HEADER LIGASE 26-SEP-23 8UCF TITLE THERMOPHILIC RNA LIGASE FROM PALAEOCOCCUS PACIFICUS K238G COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP DEPENDENT DNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 EC: 6.5.1.3; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PALAEOCOCCUS PACIFICUS DY20341; SOURCE 3 ORGANISM_TAXID: 1343739; SOURCE 4 GENE: PAP_02190; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS RNA LIGASE, THERMOPHILIC, ARCHAEA, RNL3, NUCLEOTIDYL-TRANSFERASE, KEYWDS 2 LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR M.D.ROUSSEAU,J.L.HICKS,T.OULAVALLICKAL,A.WILLIAMSON,V.L.ARCUS, AUTHOR 2 M.W.PATRICK REVDAT 3 08-MAY-24 8UCF 1 JRNL REVDAT 2 13-MAR-24 8UCF 1 JRNL REVDAT 1 21-FEB-24 8UCF 0 JRNL AUTH M.ROUSSEAU,T.OULAVALLICKAL,A.WILLIAMSON,V.ARCUS,W.M.PATRICK, JRNL AUTH 2 J.HICKS JRNL TITL CHARACTERISATION AND ENGINEERING OF A THERMOPHILIC RNA JRNL TITL 2 LIGASE FROM PALAEOCOCCUS PACIFICUS. JRNL REF NUCLEIC ACIDS RES. V. 52 3924 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 38421610 JRNL DOI 10.1093/NAR/GKAE149 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 44023 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 2223 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 46.5700 - 4.7900 1.00 2755 157 0.2053 0.2334 REMARK 3 2 4.7900 - 3.8000 1.00 2689 124 0.1576 0.1661 REMARK 3 3 3.8000 - 3.3200 1.00 2618 142 0.1597 0.1658 REMARK 3 4 3.3200 - 3.0200 1.00 2610 151 0.1691 0.1844 REMARK 3 5 3.0200 - 2.8000 1.00 2638 128 0.1711 0.2079 REMARK 3 6 2.8000 - 2.6300 1.00 2610 123 0.1718 0.1853 REMARK 3 7 2.6300 - 2.5000 1.00 2610 153 0.1701 0.2086 REMARK 3 8 2.5000 - 2.3900 1.00 2616 128 0.1690 0.1956 REMARK 3 9 2.3900 - 2.3000 1.00 2608 123 0.1586 0.1899 REMARK 3 10 2.3000 - 2.2200 1.00 2580 147 0.1590 0.1728 REMARK 3 11 2.2200 - 2.1500 1.00 2553 164 0.1605 0.2042 REMARK 3 12 2.1500 - 2.0900 1.00 2589 136 0.1648 0.2176 REMARK 3 13 2.0900 - 2.0400 1.00 2570 148 0.1637 0.2067 REMARK 3 14 2.0400 - 1.9900 1.00 2567 133 0.1716 0.2162 REMARK 3 15 1.9900 - 1.9400 1.00 2598 133 0.1819 0.2125 REMARK 3 16 1.9400 - 1.9000 1.00 2589 133 0.2128 0.2610 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.168 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.779 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.47 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 3126 REMARK 3 ANGLE : 0.887 4214 REMARK 3 CHIRALITY : 0.060 458 REMARK 3 PLANARITY : 0.015 539 REMARK 3 DIHEDRAL : 8.004 432 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -16.9275 -27.8223 21.7697 REMARK 3 T TENSOR REMARK 3 T11: 0.1108 T22: 0.0956 REMARK 3 T33: 0.1264 T12: -0.0146 REMARK 3 T13: -0.0083 T23: 0.0263 REMARK 3 L TENSOR REMARK 3 L11: 0.8002 L22: 0.4402 REMARK 3 L33: 0.7796 L12: 0.0665 REMARK 3 L13: 0.3022 L23: 0.2121 REMARK 3 S TENSOR REMARK 3 S11: 0.0275 S12: 0.0323 S13: -0.0688 REMARK 3 S21: -0.0289 S22: 0.0298 S23: 0.0795 REMARK 3 S31: 0.0811 S32: -0.1122 S33: -0.0357 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 8UCF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1000277725. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-23 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ZANUDA V7.1 REMARK 200 DATA SCALING SOFTWARE : XDS V7.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44026 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 46.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : 0.07396 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 14.20 REMARK 200 R MERGE FOR SHELL (I) : 0.06594 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.730 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.19.2_4158 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 80 MM POTASSIUM CHLORIDE, 20 MM REMARK 280 MAGNESIUM CHLORIDE HEXAHYDRATE, 40 MM SODIUM CACODYLATE REMARK 280 TRIHYDRATE PH 6.5, 40% V/V (+/-)-2-METHYL-2,4-PENTANEDIOL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.72700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.72700 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 40.97500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.42950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.97500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.42950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 69.72700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.97500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.42950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.72700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.97500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.42950 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -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 69.72700 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 523 LIES ON A SPECIAL POSITION. 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 -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 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 LEU A 11 CG CD1 CD2 REMARK 470 ASP A 16 CG OD1 OD2 REMARK 470 GLU A 17 CG CD OE1 OE2 REMARK 470 GLU A 18 CB CG CD OE1 OE2 REMARK 470 GLU A 21 CB CG CD OE1 OE2 REMARK 470 VAL A 22 CG1 CG2 REMARK 470 LYS A 26 CG CD CE NZ REMARK 470 SER A 45 OG REMARK 470 ARG A 47 CG CD NE CZ NH1 NH2 REMARK 470 SER A 48 OG REMARK 470 ARG A 51 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 67 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 70 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 83 CD CE NZ REMARK 470 LYS A 85 CD CE NZ REMARK 470 LYS A 134 CG CD CE NZ REMARK 470 LYS A 161 CE NZ REMARK 470 LYS A 175 CG CD CE NZ REMARK 470 GLU A 183 CG CD OE1 OE2 REMARK 470 GLU A 184 CG CD OE1 OE2 REMARK 470 LYS A 187 CG CD CE NZ REMARK 470 LYS A 235 CG CD CE NZ REMARK 470 ARG A 290 CG CD NE CZ NH1 NH2 REMARK 470 SER A 309 O REMARK 470 ASP A 311 CG OD1 OD2 REMARK 470 ASP A 312 CG OD1 OD2 REMARK 470 LYS A 324 CE NZ REMARK 470 GLU A 336 CG CD OE1 OE2 REMARK 470 ARG A 337 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 339 CB CG CD NE CZ NH1 NH2 REMARK 470 ASP A 381 CG OD1 OD2 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 A 518 O HOH A 676 1.85 REMARK 500 O HOH A 689 O HOH A 705 2.04 REMARK 500 O HOH A 519 O HOH A 705 2.05 REMARK 500 O HOH A 596 O HOH A 705 2.06 REMARK 500 O HOH A 604 O HOH A 650 2.07 REMARK 500 O HOH A 683 O HOH A 691 2.09 REMARK 500 NZ LYS A 269 O HOH A 501 2.09 REMARK 500 NH2 ARG A 217 O HOH A 502 2.12 REMARK 500 O HOH A 519 O HOH A 689 2.15 REMARK 500 O HOH A 600 O HOH A 698 2.19 REMARK 500 O HOH A 558 O HOH A 650 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 501 O HOH A 720 3555 1.95 REMARK 500 O HOH A 525 O HOH A 671 8445 2.11 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 47 -120.34 53.59 REMARK 500 LYS A 83 -130.60 53.00 REMARK 500 ASP A 163 -132.03 58.41 REMARK 500 LYS A 175 -48.72 73.77 REMARK 500 PHE A 256 -58.36 67.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 38 0.09 SIDE CHAIN REMARK 500 ARG A 112 0.11 SIDE CHAIN 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 724 DISTANCE = 6.73 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 A 407 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 94 OD2 REMARK 620 2 GLU A 155 OE2 90.3 REMARK 620 3 ASP A 248 OD1 176.0 91.4 REMARK 620 4 HOH A 519 O 88.5 84.7 95.3 REMARK 620 5 HOH A 559 O 91.1 177.1 87.4 92.8 REMARK 620 6 HOH A 560 O 89.1 88.3 87.2 172.6 94.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 408 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 509 O REMARK 620 2 HOH A 531 O 103.7 REMARK 620 3 HOH A 537 O 171.4 84.9 REMARK 620 4 HOH A 685 O 78.7 159.1 92.9 REMARK 620 5 HOH A 715 O 95.1 82.9 84.4 76.2 REMARK 620 N 1 2 3 4 DBREF1 8UCF A 1 381 UNP A0A075LQ94_9EURY DBREF2 8UCF A A0A075LQ94 1 381 SEQADV 8UCF MET A -20 UNP A0A075LQ9 INITIATING METHIONINE SEQADV 8UCF GLY A -19 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF SER A -18 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF SER A -17 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF HIS A -16 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF HIS A -15 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF HIS A -14 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF HIS A -13 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF HIS A -12 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF HIS A -11 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF SER A -10 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF SER A -9 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF GLY A -8 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF LEU A -7 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF VAL A -6 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF PRO A -5 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF ARG A -4 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF GLY A -3 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF SER A -2 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF HIS A -1 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF MET A 0 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCF GLY A 238 UNP A0A075LQ9 LYS 238 ENGINEERED MUTATION SEQRES 1 A 402 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 402 LEU VAL PRO ARG GLY SER HIS MET MET VAL SER SER TYR SEQRES 3 A 402 PHE LYS GLY ILE LEU LEU ASN LEU GLY LEU ASP GLU GLU SEQRES 4 A 402 ARG ILE GLU VAL LEU GLU ASN LYS GLY GLY ILE VAL GLU SEQRES 5 A 402 ASP GLU PHE GLU GLY MET ARG TYR LEU ARG LEU LYS ASP SEQRES 6 A 402 SER ALA ARG SER LEU ARG ARG GLY THR VAL VAL PHE ASP SEQRES 7 A 402 GLU HIS ASN ILE ILE LEU GLY PHE PRO HIS ILE LYS ARG SEQRES 8 A 402 VAL VAL GLN LEU GLU ASN GLY ILE ARG ARG ALA PHE LYS SEQRES 9 A 402 ARG LYS PRO PHE TYR VAL GLU GLU LYS VAL ASP GLY TYR SEQRES 10 A 402 ASN VAL ARG VAL ALA LYS ILE GLY GLU LYS ILE LEU VAL SEQRES 11 A 402 PHE THR ARG GLY GLY PHE VAL CYS PRO PHE THR THR GLU SEQRES 12 A 402 ARG ILE GLU ASP PHE ILE THR LEU ASP PHE PHE LYS ASP SEQRES 13 A 402 TYR PRO ASN MET VAL LEU CYS GLY GLU MET ALA GLY PRO SEQRES 14 A 402 GLU SER PRO TYR LEU VAL GLU GLY PRO PRO TYR VAL LYS SEQRES 15 A 402 GLU ASP ILE GLN PHE PHE LEU PHE ASP ILE GLN GLU LYS SEQRES 16 A 402 LYS THR GLY ARG SER LEU PRO VAL GLU GLU ARG LEU LYS SEQRES 17 A 402 LEU ALA GLU GLU TYR GLY ILE PRO SER VAL GLU VAL PHE SEQRES 18 A 402 GLY LEU TYR ASP LEU SER ARG ILE ASP GLU LEU HIS ALA SEQRES 19 A 402 LEU ILE ASP ARG LEU THR LYS GLU LYS ARG GLU GLY ILE SEQRES 20 A 402 VAL MET LYS SER PRO ASP MET LYS LYS ILE VAL GLY TYR SEQRES 21 A 402 VAL THR PRO TYR ALA ASN ILE ASN ASP ILE LYS ILE GLY SEQRES 22 A 402 ALA ARG ILE PHE PHE ASP LEU PRO HIS GLY TYR PHE MET SEQRES 23 A 402 GLN ARG ILE LYS ARG LEU ALA PHE TYR LEU ALA GLU ARG SEQRES 24 A 402 LYS ILE ARG GLY GLU GLU PHE ASP GLU TYR ALA ARG ALA SEQRES 25 A 402 LEU GLY LYS VAL LEU LEU GLU PRO PHE VAL GLU SER ILE SEQRES 26 A 402 TRP ASP ILE SER SER GLY ASP ASP GLU ILE ALA GLU LEU SEQRES 27 A 402 PHE THR VAL ARG VAL LYS LYS LEU GLU THR ALA HIS LYS SEQRES 28 A 402 MET VAL THR HIS PHE GLU ARG LEU ARG LEU LYS ILE HIS SEQRES 29 A 402 ILE ASP ASP ILE GLU VAL LEU ASP ASN GLY TYR TRP ARG SEQRES 30 A 402 ILE THR PHE LYS ARG VAL TYR PRO ASP ALA THR LYS GLU SEQRES 31 A 402 MET ARG GLU LEU TRP ASN GLY HIS ALA PHE VAL ASP HET GOL A 401 6 HET GOL A 402 6 HET GOL A 403 6 HET GOL A 404 6 HET GOL A 405 6 HET GOL A 406 6 HET MG A 407 1 HET MG A 408 1 HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 6(C3 H8 O3) FORMUL 8 MG 2(MG 2+) FORMUL 10 HOH *224(H2 O) HELIX 1 AA1 SER A 3 LEU A 13 1 11 HELIX 2 AA2 ASP A 16 LYS A 26 1 11 HELIX 3 AA3 GLN A 73 LYS A 83 1 11 HELIX 4 AA4 CYS A 117 ILE A 124 1 8 HELIX 5 AA5 GLU A 125 PHE A 127 5 3 HELIX 6 AA6 LEU A 130 TYR A 136 1 7 HELIX 7 AA7 PRO A 181 GLY A 193 1 13 HELIX 8 AA8 ASP A 204 SER A 206 5 3 HELIX 9 AA9 ARG A 207 GLU A 221 1 15 HELIX 10 AB1 THR A 241 ARG A 254 1 14 HELIX 11 AB2 GLY A 262 ARG A 278 1 17 HELIX 12 AB3 ARG A 281 SER A 308 1 28 HELIX 13 AB4 LYS A 324 LEU A 338 1 15 HELIX 14 AB5 TYR A 363 ASN A 375 1 13 SHEET 1 AA1 4 ILE A 29 PHE A 34 0 SHEET 2 AA1 4 MET A 37 LEU A 42 -1 O ARG A 41 N VAL A 30 SHEET 3 AA1 4 VAL A 54 VAL A 55 -1 O VAL A 55 N LEU A 40 SHEET 4 AA1 4 ILE A 61 ILE A 62 -1 O ILE A 62 N VAL A 54 SHEET 1 AA2 5 LYS A 69 ARG A 70 0 SHEET 2 AA2 5 ILE A 236 VAL A 240 1 O GLY A 238 N LYS A 69 SHEET 3 AA2 5 GLY A 225 LYS A 229 -1 N MET A 228 O VAL A 237 SHEET 4 AA2 5 PHE A 87 LYS A 92 -1 N TYR A 88 O LYS A 229 SHEET 5 AA2 5 VAL A 199 TYR A 203 -1 O TYR A 203 N PHE A 87 SHEET 1 AA3 4 LYS A 106 PHE A 110 0 SHEET 2 AA3 4 TYR A 96 ILE A 103 -1 N ILE A 103 O LYS A 106 SHEET 3 AA3 4 MET A 139 ALA A 146 -1 O LEU A 141 N VAL A 100 SHEET 4 AA3 4 GLN A 165 GLU A 173 -1 O GLN A 172 N VAL A 140 SHEET 1 AA4 3 ALA A 315 VAL A 322 0 SHEET 2 AA4 3 TRP A 355 VAL A 362 -1 O TRP A 355 N VAL A 322 SHEET 3 AA4 3 LYS A 341 VAL A 349 -1 N GLU A 348 O ARG A 356 LINK OD2 ASP A 94 MG MG A 407 1555 1555 2.08 LINK OE2 GLU A 155 MG MG A 407 1555 1555 2.08 LINK OD1 ASP A 248 MG MG A 407 1555 1555 2.04 LINK MG MG A 407 O HOH A 519 1555 1555 2.19 LINK MG MG A 407 O HOH A 559 1555 1555 2.06 LINK MG MG A 407 O HOH A 560 1555 1555 2.05 LINK MG MG A 408 O HOH A 509 1555 1555 2.00 LINK MG MG A 408 O HOH A 531 1555 1555 2.13 LINK MG MG A 408 O HOH A 537 1555 1555 2.12 LINK MG MG A 408 O HOH A 685 1555 1555 2.23 LINK MG MG A 408 O HOH A 715 1555 1555 2.51 CRYST1 81.950 96.859 139.454 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012203 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010324 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007171 0.00000