PDB Short entry for 4TS9 HEADER TRANSFERASE 18-JUN-14 4TS9 TITLE CRYSTAL STRUCTURE OF WILD TYPE E. COLI PURINE NUCLEOSIDE PHOSPHORYLASE TITLE 2 WITH 6 FMC MOLECULES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PURINE NUCLEOSIDE PHOSPHORYLASE DEOD-TYPE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: PNP; COMPND 5 EC: 2.4.2.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS PURINE NUCLEOSIDE PHOSPHORYLASE, FORMICYN A, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.STEFANIC,A.BZOWSKA REVDAT 3 31-OCT-18 4TS9 1 JRNL REVDAT 2 16-MAR-16 4TS9 1 AUTHOR JRNL REVDAT 1 08-JUL-15 4TS9 0 JRNL AUTH Z.STEFANIC,M.NARCZYK,G.MIKLEUSEVIC,S.KAZAZIC,A.BZOWSKA, JRNL AUTH 2 M.LUIC JRNL TITL CRYSTALLOGRAPHIC SNAPSHOTS OF LIGAND BINDING TO HEXAMERIC JRNL TITL 2 PURINE NUCLEOSIDE PHOSPHORYLASE AND KINETIC STUDIES GIVE JRNL TITL 3 INSIGHT INTO THE MECHANISM OF CATALYSIS. JRNL REF SCI REP V. 8 15427 2018 JRNL REFN ESSN 2045-2322 JRNL PMID 30337572 JRNL DOI 10.1038/S41598-018-33723-1 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 98260 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4914 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 48.1778 - 5.4898 1.00 3534 187 0.2025 0.2008 REMARK 3 2 5.4898 - 4.3584 1.00 3347 176 0.1522 0.1611 REMARK 3 3 4.3584 - 3.8077 1.00 3299 173 0.1334 0.1505 REMARK 3 4 3.8077 - 3.4597 1.00 3265 172 0.1426 0.1633 REMARK 3 5 3.4597 - 3.2117 1.00 3231 170 0.1505 0.1567 REMARK 3 6 3.2117 - 3.0224 1.00 3219 170 0.1542 0.1820 REMARK 3 7 3.0224 - 2.8711 1.00 3205 168 0.1637 0.1812 REMARK 3 8 2.8711 - 2.7461 1.00 3195 169 0.1603 0.1938 REMARK 3 9 2.7461 - 2.6404 1.00 3208 169 0.1557 0.1801 REMARK 3 10 2.6404 - 2.5493 0.99 3178 167 0.1553 0.1935 REMARK 3 11 2.5493 - 2.4696 0.99 3157 166 0.1552 0.1660 REMARK 3 12 2.4696 - 2.3990 0.99 3175 167 0.1536 0.1657 REMARK 3 13 2.3990 - 2.3358 0.99 3159 166 0.1529 0.1883 REMARK 3 14 2.3358 - 2.2788 0.99 3147 166 0.1499 0.1913 REMARK 3 15 2.2788 - 2.2270 0.99 3161 166 0.1569 0.1888 REMARK 3 16 2.2270 - 2.1796 0.99 3134 165 0.1538 0.1889 REMARK 3 17 2.1796 - 2.1360 0.99 3154 166 0.1533 0.1919 REMARK 3 18 2.1360 - 2.0957 0.99 3135 165 0.1562 0.1717 REMARK 3 19 2.0957 - 2.0583 0.99 3131 165 0.1509 0.1769 REMARK 3 20 2.0583 - 2.0234 0.99 3122 164 0.1545 0.1749 REMARK 3 21 2.0234 - 1.9908 0.99 3131 165 0.1527 0.1750 REMARK 3 22 1.9908 - 1.9601 0.99 3119 164 0.1524 0.1678 REMARK 3 23 1.9601 - 1.9313 0.99 3097 163 0.1538 0.1854 REMARK 3 24 1.9313 - 1.9041 0.99 3100 163 0.1509 0.1794 REMARK 3 25 1.9041 - 1.8784 0.98 3107 164 0.1517 0.1703 REMARK 3 26 1.8784 - 1.8540 0.98 3051 161 0.1477 0.1858 REMARK 3 27 1.8540 - 1.8308 0.96 3024 159 0.1618 0.1909 REMARK 3 28 1.8308 - 1.8088 0.87 2773 146 0.1719 0.2016 REMARK 3 29 1.8088 - 1.7877 0.81 2524 133 0.1775 0.2099 REMARK 3 30 1.7877 - 1.7676 0.72 2264 119 0.1913 0.2242 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.44 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 : 0.007 5662 REMARK 3 ANGLE : 1.224 7662 REMARK 3 CHIRALITY : 0.082 872 REMARK 3 PLANARITY : 0.005 987 REMARK 3 DIHEDRAL : 13.911 2094 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 4TS9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000202192. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97977 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 98266 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 48.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 39.00 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 42.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 9.600 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: 1K9S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM CITRIC BUFFER, 32 % AMMONIUM REMARK 280 SULPHATE, PH 5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 80.00200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 160.00400 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 120.00300 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 200.00500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.00100 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 80.00200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 160.00400 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 200.00500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 120.00300 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 40.00100 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A HEXAMER GENERATED FROM THE REMARK 300 TRIMER IN THE ASYMMETRIC UNIT BY THE OPERATION: -X+Y, Y, -Z+1/2 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 26380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -167.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 120.00300 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 452 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 476 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 411 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 412 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 462 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 423 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 432 LIES ON A SPECIAL POSITION. 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 99 CD CE NZ REMARK 470 LYS A 237 CG CD CE NZ REMARK 470 ALA B 89 CB REMARK 470 ALA C 89 CB 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 402 O HOH C 434 2.12 REMARK 500 O HOH C 414 O HOH C 438 2.14 REMARK 500 OG SER C 203 O HOH C 653 2.14 REMARK 500 O HOH C 439 O HOH C 445 2.17 REMARK 500 O HOH C 443 O HOH C 445 2.17 REMARK 500 OE1 GLU A 210 O HOH A 606 2.19 REMARK 500 O HOH B 627 O HOH B 632 2.19 REMARK 500 O HOH A 611 O HOH A 613 2.19 REMARK 500 O GLY C 164 O HOH C 630 2.19 REMARK 500 O HOH B 531 O HOH B 605 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 450 O HOH A 465 11555 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ALA A 89 CA ALA A 89 CB -0.156 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 A 41 12.51 -142.90 REMARK 500 ARG A 43 18.95 57.50 REMARK 500 ALA A 89 -156.45 -144.05 REMARK 500 ASP A 163 78.88 -112.11 REMARK 500 GLU A 179 -158.81 -136.94 REMARK 500 GLU A 181 -36.12 -139.87 REMARK 500 PHE A 221 61.93 -109.85 REMARK 500 ARG B 43 19.83 57.32 REMARK 500 ARG B 101 -2.26 74.36 REMARK 500 ASP B 163 79.42 -102.37 REMARK 500 GLU B 179 -156.07 -139.32 REMARK 500 GLU B 181 -38.15 -139.71 REMARK 500 ARG B 207 -70.88 -63.12 REMARK 500 THR B 208 -146.28 -80.26 REMARK 500 HIS B 209 87.29 -179.36 REMARK 500 ARG C 43 19.54 58.68 REMARK 500 ASP C 163 -74.53 -70.47 REMARK 500 GLU C 179 -153.93 -136.49 REMARK 500 GLU C 181 -37.53 -140.39 REMARK 500 ALA C 194 -168.24 -118.05 REMARK 500 ILE C 206 83.55 -67.81 REMARK 500 ARG C 207 -150.42 160.02 REMARK 500 THR C 208 -162.40 -65.05 REMARK 500 GLN C 211 112.79 72.32 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 ILE C 206 ARG C 207 -147.93 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 A 596 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH A 619 DISTANCE = 7.02 ANGSTROMS REMARK 525 HOH B 519 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH B 602 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH C 576 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH C 619 DISTANCE = 7.07 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMC A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMC B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMC C 302 DBREF 4TS9 A 1 237 UNP U0SVH6 U0SVH6_ECOLX 2 238 DBREF 4TS9 B 1 237 UNP U0SVH6 U0SVH6_ECOLX 2 238 DBREF 4TS9 C 1 237 UNP U0SVH6 U0SVH6_ECOLX 2 238 SEQADV 4TS9 ALA A 89 UNP U0SVH6 GLY 90 CONFLICT SEQADV 4TS9 ALA B 89 UNP U0SVH6 GLY 90 CONFLICT SEQADV 4TS9 ALA C 89 UNP U0SVH6 GLY 90 CONFLICT SEQRES 1 A 237 ALA THR PRO HIS ILE ASN ALA GLU MET GLY ASP PHE ALA SEQRES 2 A 237 ASP VAL VAL LEU MET PRO GLY ASP PRO LEU ARG ALA LYS SEQRES 3 A 237 TYR ILE ALA GLU THR PHE LEU GLU ASP ALA ARG GLU VAL SEQRES 4 A 237 ASN ASN VAL ARG GLY MET LEU GLY PHE THR GLY THR TYR SEQRES 5 A 237 LYS GLY ARG LYS ILE SER VAL MET GLY HIS GLY MET GLY SEQRES 6 A 237 ILE PRO SER CYS SER ILE TYR THR LYS GLU LEU ILE THR SEQRES 7 A 237 ASP PHE GLY VAL LYS LYS ILE ILE ARG VAL ALA SER CYS SEQRES 8 A 237 GLY ALA VAL LEU PRO HIS VAL LYS LEU ARG ASP VAL VAL SEQRES 9 A 237 ILE GLY MET GLY ALA CYS THR ASP SER LYS VAL ASN ARG SEQRES 10 A 237 ILE ARG PHE LYS ASP HIS ASP PHE ALA ALA ILE ALA ASP SEQRES 11 A 237 PHE ASP MET VAL ARG ASN ALA VAL ASP ALA ALA LYS ALA SEQRES 12 A 237 LEU GLY ILE ASP ALA ARG VAL GLY ASN LEU PHE SER ALA SEQRES 13 A 237 ASP LEU PHE TYR SER PRO ASP GLY GLU MET PHE ASP VAL SEQRES 14 A 237 MET GLU LYS TYR GLY ILE LEU GLY VAL GLU MET GLU ALA SEQRES 15 A 237 ALA GLY ILE TYR GLY VAL ALA ALA GLU PHE GLY ALA LYS SEQRES 16 A 237 ALA LEU THR ILE CYS THR VAL SER ASP HIS ILE ARG THR SEQRES 17 A 237 HIS GLU GLN THR THR ALA ALA GLU ARG GLN THR THR PHE SEQRES 18 A 237 ASN ASP MET ILE LYS ILE ALA LEU GLU SER VAL LEU LEU SEQRES 19 A 237 GLY ASP LYS SEQRES 1 B 237 ALA THR PRO HIS ILE ASN ALA GLU MET GLY ASP PHE ALA SEQRES 2 B 237 ASP VAL VAL LEU MET PRO GLY ASP PRO LEU ARG ALA LYS SEQRES 3 B 237 TYR ILE ALA GLU THR PHE LEU GLU ASP ALA ARG GLU VAL SEQRES 4 B 237 ASN ASN VAL ARG GLY MET LEU GLY PHE THR GLY THR TYR SEQRES 5 B 237 LYS GLY ARG LYS ILE SER VAL MET GLY HIS GLY MET GLY SEQRES 6 B 237 ILE PRO SER CYS SER ILE TYR THR LYS GLU LEU ILE THR SEQRES 7 B 237 ASP PHE GLY VAL LYS LYS ILE ILE ARG VAL ALA SER CYS SEQRES 8 B 237 GLY ALA VAL LEU PRO HIS VAL LYS LEU ARG ASP VAL VAL SEQRES 9 B 237 ILE GLY MET GLY ALA CYS THR ASP SER LYS VAL ASN ARG SEQRES 10 B 237 ILE ARG PHE LYS ASP HIS ASP PHE ALA ALA ILE ALA ASP SEQRES 11 B 237 PHE ASP MET VAL ARG ASN ALA VAL ASP ALA ALA LYS ALA SEQRES 12 B 237 LEU GLY ILE ASP ALA ARG VAL GLY ASN LEU PHE SER ALA SEQRES 13 B 237 ASP LEU PHE TYR SER PRO ASP GLY GLU MET PHE ASP VAL SEQRES 14 B 237 MET GLU LYS TYR GLY ILE LEU GLY VAL GLU MET GLU ALA SEQRES 15 B 237 ALA GLY ILE TYR GLY VAL ALA ALA GLU PHE GLY ALA LYS SEQRES 16 B 237 ALA LEU THR ILE CYS THR VAL SER ASP HIS ILE ARG THR SEQRES 17 B 237 HIS GLU GLN THR THR ALA ALA GLU ARG GLN THR THR PHE SEQRES 18 B 237 ASN ASP MET ILE LYS ILE ALA LEU GLU SER VAL LEU LEU SEQRES 19 B 237 GLY ASP LYS SEQRES 1 C 237 ALA THR PRO HIS ILE ASN ALA GLU MET GLY ASP PHE ALA SEQRES 2 C 237 ASP VAL VAL LEU MET PRO GLY ASP PRO LEU ARG ALA LYS SEQRES 3 C 237 TYR ILE ALA GLU THR PHE LEU GLU ASP ALA ARG GLU VAL SEQRES 4 C 237 ASN ASN VAL ARG GLY MET LEU GLY PHE THR GLY THR TYR SEQRES 5 C 237 LYS GLY ARG LYS ILE SER VAL MET GLY HIS GLY MET GLY SEQRES 6 C 237 ILE PRO SER CYS SER ILE TYR THR LYS GLU LEU ILE THR SEQRES 7 C 237 ASP PHE GLY VAL LYS LYS ILE ILE ARG VAL ALA SER CYS SEQRES 8 C 237 GLY ALA VAL LEU PRO HIS VAL LYS LEU ARG ASP VAL VAL SEQRES 9 C 237 ILE GLY MET GLY ALA CYS THR ASP SER LYS VAL ASN ARG SEQRES 10 C 237 ILE ARG PHE LYS ASP HIS ASP PHE ALA ALA ILE ALA ASP SEQRES 11 C 237 PHE ASP MET VAL ARG ASN ALA VAL ASP ALA ALA LYS ALA SEQRES 12 C 237 LEU GLY ILE ASP ALA ARG VAL GLY ASN LEU PHE SER ALA SEQRES 13 C 237 ASP LEU PHE TYR SER PRO ASP GLY GLU MET PHE ASP VAL SEQRES 14 C 237 MET GLU LYS TYR GLY ILE LEU GLY VAL GLU MET GLU ALA SEQRES 15 C 237 ALA GLY ILE TYR GLY VAL ALA ALA GLU PHE GLY ALA LYS SEQRES 16 C 237 ALA LEU THR ILE CYS THR VAL SER ASP HIS ILE ARG THR SEQRES 17 C 237 HIS GLU GLN THR THR ALA ALA GLU ARG GLN THR THR PHE SEQRES 18 C 237 ASN ASP MET ILE LYS ILE ALA LEU GLU SER VAL LEU LEU SEQRES 19 C 237 GLY ASP LYS HET FMC A 300 19 HET PO4 A 301 5 HET PO4 B 301 5 HET FMC B 302 19 HET PO4 C 301 5 HET FMC C 302 19 HETNAM FMC (1S)-1-(7-AMINO-1H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-1,4- HETNAM 2 FMC ANHYDRO-D-RIBITOL HETNAM PO4 PHOSPHATE ION FORMUL 4 FMC 3(C10 H13 N5 O4) FORMUL 5 PO4 3(O4 P 3-) FORMUL 10 HOH *718(H2 O) HELIX 1 AA1 ASP A 21 LEU A 33 1 13 HELIX 2 AA2 ASN A 41 MET A 45 5 5 HELIX 3 AA3 GLY A 65 PHE A 80 1 16 HELIX 4 AA4 LYS A 114 PHE A 120 1 7 HELIX 5 AA5 ASP A 130 GLY A 145 1 16 HELIX 6 AA6 GLU A 165 TYR A 173 1 9 HELIX 7 AA7 GLU A 181 GLY A 193 1 13 HELIX 8 AA8 THR A 213 THR A 220 1 8 HELIX 9 AA9 PHE A 221 LYS A 237 1 17 HELIX 10 AB1 PRO B 22 LEU B 33 1 12 HELIX 11 AB2 ASN B 41 MET B 45 5 5 HELIX 12 AB3 GLY B 65 GLY B 81 1 17 HELIX 13 AB4 LYS B 114 PHE B 120 1 7 HELIX 14 AB5 ASP B 130 LEU B 144 1 15 HELIX 15 AB6 GLU B 165 TYR B 173 1 9 HELIX 16 AB7 GLU B 181 GLY B 193 1 13 HELIX 17 AB8 THR B 213 ASP B 236 1 24 HELIX 18 AB9 ASP C 21 LEU C 33 1 13 HELIX 19 AC1 ASN C 41 MET C 45 5 5 HELIX 20 AC2 GLY C 65 PHE C 80 1 16 HELIX 21 AC3 LYS C 114 PHE C 120 1 7 HELIX 22 AC4 ASP C 130 LEU C 144 1 15 HELIX 23 AC5 GLY C 164 TYR C 173 1 10 HELIX 24 AC6 GLU C 181 GLY C 193 1 13 HELIX 25 AC7 THR C 213 LYS C 237 1 25 SHEET 1 AA110 GLU A 34 ASN A 40 0 SHEET 2 AA110 GLY A 47 TYR A 52 -1 O GLY A 47 N VAL A 39 SHEET 3 AA110 ARG A 55 MET A 60 -1 O VAL A 59 N PHE A 48 SHEET 4 AA110 VAL A 15 MET A 18 1 N LEU A 17 O SER A 58 SHEET 5 AA110 LYS A 84 ALA A 93 1 O ILE A 86 N MET A 18 SHEET 6 AA110 LYS A 195 HIS A 205 1 O THR A 201 N ALA A 89 SHEET 7 AA110 VAL A 103 THR A 111 -1 N VAL A 104 O CYS A 200 SHEET 8 AA110 ALA A 148 SER A 155 1 O ARG A 149 N ILE A 105 SHEET 9 AA110 GLY A 177 GLU A 179 1 O GLU A 179 N PHE A 154 SHEET 10 AA110 LYS A 84 ALA A 93 -1 N GLY A 92 O VAL A 178 SHEET 1 AA210 GLU B 34 ASN B 40 0 SHEET 2 AA210 GLY B 47 TYR B 52 -1 O GLY B 47 N VAL B 39 SHEET 3 AA210 ARG B 55 MET B 60 -1 O ILE B 57 N GLY B 50 SHEET 4 AA210 VAL B 15 MET B 18 1 N LEU B 17 O SER B 58 SHEET 5 AA210 LYS B 84 ALA B 93 1 O ILE B 86 N MET B 18 SHEET 6 AA210 LYS B 195 HIS B 205 1 O ILE B 199 N ARG B 87 SHEET 7 AA210 VAL B 103 THR B 111 -1 N VAL B 104 O CYS B 200 SHEET 8 AA210 ARG B 149 SER B 155 1 O SER B 155 N CYS B 110 SHEET 9 AA210 GLY B 177 GLU B 179 1 O GLU B 179 N PHE B 154 SHEET 10 AA210 LYS B 84 ALA B 93 -1 N GLY B 92 O VAL B 178 SHEET 1 AA310 GLU C 34 ASN C 40 0 SHEET 2 AA310 GLY C 47 TYR C 52 -1 O GLY C 47 N VAL C 39 SHEET 3 AA310 ARG C 55 MET C 60 -1 O VAL C 59 N PHE C 48 SHEET 4 AA310 VAL C 15 MET C 18 1 N LEU C 17 O SER C 58 SHEET 5 AA310 LYS C 84 ALA C 93 1 O ILE C 86 N MET C 18 SHEET 6 AA310 LYS C 195 HIS C 205 1 O ASP C 204 N ALA C 93 SHEET 7 AA310 VAL C 103 THR C 111 -1 N VAL C 104 O CYS C 200 SHEET 8 AA310 ARG C 149 SER C 155 1 O SER C 155 N CYS C 110 SHEET 9 AA310 GLY C 177 GLU C 179 1 O GLU C 179 N PHE C 154 SHEET 10 AA310 LYS C 84 ALA C 93 -1 N GLY C 92 O VAL C 178 SITE 1 AC1 17 MET A 64 ARG A 87 SER A 90 CYS A 91 SITE 2 AC1 17 GLY A 92 PHE A 159 VAL A 178 GLU A 179 SITE 3 AC1 17 MET A 180 GLU A 181 SER A 203 ASP A 204 SITE 4 AC1 17 ARG A 217 PO4 A 301 HOH A 500 HIS C 4 SITE 5 AC1 17 ARG C 43 SITE 1 AC2 8 PRO A 19 GLY A 20 ARG A 24 ARG A 87 SITE 2 AC2 8 ALA A 89 SER A 90 FMC A 300 ARG C 43 SITE 1 AC3 8 GLY B 20 ARG B 43 ARG B 87 ALA B 89 SITE 2 AC3 8 SER B 90 FMC B 302 HOH B 401 HOH B 420 SITE 1 AC4 16 HIS B 4 ARG B 43 MET B 64 ARG B 87 SITE 2 AC4 16 SER B 90 CYS B 91 GLY B 92 PHE B 159 SITE 3 AC4 16 VAL B 178 GLU B 179 MET B 180 GLU B 181 SITE 4 AC4 16 ASP B 204 ILE B 206 PO4 B 301 HOH B 572 SITE 1 AC5 9 ARG A 43 GLY C 20 ARG C 87 ALA C 89 SITE 2 AC5 9 SER C 90 FMC C 302 HOH C 450 HOH C 516 SITE 3 AC5 9 HOH C 652 SITE 1 AC6 15 HIS A 4 ARG A 43 ARG C 87 SER C 90 SITE 2 AC6 15 CYS C 91 GLY C 92 PHE C 159 VAL C 178 SITE 3 AC6 15 GLU C 179 MET C 180 GLU C 181 ASP C 204 SITE 4 AC6 15 PO4 C 301 HOH C 561 HOH C 644 CRYST1 120.625 120.625 240.006 90.00 90.00 120.00 P 61 2 2 36 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 0.008290 0.004786 0.000000 0.00000 SCALE2 0.000000 0.009573 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004167 0.00000