2Q0G - Header Asymmetric Unit

HEADER TRANSFERASE 21-MAY-07 2Q0G

TITLE TERMINAL URIDYLYL TRANSFERASE 4 FROM TRYPANOSOMA BRUCEI TITLE 2 WITH BOUND UPU

COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA URIDYLYL TRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RNA URIDYLYLTRANSFERASE 4; COMPND 5 EC: 2.7.7.52; COMPND 6 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 3 ORGANISM_TAXID: 5691; SOURCE 4 GENE: TUT4; 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, KEYWDS 2 RNA-EDITING

EXPDTA X-RAY DIFFRACTION

AUTHOR J.STAGNO,H.LUECKE

REVDAT 3 24-FEB-09 2Q0G 1 VERSN REVDAT 2 09-OCT-07 2Q0G 1 JRNL REVDAT 1 28-AUG-07 2Q0G 0

JRNL AUTH J.STAGNO,I.APHASIZHEVA,R.APHASIZHEV,H.LUECKE JRNL TITL DUAL ROLE OF THE RNA SUBSTRATE IN SELECTIVITY AND JRNL TITL 2 CATALYSIS BY TERMINAL URIDYLYL TRANSFERASES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 14634 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17785418 JRNL DOI 10.1073/PNAS.0704259104

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 32469 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : TEST SET TAKEN FROM 2IKF REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1681 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2248 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE SET COUNT : 124 REMARK 3 BIN FREE R VALUE : 0.3740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5174 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.17000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.412 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.291 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.261 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.926 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5368 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7294 ; 1.608 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 645 ; 6.522 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 252 ;36.333 ;23.135 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 898 ;19.281 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 49 ;17.443 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 821 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4055 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2156 ; 0.213 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3562 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 218 ; 0.215 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.136 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 63 ; 0.205 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.181 ; 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): 3325 ; 0.727 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5238 ; 1.289 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2321 ; 1.650 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2056 ; 2.569 ; 4.500 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 REMARK 3 RIDING POSITIONS

REMARK 4 REMARK 4 2Q0G COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAY-07. REMARK 100 THE RCSB ID CODE IS RCSB042993.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : NULL 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 : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32493 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 46.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.650 REMARK 200 R MERGE (I) : 0.14100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.68 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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: PDB ENTRY 2IKF REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CACODYLATE, 200 MM REMARK 280 CALCIUM ACETATE, 18% PEG-8000, 4 MM MGCL2, 50 UM UTP, CRYSTALS REMARK 280 SOAKED IN 10 MM UPU FOR 30 MINUTES, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING 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 20.97650 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 LYS A 22 REMARK 465 ASP A 23 REMARK 465 LEU A 24 REMARK 465 HIS A 25 REMARK 465 THR A 26 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 MET B 1 REMARK 465 PRO B 2 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 333

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 LEU A 235 OG1 THR A 239 2.19 REMARK 500 OH TYR A 154 O HOH A 526 2.19 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 GLU A 62 -153.42 -76.47 REMARK 500 ASP A 79 56.73 -66.03 REMARK 500 ASN A 158 79.69 -156.73 REMARK 500 TRP A 274 63.92 -104.57 REMARK 500 ASN A 285 49.24 78.81 REMARK 500 ALA A 328 73.61 39.21 REMARK 500 LEU A 329 52.17 39.07 REMARK 500 VAL B 43 -55.66 -120.08 REMARK 500 PHE B 52 -159.83 -150.92 REMARK 500 LYS B 63 40.76 -73.65 REMARK 500 ASP B 79 56.48 -94.83 REMARK 500 THR B 138 -167.58 -123.87 REMARK 500 PRO B 160 -6.33 -59.32 REMARK 500 ASN B 203 11.89 89.80 REMARK 500 GLU B 233 34.97 72.32 REMARK 500 ASP B 273 33.20 71.00 REMARK 500 TRP B 274 56.88 -106.44 REMARK 500 VAL B 289 123.85 -175.62 REMARK 500 TYR B 299 -42.45 -130.68 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 ARG A 27 HIS A 28 149.11 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 OD1 REMARK 620 2 ASP A 68 OD1 143.0 REMARK 620 3 ASP A 136 OD2 96.1 73.3 REMARK 620 4 UPU A 501 O1 124.6 89.0 123.2 REMARK 620 5 HOH A 552 O 67.3 143.2 135.6 57.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 66 OD1 REMARK 620 2 UPU B 502 O1 105.3 REMARK 620 3 ASP B 68 OD1 114.2 99.7 REMARK 620 4 ASP B 68 OD2 78.4 84.7 44.6 REMARK 620 5 ASP B 136 OD1 95.4 142.9 99.3 130.2 REMARK 620 6 UPU B 502 O3'B 156.5 51.2 75.6 97.9 104.3 REMARK 620 7 ASP B 66 OD2 44.5 84.6 158.0 115.3 89.4 121.9 REMARK 620 N 1 2 3 4 5 6

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 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 402 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 403 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 404 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UPU A 501 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UPU B 502

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IKF RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH BOUND UTP SUBSTRATE. REMARK 900 RELATED ID: 2NOM RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH BOUND DUTP SUBSTRATE. REMARK 900 RELATED ID: 2Q0C RELATED DB: PDB REMARK 900 RELATED ID: 2Q0D RELATED DB: PDB REMARK 900 RELATED ID: 2Q0E RELATED DB: PDB REMARK 900 RELATED ID: 2Q0F RELATED DB: PDB

DBREF 2Q0G A 1 333 UNP Q381M1 Q381M1_9TRYP 1 333 DBREF 2Q0G B 1 333 UNP Q381M1 Q381M1_9TRYP 1 333

SEQADV 2Q0G MET A -19 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G GLY A -18 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G SER A -17 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G SER A -16 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G HIS A -15 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0G HIS A -14 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0G HIS A -13 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0G HIS A -12 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0G HIS A -11 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0G HIS A -10 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0G SER A -9 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G SER A -8 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G GLY A -7 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G LEU A -6 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G VAL A -5 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G PRO A -4 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G ARG A -3 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G GLY A -2 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G SER A -1 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G HIS A 0 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G MET B -19 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G GLY B -18 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G SER B -17 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G SER B -16 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G HIS B -15 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0G HIS B -14 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0G HIS B -13 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0G HIS B -12 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0G HIS B -11 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0G HIS B -10 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0G SER B -9 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G SER B -8 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G GLY B -7 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G LEU B -6 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G VAL B -5 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G PRO B -4 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G ARG B -3 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G GLY B -2 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G SER B -1 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0G 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 B 402 1 HET CL A 403 1 HET CL B 404 1 HET UPU A 501 37 HET UPU B 502 37

HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM UPU [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN- HETNAM 2 UPU 1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL HETNAM 3 UPU (2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)- HETNAM 4 UPU YL)-4-HYDROXY-2-(HYDROXYMETHYL)TETRAHYDROFURAN-3-YL HETNAM 5 UPU HYDROGEN (S)-PHOSPHATE

FORMUL 3 MG 2(MG 2+) FORMUL 5 CL 2(CL 1-) FORMUL 7 UPU 2(C18 H23 N4 O14 P) FORMUL 9 HOH *175(H2 O)

HELIX 1 1 SER A 4 PHE A 16 1 13 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 ASN A 158 1 17 HELIX 7 7 CYS A 161 THR A 175 1 15 HELIX 8 8 THR A 187 ARG A 202 1 16 HELIX 9 9 PRO A 209 ILE A 213 5 5 HELIX 10 10 ASP A 214 VAL A 218 5 5 HELIX 11 11 GLY A 234 GLU A 251 1 18 HELIX 12 12 LYS A 269 ASP A 273 1 5 HELIX 13 13 THR A 275 ASP A 280 1 6 HELIX 14 14 THR A 310 ALA A 324 1 15 HELIX 15 15 SER B 4 SER B 15 1 12 HELIX 16 16 VAL B 29 ALA B 42 1 14 HELIX 17 17 GLY B 53 GLY B 59 1 7 HELIX 18 18 ASN B 73 ASP B 79 1 7 HELIX 19 19 THR B 87 ASP B 96 1 10 HELIX 20 20 ILE B 97 HIS B 109 1 13 HELIX 21 21 ARG B 142 ASN B 158 1 17 HELIX 22 22 CYS B 161 THR B 175 1 15 HELIX 23 23 THR B 187 ARG B 202 1 16 HELIX 24 24 PRO B 209 ILE B 213 5 5 HELIX 25 25 GLY B 234 GLU B 251 1 18 HELIX 26 26 THR B 275 ASN B 285 1 11 HELIX 27 27 THR B 310 THR B 327 1 18

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 GLU A 115 O ARG A 126 SHEET 1 B 3 THR A 267 THR A 268 0 SHEET 2 B 3 GLN A 257 ILE A 259 -1 N VAL A 258 O THR A 267 SHEET 3 B 3 CYS A 294 ILE A 295 1 O CYS A 294 N ILE A 259 SHEET 1 C 5 ARG B 48 PHE B 52 0 SHEET 2 C 5 VAL B 67 LEU B 72 -1 O LEU B 72 N ARG B 48 SHEET 3 C 5 ASP B 134 ALA B 139 1 O ASP B 136 N PHE B 69 SHEET 4 C 5 VAL B 124 LYS B 128 -1 N VAL B 127 O PHE B 135 SHEET 5 C 5 ASN B 113 VAL B 117 -1 N VAL B 117 O VAL B 124 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 MG MG A 401 OD1 ASP A 66 1555 1555 2.74 LINK MG MG A 401 OD1 ASP A 68 1555 1555 2.29 LINK MG MG A 401 OD2 ASP A 136 1555 1555 1.99 LINK MG MG A 401 O1 UPU A 501 1555 1555 2.75 LINK MG MG A 401 O HOH A 552 1555 1555 2.90 LINK MG MG B 402 OD1 ASP B 66 1555 1555 1.80 LINK MG MG B 402 O1 UPU B 502 1555 1555 2.64 LINK MG MG B 402 OD1 ASP B 68 1555 1555 2.23 LINK MG MG B 402 OD2 ASP B 68 1555 1555 3.15 LINK MG MG B 402 OD1 ASP B 136 1555 1555 2.76 LINK MG MG B 402 O3'B UPU B 502 1555 1555 3.14 LINK MG MG B 402 OD2 ASP B 66 1555 1555 3.09

SITE 1 AC1 5 ASP A 66 ASP A 68 ASP A 136 UPU A 501 SITE 2 AC1 5 HOH A 552 SITE 1 AC2 4 ASP B 66 ASP B 68 ASP B 136 UPU B 502 SITE 1 AC3 4 HIS A 246 HIS A 250 HOH A 523 HOH A 610 SITE 1 AC4 4 HIS B 246 HIS B 250 HOH B 504 HOH B 552 SITE 1 AC5 18 PHE A 52 GLY A 53 ASP A 68 ARG A 121 SITE 2 AC5 18 ARG A 126 ASP A 136 GLY A 144 ASN A 147 SITE 3 AC5 18 SER A 148 TYR A 189 MG A 401 HOH A 502 SITE 4 AC5 18 HOH A 505 HOH A 512 HOH A 535 HOH A 552 SITE 5 AC5 18 HOH A 592 HOH A 600 SITE 1 AC6 15 PHE B 52 GLY B 53 ASP B 66 ASP B 68 SITE 2 AC6 15 ARG B 121 VAL B 122 GLY B 144 ASN B 147 SITE 3 AC6 15 SER B 148 TYR B 189 MG B 402 HOH B 503 SITE 4 AC6 15 HOH B 517 HOH B 532 HOH B 535

CRYST1 81.544 41.953 106.593 90.00 95.62 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 0.012263 0.000000 0.001206 0.00000

SCALE2 0.000000 0.023836 0.000000 0.00000

SCALE3 0.000000 0.000000 0.009427 0.00000