HEADER TRANSFERASE 25-OCT-06 2NOM TITLE TERMINAL URIDYLYL TRANSFERASE 4 FROM TRYPANOSOMA BRUCEI WITH BOUND TITLE 2 DUTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA URIDYLYL TRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.7.7.52; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 3 ORGANISM_TAXID: 5691; SOURCE 4 GENE: 841358, TB11.01.7300; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS TUTASE, TRYPANOSOMA, NUCLEOTIDYLTRANSFERASE, UTP-BINDING, RNA- KEYWDS 2 EDITING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.LUECKE,J.STAGNO REVDAT 4 30-AUG-23 2NOM 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2NOM 1 VERSN REVDAT 2 07-AUG-07 2NOM 1 HEADER REVDAT 1 20-FEB-07 2NOM 0 JRNL AUTH J.STAGNO,I.APHASIZHEVA,A.ROSENGARTH,H.LUECKE,R.APHASIZHEV JRNL TITL UTP-BOUND AND APO STRUCTURES OF A MINIMAL RNA JRNL TITL 2 URIDYLYLTRANSFERASE. JRNL REF J.MOL.BIOL. V. 366 882 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17189640 JRNL DOI 10.1016/J.JMB.2006.11.065 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 26857 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) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.301 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1393 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1850 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4645 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 125 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.07000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.499 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.320 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.266 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.434 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.912 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.864 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4807 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6530 ; 1.422 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 572 ; 5.775 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 229 ;36.299 ;23.275 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 799 ;19.412 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;18.144 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 724 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3633 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2340 ; 0.221 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3249 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 229 ; 0.186 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.108 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 58 ; 0.259 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.185 ; 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): 2952 ; 0.730 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4678 ; 1.292 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2089 ; 1.591 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1852 ; 2.541 ; 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 : 1.20 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 2NOM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000040116. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAR-06 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 : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK 9.2L REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26868 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 41.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.480 REMARK 200 R MERGE (I) : 0.17800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.56 REMARK 200 R MERGE FOR SHELL (I) : 0.50900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2IKF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CACODYLATE PH 6.5, 200 REMARK 280 MM MAGNESIUM CHLORIDE, 18% PEG-8000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277K 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 20.82950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 VAL A 20 REMARK 465 SER A 21 REMARK 465 LYS A 22 REMARK 465 ASP A 23 REMARK 465 LEU A 24 REMARK 465 VAL A 333 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 ASP B 23 REMARK 465 LEU B 24 REMARK 465 HIS B 25 REMARK 465 THR B 26 REMARK 465 ARG B 27 REMARK 465 HIS B 28 REMARK 465 VAL B 29 REMARK 465 ASP B 30 REMARK 465 ALA B 31 REMARK 465 THR B 32 REMARK 465 TYR B 33 REMARK 465 ARG B 34 REMARK 465 LEU B 35 REMARK 465 VAL B 36 REMARK 465 LEU B 37 REMARK 465 ASP B 38 REMARK 465 CYS B 39 REMARK 465 VAL B 40 REMARK 465 ALA B 41 REMARK 465 ALA B 42 REMARK 465 VAL B 43 REMARK 465 ASP B 44 REMARK 465 PRO B 45 REMARK 465 LEU B 46 REMARK 465 MET B 47 REMARK 465 ARG B 48 REMARK 465 LEU B 49 REMARK 465 HIS B 61 REMARK 465 GLU B 62 REMARK 465 LYS B 63 REMARK 465 GLY B 64 REMARK 465 SER B 65 REMARK 465 THR B 75 REMARK 465 ASP B 76 REMARK 465 VAL B 77 REMARK 465 GLU B 78 REMARK 465 ASP B 79 REMARK 465 GLY B 80 REMARK 465 ALA B 86 REMARK 465 THR B 87 REMARK 465 GLN B 88 REMARK 465 VAL B 89 REMARK 465 ALA B 90 REMARK 465 LYS B 91 REMARK 465 ALA B 99 REMARK 465 LYS B 100 REMARK 465 LEU B 101 REMARK 465 ALA B 102 REMARK 465 ARG B 103 REMARK 465 VAL B 104 REMARK 465 ILE B 105 REMARK 465 ARG B 106 REMARK 465 GLN B 107 REMARK 465 LYS B 108 REMARK 465 HIS B 109 REMARK 465 LEU B 110 REMARK 465 SER B 111 REMARK 465 TRP B 112 REMARK 465 ASN B 113 REMARK 465 VAL B 114 REMARK 465 GLU B 115 REMARK 465 GLU B 116 REMARK 465 VAL B 117 REMARK 465 ARG B 118 REMARK 465 ARG B 119 REMARK 465 THR B 120 REMARK 465 ARG B 121 REMARK 465 VAL B 122 REMARK 465 PRO B 123 REMARK 465 VAL B 124 REMARK 465 VAL B 125 REMARK 465 ARG B 126 REMARK 465 VAL B 127 REMARK 465 LYS B 128 REMARK 465 GLY B 129 REMARK 465 GLY B 130 REMARK 465 GLY B 131 REMARK 465 ALA B 132 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 OD1 ASP A 68 O HOH A 581 2.16 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 27 -76.90 -56.32 REMARK 500 ASP A 66 -168.28 -69.85 REMARK 500 ASP A 79 68.79 -100.02 REMARK 500 TRP A 274 66.94 -104.09 REMARK 500 ARG A 283 84.66 -176.35 REMARK 500 LEU B 72 -155.66 -152.22 REMARK 500 ASN B 73 82.32 49.86 REMARK 500 ILE B 97 38.25 -98.71 REMARK 500 ASN B 203 18.03 59.14 REMARK 500 ASP B 232 32.70 -78.26 REMARK 500 ILE B 332 41.55 -89.21 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 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 66 OD2 REMARK 620 2 ASP A 68 OD2 92.5 REMARK 620 3 DUT A 501 O1B 144.8 83.2 REMARK 620 4 DUT A 501 O3G 91.8 140.0 70.9 REMARK 620 5 HOH A 556 O 128.9 121.4 81.2 84.9 REMARK 620 6 HOH A 590 O 80.5 75.1 64.6 66.4 140.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 66 OD1 REMARK 620 2 ASP A 66 OD2 47.3 REMARK 620 3 ASP A 68 OD1 124.4 105.4 REMARK 620 4 ASP A 68 OD2 104.9 64.0 47.8 REMARK 620 5 ASP A 136 OD2 75.2 116.8 84.5 123.4 REMARK 620 6 HOH A 588 O 139.7 172.3 73.6 111.7 70.9 REMARK 620 7 HOH A 589 O 67.3 94.4 159.8 150.6 83.2 87.3 REMARK 620 8 HOH A 590 O 104.7 68.6 104.6 68.3 168.1 104.1 85.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUT A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUT B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IKF RELATED DB: PDB REMARK 900 SAME ENZYME WITH DIFFERENT SUBSTRATE. DBREF 2NOM A 1 333 UNP Q381M1 Q381M1_9TRYP 1 333 DBREF 2NOM B 1 333 UNP Q381M1 Q381M1_9TRYP 1 333 SEQADV 2NOM MET A -19 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM GLY A -18 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM SER A -17 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM SER A -16 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM HIS A -15 UNP Q381M1 EXPRESSION TAG SEQADV 2NOM HIS A -14 UNP Q381M1 EXPRESSION TAG SEQADV 2NOM HIS A -13 UNP Q381M1 EXPRESSION TAG SEQADV 2NOM HIS A -12 UNP Q381M1 EXPRESSION TAG SEQADV 2NOM HIS A -11 UNP Q381M1 EXPRESSION TAG SEQADV 2NOM HIS A -10 UNP Q381M1 EXPRESSION TAG SEQADV 2NOM SER A -9 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM SER A -8 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM GLY A -7 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM LEU A -6 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM VAL A -5 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM PRO A -4 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM ARG A -3 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM GLY A -2 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM SER A -1 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM HIS A 0 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM MET B -19 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM GLY B -18 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM SER B -17 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM SER B -16 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM HIS B -15 UNP Q381M1 EXPRESSION TAG SEQADV 2NOM HIS B -14 UNP Q381M1 EXPRESSION TAG SEQADV 2NOM HIS B -13 UNP Q381M1 EXPRESSION TAG SEQADV 2NOM HIS B -12 UNP Q381M1 EXPRESSION TAG SEQADV 2NOM HIS B -11 UNP Q381M1 EXPRESSION TAG SEQADV 2NOM HIS B -10 UNP Q381M1 EXPRESSION TAG SEQADV 2NOM SER B -9 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM SER B -8 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM GLY B -7 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM LEU B -6 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM VAL B -5 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM PRO B -4 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM ARG B -3 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM GLY B -2 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM SER B -1 UNP Q381M1 CLONING ARTIFACT SEQADV 2NOM HIS B 0 UNP Q381M1 CLONING ARTIFACT SEQRES 1 A 353 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 353 LEU VAL PRO ARG GLY SER HIS MET PRO PRO SER PRO ALA SEQRES 3 A 353 VAL VAL GLY ARG SER LEU VAL ASN SER PHE LYS GLN PHE SEQRES 4 A 353 VAL SER LYS ASP LEU HIS THR ARG HIS VAL ASP ALA THR SEQRES 5 A 353 TYR ARG LEU VAL LEU ASP CYS VAL ALA ALA VAL ASP PRO SEQRES 6 A 353 LEU MET ARG LEU TYR THR PHE GLY SER THR VAL VAL TYR SEQRES 7 A 353 GLY VAL HIS GLU LYS GLY SER ASP VAL ASP PHE VAL VAL SEQRES 8 A 353 LEU ASN LYS THR ASP VAL GLU ASP GLY LYS GLY GLY ASP SEQRES 9 A 353 ALA ALA THR GLN VAL ALA LYS GLY LEU GLN ALA ASP ILE SEQRES 10 A 353 LEU ALA LYS LEU ALA ARG VAL ILE ARG GLN LYS HIS LEU SEQRES 11 A 353 SER TRP ASN VAL GLU GLU VAL ARG ARG THR ARG VAL PRO SEQRES 12 A 353 VAL VAL ARG VAL LYS GLY GLY GLY ALA VAL ASP PHE ASP SEQRES 13 A 353 ILE THR ALA TYR ARG ARG ASN GLY VAL ARG ASN SER ALA SEQRES 14 A 353 LEU LEU ARG ALA TYR PHE GLU GLN ASN PRO PRO CYS ARG SEQRES 15 A 353 TRP LEU SER MET SER ILE LYS ARG TRP SER LYS GLN THR SEQRES 16 A 353 GLY LEU ASN ALA SER VAL ILE GLY GLY SER ILE THR SER SEQRES 17 A 353 TYR GLY PHE ASN LEU MET VAL VAL TYR TYR LEU LEU GLN SEQRES 18 A 353 ARG ASN HIS LEU GLN PHE VAL PRO PRO SER THR ILE ASP SEQRES 19 A 353 VAL SER ARG VAL GLU PRO LEU PRO PRO HIS LEU PRO LEU SEQRES 20 A 353 GLU GLU PRO ALA ASP GLU GLY LEU GLU LEU GLY THR GLN SEQRES 21 A 353 VAL LEU ASP PHE LEU HIS PHE PHE LEU HIS GLU PHE ASP SEQRES 22 A 353 SER ASP LYS GLN VAL ILE SER LEU ASN ARG PRO GLY ILE SEQRES 23 A 353 THR THR LYS GLU GLU LEU ASP TRP THR LYS SER ALA GLU SEQRES 24 A 353 ASP PHE ALA ARG MET ASN GLY GLU LYS VAL HIS TYR GLN SEQRES 25 A 353 TRP CYS ILE GLU ASP PRO TYR GLU LEU ASN LEU ASN VAL SEQRES 26 A 353 GLY ARG ASN VAL THR PRO LEU LYS ARG ASP PHE LEU ARG SEQRES 27 A 353 ARG HIS LEU GLU LYS ALA ARG ASP THR ALA LEU LEU THR SEQRES 28 A 353 ILE VAL SEQRES 1 B 353 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 353 LEU VAL PRO ARG GLY SER HIS MET PRO PRO SER PRO ALA SEQRES 3 B 353 VAL VAL GLY ARG SER LEU VAL ASN SER PHE LYS GLN PHE SEQRES 4 B 353 VAL SER LYS ASP LEU HIS THR ARG HIS VAL ASP ALA THR SEQRES 5 B 353 TYR ARG LEU VAL LEU ASP CYS VAL ALA ALA VAL ASP PRO SEQRES 6 B 353 LEU MET ARG LEU TYR THR PHE GLY SER THR VAL VAL TYR SEQRES 7 B 353 GLY VAL HIS GLU LYS GLY SER ASP VAL ASP PHE VAL VAL SEQRES 8 B 353 LEU ASN LYS THR ASP VAL GLU ASP GLY LYS GLY GLY ASP SEQRES 9 B 353 ALA ALA THR GLN VAL ALA LYS GLY LEU GLN ALA ASP ILE SEQRES 10 B 353 LEU ALA LYS LEU ALA ARG VAL ILE ARG GLN LYS HIS LEU SEQRES 11 B 353 SER TRP ASN VAL GLU GLU VAL ARG ARG THR ARG VAL PRO SEQRES 12 B 353 VAL VAL ARG VAL LYS GLY GLY GLY ALA VAL ASP PHE ASP SEQRES 13 B 353 ILE THR ALA TYR ARG ARG ASN GLY VAL ARG ASN SER ALA SEQRES 14 B 353 LEU LEU ARG ALA TYR PHE GLU GLN ASN PRO PRO CYS ARG SEQRES 15 B 353 TRP LEU SER MET SER ILE LYS ARG TRP SER LYS GLN THR SEQRES 16 B 353 GLY LEU ASN ALA SER VAL ILE GLY GLY SER ILE THR SER SEQRES 17 B 353 TYR GLY PHE ASN LEU MET VAL VAL TYR TYR LEU LEU GLN SEQRES 18 B 353 ARG ASN HIS LEU GLN PHE VAL PRO PRO SER THR ILE ASP SEQRES 19 B 353 VAL SER ARG VAL GLU PRO LEU PRO PRO HIS LEU PRO LEU SEQRES 20 B 353 GLU GLU PRO ALA ASP GLU GLY LEU GLU LEU GLY THR GLN SEQRES 21 B 353 VAL LEU ASP PHE LEU HIS PHE PHE LEU HIS GLU PHE ASP SEQRES 22 B 353 SER ASP LYS GLN VAL ILE SER LEU ASN ARG PRO GLY ILE SEQRES 23 B 353 THR THR LYS GLU GLU LEU ASP TRP THR LYS SER ALA GLU SEQRES 24 B 353 ASP PHE ALA ARG MET ASN GLY GLU LYS VAL HIS TYR GLN SEQRES 25 B 353 TRP CYS ILE GLU ASP PRO TYR GLU LEU ASN LEU ASN VAL SEQRES 26 B 353 GLY ARG ASN VAL THR PRO LEU LYS ARG ASP PHE LEU ARG SEQRES 27 B 353 ARG HIS LEU GLU LYS ALA ARG ASP THR ALA LEU LEU THR SEQRES 28 B 353 ILE VAL HET MG A 401 1 HET MG A 402 1 HET DUT A 501 28 HET DUT B 502 28 HETNAM MG MAGNESIUM ION HETNAM DUT DEOXYURIDINE-5'-TRIPHOSPHATE FORMUL 3 MG 2(MG 2+) FORMUL 5 DUT 2(C9 H15 N2 O14 P3) FORMUL 7 HOH *125(H2 O) HELIX 1 1 SER A 4 SER A 15 1 12 HELIX 2 2 HIS A 28 ASP A 44 1 17 HELIX 3 3 GLY A 53 GLY A 59 1 7 HELIX 4 4 ASN A 73 ASP A 79 1 7 HELIX 5 5 THR A 87 HIS A 109 1 23 HELIX 6 6 ARG A 142 GLU A 156 1 15 HELIX 7 7 ASN A 158 PRO A 160 5 3 HELIX 8 8 CYS A 161 THR A 175 1 15 HELIX 9 9 THR A 187 ARG A 202 1 16 HELIX 10 10 PRO A 209 ILE A 213 5 5 HELIX 11 11 ASP A 214 VAL A 218 5 5 HELIX 12 12 GLY A 234 GLU A 251 1 18 HELIX 13 13 THR A 268 ASP A 273 1 6 HELIX 14 14 THR A 275 ASP A 280 1 6 HELIX 15 15 ARG A 283 GLU A 287 5 5 HELIX 16 16 THR A 310 ASP A 326 1 17 HELIX 17 17 SER B 4 LYS B 17 1 14 HELIX 18 18 GLY B 53 GLY B 59 1 7 HELIX 19 19 GLN B 94 LEU B 98 5 5 HELIX 20 20 ARG B 142 ASN B 158 1 17 HELIX 21 21 CYS B 161 THR B 175 1 15 HELIX 22 22 THR B 187 ARG B 202 1 16 HELIX 23 23 PRO B 209 ILE B 213 5 5 HELIX 24 24 GLY B 234 GLU B 251 1 18 HELIX 25 25 LYS B 269 ASP B 273 1 5 HELIX 26 26 THR B 275 ASN B 285 1 11 HELIX 27 27 THR B 310 ALA B 328 1 19 SHEET 1 A 5 ARG A 48 PHE A 52 0 SHEET 2 A 5 VAL A 67 LEU A 72 -1 O LEU A 72 N ARG A 48 SHEET 3 A 5 ASP A 134 ALA A 139 1 O ASP A 136 N PHE A 69 SHEET 4 A 5 VAL A 124 LYS A 128 -1 N VAL A 127 O PHE A 135 SHEET 5 A 5 ASN A 113 VAL A 117 -1 N VAL A 117 O VAL A 124 SHEET 1 B 2 VAL A 258 ILE A 259 0 SHEET 2 B 2 CYS A 294 ILE A 295 1 O CYS A 294 N ILE A 259 SHEET 1 C 3 THR B 51 PHE B 52 0 SHEET 2 C 3 VAL B 67 VAL B 71 -1 O ASP B 68 N PHE B 52 SHEET 3 C 3 PHE B 135 ALA B 139 1 O THR B 138 N PHE B 69 SHEET 1 D 2 GLN B 257 VAL B 258 0 SHEET 2 D 2 THR B 267 THR B 268 -1 O THR B 267 N VAL B 258 LINK OD2 ASP A 66 MG MG A 401 1555 1555 2.06 LINK OD1 ASP A 66 MG MG A 402 1555 1555 2.35 LINK OD2 ASP A 66 MG MG A 402 1555 1555 2.97 LINK OD2 ASP A 68 MG MG A 401 1555 1555 2.24 LINK OD1 ASP A 68 MG MG A 402 1555 1555 2.24 LINK OD2 ASP A 68 MG MG A 402 1555 1555 2.89 LINK OD2 ASP A 136 MG MG A 402 1555 1555 2.24 LINK MG MG A 401 O1B DUT A 501 1555 1555 2.31 LINK MG MG A 401 O3G DUT A 501 1555 1555 2.21 LINK MG MG A 401 O HOH A 556 1555 1555 1.88 LINK MG MG A 401 O HOH A 590 1555 1555 2.49 LINK MG MG A 402 O HOH A 588 1555 1555 2.37 LINK MG MG A 402 O HOH A 589 1555 1555 2.36 LINK MG MG A 402 O HOH A 590 1555 1555 2.13 SITE 1 AC1 6 ASP A 66 ASP A 68 MG A 402 DUT A 501 SITE 2 AC1 6 HOH A 556 HOH A 590 SITE 1 AC2 7 ASP A 66 ASP A 68 ASP A 136 MG A 401 SITE 2 AC2 7 HOH A 588 HOH A 589 HOH A 590 SITE 1 AC3 25 PHE A 52 GLY A 53 SER A 54 VAL A 57 SITE 2 AC3 25 SER A 65 ASP A 66 ASP A 68 ASN A 147 SITE 3 AC3 25 SER A 148 LEU A 151 LYS A 169 LYS A 173 SITE 4 AC3 25 THR A 187 SER A 188 TYR A 189 MG A 401 SITE 5 AC3 25 HOH A 525 HOH A 540 HOH A 556 HOH A 558 SITE 6 AC3 25 HOH A 573 HOH A 574 HOH A 576 HOH A 587 SITE 7 AC3 25 HOH A 590 SITE 1 AC4 12 GLY B 53 SER B 54 ASP B 66 ASP B 68 SITE 2 AC4 12 ASN B 147 SER B 148 LYS B 169 LYS B 173 SITE 3 AC4 12 THR B 187 SER B 188 TYR B 189 HOH B 533 CRYST1 79.142 41.659 104.286 90.00 96.46 90.00 P 1 21 1 4 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 0.012636 0.000000 0.001430 0.00000 SCALE2 0.000000 0.024004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009650 0.00000