HEADER HYDROLASE 23-SEP-19 6KZ6 TITLE CRYSTAL STRUCTURE OF ASFV DUTPASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: E165R; COMPND 3 CHAIN: C, A, B; COMPND 4 SYNONYM: E165R CDS PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AFRICAN SWINE FEVER VIRUS; SOURCE 3 ORGANISM_COMMON: ASFV; SOURCE 4 ORGANISM_TAXID: 10497; SOURCE 5 GENE: E165R CDS, E165R, ASFV-GEORGIA_4-154; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HOMOTRIMER, DUTPASE, DUMP, VIRAL PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.GUO,C.CHEN,G.B.LI,L.CAO,C.W.WANG REVDAT 4 27-MAR-24 6KZ6 1 LINK REVDAT 3 12-FEB-20 6KZ6 1 JRNL REVDAT 2 04-DEC-19 6KZ6 1 JRNL REVDAT 1 13-NOV-19 6KZ6 0 JRNL AUTH G.LI,C.WANG,M.YANG,L.CAO,D.FU,X.LIU,D.SUN,C.CHEN,Y.WANG, JRNL AUTH 2 Z.JIA,C.YANG,Y.GUO,Z.RAO JRNL TITL STRUCTURAL INSIGHT INTO AFRICAN SWINE FEVER VIRUS DUTPASE JRNL TITL 2 REVEALS A NOVEL FOLDING PATTERN IN THE DUTPASE FAMILY. JRNL REF J.VIROL. V. 94 2020 JRNL REFN ESSN 1098-5514 JRNL PMID 31748385 JRNL DOI 10.1128/JVI.01698-19 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 27086 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1389 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.1280 - 4.7080 0.99 2749 152 0.1748 0.1943 REMARK 3 2 4.7080 - 3.7385 1.00 2691 129 0.1555 0.1845 REMARK 3 3 3.7385 - 3.2664 1.00 2615 158 0.1774 0.2144 REMARK 3 4 3.2664 - 2.9680 1.00 2661 116 0.2062 0.2484 REMARK 3 5 2.9680 - 2.7554 1.00 2613 129 0.2213 0.2333 REMARK 3 6 2.7554 - 2.5930 1.00 2593 129 0.2302 0.2550 REMARK 3 7 2.5930 - 2.4632 1.00 2610 150 0.2285 0.2610 REMARK 3 8 2.4632 - 2.3560 1.00 2525 168 0.2315 0.3138 REMARK 3 9 2.3560 - 2.2653 0.99 2546 152 0.2478 0.2600 REMARK 3 10 2.2653 - 2.1871 0.81 2094 106 0.2652 0.3118 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6KZ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1300013892. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27729 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08 M HEPES PH 7.5, 0.02 M SODIUM REMARK 280 CITRATE TRIBASIC DIHYDRATE, 17% W/V POLYETHYLENE GLYCOL 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 33.12800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.45600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.63900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.45600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.12800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.63900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET C -20 REMARK 465 GLY C -19 REMARK 465 SER C -18 REMARK 465 SER C -17 REMARK 465 HIS C -16 REMARK 465 HIS C -15 REMARK 465 HIS C -14 REMARK 465 HIS C -13 REMARK 465 HIS C -12 REMARK 465 HIS C -11 REMARK 465 SER C -10 REMARK 465 SER C -9 REMARK 465 GLY C -8 REMARK 465 LEU C -7 REMARK 465 VAL C -6 REMARK 465 PRO C -5 REMARK 465 ARG C -4 REMARK 465 GLY C -3 REMARK 465 SER C -2 REMARK 465 HIS C -1 REMARK 465 MET C 0 REMARK 465 MET C 1 REMARK 465 THR C 147 REMARK 465 PRO C 148 REMARK 465 ARG C 149 REMARK 465 GLY C 150 REMARK 465 GLU C 151 REMARK 465 GLY C 152 REMARK 465 ARG C 153 REMARK 465 PHE C 154 REMARK 465 GLY C 155 REMARK 465 SER C 156 REMARK 465 THR C 157 REMARK 465 GLY C 158 REMARK 465 GLU C 159 REMARK 465 ALA C 160 REMARK 465 GLY C 161 REMARK 465 ILE C 162 REMARK 465 MET C 163 REMARK 465 ARG C 164 REMARK 465 THR C 165 REMARK 465 MET A -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS 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 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 ARG A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 MET A 1 REMARK 465 LEU A 143 REMARK 465 PHE A 144 REMARK 465 ALA A 145 REMARK 465 PRO A 146 REMARK 465 THR A 147 REMARK 465 PRO A 148 REMARK 465 ARG A 149 REMARK 465 GLY A 150 REMARK 465 GLU A 151 REMARK 465 GLY A 152 REMARK 465 ARG A 153 REMARK 465 PHE A 154 REMARK 465 GLY A 155 REMARK 465 SER A 156 REMARK 465 THR A 157 REMARK 465 GLY A 158 REMARK 465 GLU A 159 REMARK 465 ALA A 160 REMARK 465 GLY A 161 REMARK 465 ILE A 162 REMARK 465 MET A 163 REMARK 465 ARG A 164 REMARK 465 THR A 165 REMARK 465 MET B -20 REMARK 465 GLY B -19 REMARK 465 SER B -18 REMARK 465 SER B -17 REMARK 465 HIS 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 SER B -10 REMARK 465 SER B -9 REMARK 465 GLY B -8 REMARK 465 LEU B -7 REMARK 465 VAL B -6 REMARK 465 PRO B -5 REMARK 465 ARG B -4 REMARK 465 GLY B -3 REMARK 465 ALA B 145 REMARK 465 PRO B 146 REMARK 465 THR B 147 REMARK 465 PRO B 148 REMARK 465 ARG B 149 REMARK 465 GLY B 150 REMARK 465 GLU B 151 REMARK 465 GLY B 152 REMARK 465 ARG B 153 REMARK 465 PHE B 154 REMARK 465 GLY B 155 REMARK 465 SER B 156 REMARK 465 THR B 157 REMARK 465 GLY B 158 REMARK 465 GLU B 159 REMARK 465 ALA B 160 REMARK 465 GLY B 161 REMARK 465 ILE B 162 REMARK 465 MET B 163 REMARK 465 ARG B 164 REMARK 465 THR B 165 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 PRO A 142 CG CD 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 C 436 O HOH C 442 1.85 REMARK 500 O HOH C 383 O HOH B 514 1.87 REMARK 500 O HOH C 361 O HOH C 429 1.90 REMARK 500 O HOH B 428 O HOH B 495 1.91 REMARK 500 O THR B 24 O HOH B 401 1.93 REMARK 500 OE2 GLU A 12 O HOH A 301 1.95 REMARK 500 O HOH B 503 O HOH B 513 1.97 REMARK 500 O HOH B 410 O HOH B 491 1.98 REMARK 500 O HOH C 434 O HOH C 439 1.99 REMARK 500 O HOH A 398 O HOH A 410 2.03 REMARK 500 O HOH C 409 O HOH C 435 2.04 REMARK 500 O SER C 73 O HOH C 301 2.05 REMARK 500 O HOH C 398 O HOH A 379 2.06 REMARK 500 NH1 ARG C 79 O HOH C 301 2.06 REMARK 500 OD2 ASP B 107 O HOH B 402 2.06 REMARK 500 O HOH A 401 O HOH B 476 2.09 REMARK 500 NZ LYS A 136 O HOH A 302 2.09 REMARK 500 O HOH C 390 O HOH C 437 2.11 REMARK 500 O HOH C 406 O HOH C 407 2.13 REMARK 500 O HOH B 406 O HOH B 496 2.14 REMARK 500 O HOH C 304 O HOH C 416 2.15 REMARK 500 O HOH A 348 O HOH B 502 2.16 REMARK 500 NH1 ARG A 137 O HOH A 303 2.17 REMARK 500 O PRO C 146 O HOH C 302 2.18 REMARK 500 O HOH A 308 O HOH A 393 2.19 REMARK 500 OD2 ASP B 33 O HOH B 403 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 C 405 O HOH A 405 3545 2.02 REMARK 500 O HOH A 317 O HOH B 453 2455 2.08 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 PRO A 142 N - CA - CB ANGL. DEV. = 7.8 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 ASN C 25 71.71 -103.28 REMARK 500 CYS C 37 -24.92 87.10 REMARK 500 ASN C 138 56.42 -90.01 REMARK 500 CYS A 37 -23.69 76.90 REMARK 500 ASN B 25 67.33 -102.13 REMARK 500 CYS B 37 -24.31 76.79 REMARK 500 ARG B 79 88.01 -150.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH C 443 DISTANCE = 6.59 ANGSTROMS 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 B 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 UMP C 201 OP1 REMARK 620 2 HOH C 339 O 70.0 REMARK 620 3 HOH C 396 O 91.2 91.2 REMARK 620 4 HOH B 403 O 104.2 163.6 104.5 REMARK 620 5 HOH B 423 O 80.8 79.7 169.4 84.3 REMARK 620 6 HOH B 513 O 151.6 82.4 95.6 100.6 88.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 313 O REMARK 620 2 HOH C 323 O 82.0 REMARK 620 3 HOH C 415 O 79.9 84.5 REMARK 620 4 UMP A 201 OP1 79.9 72.5 151.2 REMARK 620 5 HOH A 319 O 149.8 79.8 121.9 71.7 REMARK 620 6 HOH A 339 O 79.8 139.8 126.4 69.2 99.0 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 C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UMP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UMP B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 302 DBREF1 6KZ6 C 1 165 UNP A0A2X0SE53_ASF DBREF2 6KZ6 C A0A2X0SE53 1 165 DBREF1 6KZ6 A 1 165 UNP A0A2X0SE53_ASF DBREF2 6KZ6 A A0A2X0SE53 1 165 DBREF1 6KZ6 B 1 165 UNP A0A2X0SE53_ASF DBREF2 6KZ6 B A0A2X0SE53 1 165 SEQADV 6KZ6 MET C -20 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 GLY C -19 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 SER C -18 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 SER C -17 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS C -16 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS C -15 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS C -14 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS C -13 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS C -12 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS C -11 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 SER C -10 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 SER C -9 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 GLY C -8 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 LEU C -7 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 VAL C -6 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 PRO C -5 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 ARG C -4 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 GLY C -3 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 SER C -2 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS C -1 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 MET C 0 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 MET A -20 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 GLY A -19 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 SER A -18 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 SER A -17 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS A -16 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS A -15 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS A -14 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS A -13 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS A -12 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS A -11 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 SER A -10 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 SER A -9 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 GLY A -8 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 LEU A -7 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 VAL A -6 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 PRO A -5 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 ARG A -4 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 GLY A -3 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 SER A -2 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS A -1 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 MET A 0 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 MET B -20 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 GLY B -19 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 SER B -18 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 SER B -17 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS B -16 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS B -15 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS B -14 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS B -13 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS B -12 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS B -11 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 SER B -10 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 SER B -9 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 GLY B -8 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 LEU B -7 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 VAL B -6 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 PRO B -5 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 ARG B -4 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 GLY B -3 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 SER B -2 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 HIS B -1 UNP A0A2X0SE5 EXPRESSION TAG SEQADV 6KZ6 MET B 0 UNP A0A2X0SE5 EXPRESSION TAG SEQRES 1 C 186 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 C 186 LEU VAL PRO ARG GLY SER HIS MET MET ALA THR ASN PHE SEQRES 3 C 186 PHE ILE GLN PRO ILE THR GLU GLU ALA GLU ALA TYR TYR SEQRES 4 C 186 PRO PRO SER VAL ILE THR ASN LYS ARG LYS ASP LEU GLY SEQRES 5 C 186 VAL ASP VAL TYR CYS CYS SER ASP LEU VAL LEU GLN PRO SEQRES 6 C 186 GLY LEU ASN ILE VAL ARG LEU HIS ILE LYS VAL ALA CYS SEQRES 7 C 186 GLU HIS MET GLY LYS LYS CYS GLY PHE LYS ILE MET ALA SEQRES 8 C 186 ARG SER SER MET CYS THR HIS GLU ARG LEU LEU ILE LEU SEQRES 9 C 186 ALA ASN GLY ILE GLY LEU ILE ASP PRO GLY TYR VAL GLY SEQRES 10 C 186 GLU LEU MET LEU LYS ILE ILE ASN LEU GLY ASP THR PRO SEQRES 11 C 186 VAL GLN ILE TRP ALA LYS GLU CYS LEU VAL GLN LEU VAL SEQRES 12 C 186 ALA GLN GLY ASP HIS VAL PRO ASP HIS ILE ASN ILE LEU SEQRES 13 C 186 LYS ARG ASN GLN ILE PHE PRO LEU PHE ALA PRO THR PRO SEQRES 14 C 186 ARG GLY GLU GLY ARG PHE GLY SER THR GLY GLU ALA GLY SEQRES 15 C 186 ILE MET ARG THR SEQRES 1 A 186 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 186 LEU VAL PRO ARG GLY SER HIS MET MET ALA THR ASN PHE SEQRES 3 A 186 PHE ILE GLN PRO ILE THR GLU GLU ALA GLU ALA TYR TYR SEQRES 4 A 186 PRO PRO SER VAL ILE THR ASN LYS ARG LYS ASP LEU GLY SEQRES 5 A 186 VAL ASP VAL TYR CYS CYS SER ASP LEU VAL LEU GLN PRO SEQRES 6 A 186 GLY LEU ASN ILE VAL ARG LEU HIS ILE LYS VAL ALA CYS SEQRES 7 A 186 GLU HIS MET GLY LYS LYS CYS GLY PHE LYS ILE MET ALA SEQRES 8 A 186 ARG SER SER MET CYS THR HIS GLU ARG LEU LEU ILE LEU SEQRES 9 A 186 ALA ASN GLY ILE GLY LEU ILE ASP PRO GLY TYR VAL GLY SEQRES 10 A 186 GLU LEU MET LEU LYS ILE ILE ASN LEU GLY ASP THR PRO SEQRES 11 A 186 VAL GLN ILE TRP ALA LYS GLU CYS LEU VAL GLN LEU VAL SEQRES 12 A 186 ALA GLN GLY ASP HIS VAL PRO ASP HIS ILE ASN ILE LEU SEQRES 13 A 186 LYS ARG ASN GLN ILE PHE PRO LEU PHE ALA PRO THR PRO SEQRES 14 A 186 ARG GLY GLU GLY ARG PHE GLY SER THR GLY GLU ALA GLY SEQRES 15 A 186 ILE MET ARG THR SEQRES 1 B 186 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 186 LEU VAL PRO ARG GLY SER HIS MET MET ALA THR ASN PHE SEQRES 3 B 186 PHE ILE GLN PRO ILE THR GLU GLU ALA GLU ALA TYR TYR SEQRES 4 B 186 PRO PRO SER VAL ILE THR ASN LYS ARG LYS ASP LEU GLY SEQRES 5 B 186 VAL ASP VAL TYR CYS CYS SER ASP LEU VAL LEU GLN PRO SEQRES 6 B 186 GLY LEU ASN ILE VAL ARG LEU HIS ILE LYS VAL ALA CYS SEQRES 7 B 186 GLU HIS MET GLY LYS LYS CYS GLY PHE LYS ILE MET ALA SEQRES 8 B 186 ARG SER SER MET CYS THR HIS GLU ARG LEU LEU ILE LEU SEQRES 9 B 186 ALA ASN GLY ILE GLY LEU ILE ASP PRO GLY TYR VAL GLY SEQRES 10 B 186 GLU LEU MET LEU LYS ILE ILE ASN LEU GLY ASP THR PRO SEQRES 11 B 186 VAL GLN ILE TRP ALA LYS GLU CYS LEU VAL GLN LEU VAL SEQRES 12 B 186 ALA GLN GLY ASP HIS VAL PRO ASP HIS ILE ASN ILE LEU SEQRES 13 B 186 LYS ARG ASN GLN ILE PHE PRO LEU PHE ALA PRO THR PRO SEQRES 14 B 186 ARG GLY GLU GLY ARG PHE GLY SER THR GLY GLU ALA GLY SEQRES 15 B 186 ILE MET ARG THR HET UMP C 201 20 HET MG C 202 1 HET UMP A 201 20 HET UMP B 301 20 HET MG B 302 1 HETNAM UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN UMP DUMP FORMUL 4 UMP 3(C9 H13 N2 O8 P) FORMUL 5 MG 2(MG 2+) FORMUL 9 HOH *381(H2 O) HELIX 1 AA1 THR C 11 ALA C 16 1 6 HELIX 2 AA2 GLY C 125 HIS C 127 5 3 HELIX 3 AA3 PHE C 141 ALA C 145 5 5 HELIX 4 AA4 THR A 11 TYR A 18 1 8 HELIX 5 AA5 SER A 72 CYS A 75 5 4 HELIX 6 AA6 THR B 11 TYR B 18 1 8 HELIX 7 AA7 GLY B 125 HIS B 127 5 3 SHEET 1 AA1 5 SER C 21 THR C 24 0 SHEET 2 AA1 5 HIS C 131 ILE C 134 -1 O ILE C 132 N ILE C 23 SHEET 3 AA1 5 THR C 3 PRO C 9 1 N ILE C 7 O ASN C 133 SHEET 4 AA1 5 ILE C 53 HIS C 59 -1 O LYS C 54 N GLN C 8 SHEET 5 AA1 5 LYS C 62 CYS C 64 -1 O LYS C 62 N HIS C 59 SHEET 1 AA2 4 GLY C 31 VAL C 34 0 SHEET 2 AA2 4 VAL C 119 ALA C 123 -1 O LEU C 121 N VAL C 32 SHEET 3 AA2 4 PHE C 66 ALA C 70 -1 N MET C 69 O GLN C 120 SHEET 4 AA2 4 GLY C 88 ILE C 90 -1 O GLY C 88 N ILE C 68 SHEET 1 AA3 2 LEU C 40 LEU C 42 0 SHEET 2 AA3 2 VAL C 110 ILE C 112 -1 O VAL C 110 N LEU C 42 SHEET 1 AA4 3 GLY C 45 ARG C 50 0 SHEET 2 AA4 3 MET C 99 ASN C 104 -1 O ASN C 104 N GLY C 45 SHEET 3 AA4 3 LEU C 81 LEU C 83 -1 N ILE C 82 O ILE C 103 SHEET 1 AA5 5 SER A 21 THR A 24 0 SHEET 2 AA5 5 HIS A 131 ILE A 134 -1 O ILE A 132 N ILE A 23 SHEET 3 AA5 5 THR A 3 PRO A 9 1 N ILE A 7 O ASN A 133 SHEET 4 AA5 5 ILE A 53 HIS A 59 -1 O LYS A 54 N GLN A 8 SHEET 5 AA5 5 LYS A 62 CYS A 64 -1 O LYS A 62 N HIS A 59 SHEET 1 AA6 4 VAL A 32 VAL A 34 0 SHEET 2 AA6 4 VAL A 119 ALA A 123 -1 O LEU A 121 N VAL A 32 SHEET 3 AA6 4 PHE A 66 ALA A 70 -1 N LYS A 67 O VAL A 122 SHEET 4 AA6 4 GLY A 88 ILE A 90 -1 O GLY A 88 N ILE A 68 SHEET 1 AA7 2 LEU A 40 LEU A 42 0 SHEET 2 AA7 2 VAL A 110 ILE A 112 -1 O ILE A 112 N LEU A 40 SHEET 1 AA8 3 GLY A 45 ARG A 50 0 SHEET 2 AA8 3 MET A 99 ASN A 104 -1 O LEU A 100 N VAL A 49 SHEET 3 AA8 3 LEU A 81 LEU A 83 -1 N ILE A 82 O ILE A 103 SHEET 1 AA9 5 SER B 21 THR B 24 0 SHEET 2 AA9 5 HIS B 131 ILE B 134 -1 O ILE B 134 N SER B 21 SHEET 3 AA9 5 THR B 3 PRO B 9 1 N PHE B 5 O ASN B 133 SHEET 4 AA9 5 ILE B 53 HIS B 59 -1 O ALA B 56 N PHE B 6 SHEET 5 AA9 5 LYS B 62 CYS B 64 -1 O LYS B 62 N HIS B 59 SHEET 1 AB1 4 VAL B 32 VAL B 34 0 SHEET 2 AB1 4 VAL B 119 ALA B 123 -1 O LEU B 121 N VAL B 32 SHEET 3 AB1 4 PHE B 66 ALA B 70 -1 N LYS B 67 O VAL B 122 SHEET 4 AB1 4 GLY B 88 ILE B 90 -1 O GLY B 88 N ILE B 68 SHEET 1 AB2 2 LEU B 40 LEU B 42 0 SHEET 2 AB2 2 VAL B 110 ILE B 112 -1 O ILE B 112 N LEU B 40 SHEET 1 AB3 3 GLY B 45 ARG B 50 0 SHEET 2 AB3 3 MET B 99 ASN B 104 -1 O LEU B 100 N VAL B 49 SHEET 3 AB3 3 LEU B 81 LEU B 83 -1 N ILE B 82 O ILE B 103 LINK OP1 UMP C 201 MG MG B 302 1555 1555 2.28 LINK MG MG C 202 O HOH C 313 1555 1555 2.19 LINK MG MG C 202 O HOH C 323 1555 1555 2.17 LINK MG MG C 202 O HOH C 415 1555 1555 2.30 LINK MG MG C 202 OP1 UMP A 201 1555 1555 2.70 LINK MG MG C 202 O HOH A 319 1555 1555 2.46 LINK MG MG C 202 O HOH A 339 1555 1555 2.10 LINK O HOH C 339 MG MG B 302 1555 1555 2.48 LINK O HOH C 396 MG MG B 302 1555 1555 2.13 LINK MG MG B 302 O HOH B 403 1555 1555 2.18 LINK MG MG B 302 O HOH B 423 1555 1555 2.14 LINK MG MG B 302 O HOH B 513 1555 1555 2.23 SITE 1 AC1 16 ARG B 71 SER B 72 LYS B 136 MG B 302 SITE 2 AC1 16 HOH B 423 HOH B 434 ASN C 85 LEU C 89 SITE 3 AC1 16 ILE C 90 ASP C 91 TYR C 94 MET C 99 SITE 4 AC1 16 HOH C 309 HOH C 310 HOH C 339 HOH C 344 SITE 1 AC2 6 UMP A 201 HOH A 319 HOH A 339 HOH C 313 SITE 2 AC2 6 HOH C 323 HOH C 415 SITE 1 AC3 18 ASN A 85 GLY A 88 LEU A 89 ILE A 90 SITE 2 AC3 18 ASP A 91 TYR A 94 MET A 99 HOH A 319 SITE 3 AC3 18 HOH A 325 HOH A 339 HOH A 347 HOH A 352 SITE 4 AC3 18 ARG C 71 SER C 72 LYS C 136 MG C 202 SITE 5 AC3 18 HOH C 317 HOH C 323 SITE 1 AC4 7 ILE B 90 ASP B 91 TYR B 94 MET B 99 SITE 2 AC4 7 LYS B 101 HOH B 418 HOH B 421 SITE 1 AC5 6 HOH B 403 HOH B 423 HOH B 513 UMP C 201 SITE 2 AC5 6 HOH C 339 HOH C 396 CRYST1 66.256 67.278 116.912 90.00 90.00 90.00 P 21 21 21 12 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 0.015093 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014864 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008553 0.00000