPRESSION TAG SEQADV 4DL8 ALA A 0 UNP Q57ZH3 EXPRESSION TAG SEQRES 1 A 290 GLY PRO ALA MET LYS ASN ALA ARG ARG VAL SER LEU SER SEQRES 2 A 290 PRO LEU ILE LEU ARG SER LEU ALA GLU LEU GLN ASP GLY SEQRES 3 A 290 LEU ASN THR VAL VAL ASP LYS ASN TRP ARG GLN LEU ARG SEQRES 4 A 290 ARG PRO GLY ASP TRP SER LEU ALA ILE THR MET GLU ALA SEQRES 5 A 290 ALA GLU LEU LEU ASP SER TYR PRO TRP LYS TRP TRP LYS SEQRES 6 A 290 ASN VAL LYS ALA GLN PRO ASP LEU GLN ASN VAL LYS ILE SEQRES 7 A 290 GLU LEU THR ASP ILE LEU HIS PHE SER LEU SER GLY ALA SEQRES 8 A 290 MET GLN VAL SER ASP GLU ASN SER GLY ALA VAL HIS LYS SEQRES 9 A 290 ALA GLU ALA GLY SER ASN GLY GLU SER GLY LYS HIS TRP SEQRES 10 A 290 CYS TYR PHE ASP GLN PRO ARG ALA LEU PRO ALA ALA GLY SEQRES 11 A 290 GLY ALA GLU TYR VAL ALA CYS VAL GLU THR PRO GLY SER SEQRES 12 A 290 SER LEU SER ALA PRO VAL SER ALA ASP GLU CYS ASP LEU SEQRES 13 A 290 ALA ASP PHE MET PHE PHE PRO LEU SER ASP THR ASN ASN SEQRES 14 A 290 ALA LEU ALA SER PHE GLN ASN ILE ILE ARG LEU ALA SER SEQRES 15 A 290 LEU GLN ARG PHE GLN LEU VAL THR SER ALA VAL ILE ALA SEQRES 16 A 290 ALA ALA ASP ASP ILE GLY PHE ASN LEU VAL ALA TYR TYR SEQRES 17 A 290 VAL ALA LYS HIS THR LEU ASN GLY ILE ARG GLN MET LYS SEQRES 18 A 290 GLY TYR LYS ASP GLY THR TYR VAL LYS VAL GLN LYS GLY SEQRES 19 A 290 VAL GLU ASP ASN GLU LEU LEU HIS GLY CYS ILE SER PRO SEQRES 20 A 290 PHE SER LEU ASP ASP VAL THR ASN GLU GLY ASN TYR LYS SEQRES 21 A 290 THR LYS TRP ASP ASP ILE MET HIS ARG VAL TYR ASP ALA SEQRES 22 A 290 PHE GLY THR PRO LYS GLU GLU ARG LEU ASN ILE GLY HIS SEQRES 23 A 290 TRP LEU LYS SER HET UMP A 301 20 HET AF3 A 302 4 HET PO4 A 303 5 HET MG A 304 1 HET MG A 305 1 HET NA A 306 1 HETNAM UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE HETNAM AF3 ALUMINUM FLUORIDE HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETSYN UMP DUMP FORMUL 2 UMP C9 H13 N2 O8 P FORMUL 3 AF3 AL F3 FORMUL 4 PO4 O4 P 3- FORMUL 5 MG 2(MG 2+) FORMUL 7 NA NA 1+ FORMUL 8 HOH *166(H2 O) HELIX 1 1 SER A 10 ASP A 29 1 20 HELIX 2 2 ASN A 31 ARG A 36 1 6 HELIX 3 3 ARG A 37 ASP A 54 1 18 HELIX 4 4 ASP A 69 MET A 89 1 21 HELIX 5 5 ASP A 163 LEU A 180 1 18 HELIX 6 6 ARG A 182 GLY A 198 1 17 HELIX 7 7 ASN A 200 LYS A 218 1 19 HELIX 8 8 GLY A 219 GLY A 223 5 5 HELIX 9 9 LEU A 237 SER A 243 1 7 HELIX 10 10 SER A 246 ASN A 252 1 7 HELIX 11 11 ASN A 255 PHE A 271 1 17 HELIX 12 12 PRO A 274 ARG A 278 5 5 HELIX 13 13 ASN A 280 TRP A 284 5 5 SHEET 1 A 2 VAL A 228 GLN A 229 0 SHEET 2 A 2 VAL A 232 GLU A 233 -1 O VAL A 232 N GLN A 229 LINK OE2 GLU A 48 MG MG A 304 1555 1555 2.07 LINK OE1 GLU A 48 MG MG A 305 1555 1555 2.00 LINK OE2 GLU A 51 MG MG A 304 1555 1555 2.03 LINK OE1 GLU A 51 MG MG A 305 1555 1555 2.14 LINK OE1 GLU A 51 NA NA A 306 1555 1555 2.43 LINK OE1 GLU A 76 MG MG A 305 1555 1555 1.94 LINK OE2 GLU A 76 NA NA A 306 1555 1555 2.21 LINK OD2 ASP A 79 MG MG A 305 1555 1555 2.05 LINK OP1 UMP A 301 AL AF3 A 302 1555 1555 1.91 LINK OP2 UMP A 301 MG MG A 304 1555 1555 1.91 LINK AL AF3 A 302 O1 PO4 A 303 1555 1555 1.89 LINK AL AF3 A 302 O HOH A 401 1555 1555 1.95 LINK O2 PO4 A 303 MG MG A 304 1555 1555 1.95 LINK O1 PO4 A 303 NA NA A 306 1555 1555 2.98 LINK MG MG A 304 O HOH A 437 1555 1555 2.18 LINK MG MG A 305 O HOH A 401 1555 1555 2.06 LINK NA NA A 306 O HOH A 401 1555 1555 2.23 LINK NA NA A 306 O HOH A 402 1555 1555 2.17 LINK NA NA A 306 O HOH A 403 1555 1555 2.35 LINK NA NA A 306 O HOH A 485 1555 1555 2.87 CISPEP 1 PHE A 159 PRO A 160 0 1.41 SITE 1 AC1 20 GLN A 21 LEU A 24 ASN A 25 GLU A 48 SITE 2 AC1 20 LYS A 59 TRP A 60 TRP A 61 ASP A 79 SITE 3 AC1 20 HIS A 82 PHE A 83 ASN A 212 ARG A 215 SITE 4 AC1 20 TYR A 220 LYS A 227 AF3 A 302 PO4 A 303 SITE 5 AC1 20 MG A 304 HOH A 404 HOH A 405 HOH A 437 SITE 1 AC2 14 GLU A 48 GLU A 51 ASP A 79 LYS A 208 SITE 2 AC2 14 ARG A 215 LYS A 227 ASN A 235 UMP A 301 SITE 3 AC2 14 PO4 A 303 MG A 304 MG A 305 NA A 306 SITE 4 AC2 14 HOH A 401 HOH A 485 SITE 1 AC3 11 GLU A 51 LYS A 59 LYS A 62 LYS A 227 SITE 2 AC3 11 UMP A 301 AF3 A 302 MG A 304 NA A 306 SITE 3 AC3 11 HOH A 401 HOH A 437 HOH A 485 SITE 1 AC4 7 GLU A 48 GLU A 51 UMP A 301 AF3 A 302 SITE 2 AC4 7 PO4 A 303 MG A 305 HOH A 437 SITE 1 AC5 8 GLU A 48 GLU A 51 GLU A 76 ASP A 79 SITE 2 AC5 8 AF3 A 302 MG A 304 NA A 306 HOH A 401 SITE 1 AC6 9 GLU A 51 GLU A 76 AF3 A 302 PO4 A 303 SITE 2 AC6 9 MG A 305 HOH A 401 HOH A 402 HOH A 403 SITE 3 AC6 9 HOH A 485 CRYST1 68.590 68.590 123.759 90.00 90.00 90.00 P 43 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 0.014579 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014579 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008080 0.00000