HEADER LIGASE 26-SEP-23 8UCH TITLE THERMOPHILIC RNA LIGASE FROM PALAEOCOCCUS PACIFICUS K92A + ATP 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; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLAMSID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28B 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 8UCH 1 JRNL REVDAT 2 13-MAR-24 8UCH 1 JRNL REVDAT 1 21-FEB-24 8UCH 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. 2.14 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) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 31262 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.400 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 46.7200 - 5.1600 1.00 2215 151 0.2127 0.2198 REMARK 3 2 5.1500 - 4.0900 1.00 2135 147 0.1464 0.1626 REMARK 3 3 4.0900 - 3.5800 1.00 2094 142 0.1488 0.1901 REMARK 3 4 3.5800 - 3.2500 1.00 2108 144 0.1463 0.1830 REMARK 3 5 3.2500 - 3.0200 1.00 2080 143 0.1545 0.1825 REMARK 3 6 3.0200 - 2.8400 1.00 2101 143 0.1558 0.2069 REMARK 3 7 2.8400 - 2.7000 1.00 2055 141 0.1607 0.2137 REMARK 3 8 2.7000 - 2.5800 1.00 2080 142 0.1636 0.1824 REMARK 3 9 2.5800 - 2.4800 1.00 2068 142 0.1782 0.2184 REMARK 3 10 2.4800 - 2.3900 1.00 2078 141 0.1856 0.2533 REMARK 3 11 2.3900 - 2.3200 1.00 2048 140 0.1908 0.2356 REMARK 3 12 2.3200 - 2.2500 1.00 2084 143 0.1825 0.2595 REMARK 3 13 2.2500 - 2.1900 1.00 2031 138 0.2012 0.2346 REMARK 3 14 2.1900 - 2.1400 1.00 2085 143 0.2113 0.2616 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) : 0.186 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.55 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 3134 REMARK 3 ANGLE : 0.785 4234 REMARK 3 CHIRALITY : 0.055 459 REMARK 3 PLANARITY : 0.008 537 REMARK 3 DIHEDRAL : 9.063 440 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): 57.7906 20.7023 48.3892 REMARK 3 T TENSOR REMARK 3 T11: 0.0809 T22: 0.1677 REMARK 3 T33: 0.1590 T12: 0.0128 REMARK 3 T13: -0.0085 T23: -0.0455 REMARK 3 L TENSOR REMARK 3 L11: 1.0473 L22: 0.4773 REMARK 3 L33: 0.8976 L12: -0.1917 REMARK 3 L13: 0.3992 L23: -0.3848 REMARK 3 S TENSOR REMARK 3 S11: 0.0213 S12: -0.0112 S13: -0.0488 REMARK 3 S21: 0.0170 S22: 0.0339 S23: -0.0591 REMARK 3 S31: 0.0502 S32: 0.1498 S33: -0.0510 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 8UCH 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_1000277794. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-22 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) : 0.953659 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 : 31266 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.140 REMARK 200 RESOLUTION RANGE LOW (A) : 46.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : 0.10880 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 46.72 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.96750 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.550 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 80 MM STRONTIUM CHLORIDE HEXAHYDRATE, REMARK 280 20 MM MAGNESIUM CHLORIDE HEXAHYDRATE, 40 MM SODIUM CACODYLATE REMARK 280 TRIHYDRATE PH 7.0, 20% V/V (+/-)-2-METHYL-2,4-PENTANEDIOL, 12 MM REMARK 280 SPERMINE TETRAHYDROCHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 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 70.05050 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 70.05050 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 41.01000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.62550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.01000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.62550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 70.05050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.01000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.62550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 70.05050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.01000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.62550 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: 9510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -161.0 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 82.02000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 70.05050 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 703 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 465 ASP A 381 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 CG CD OE1 OE2 REMARK 470 GLU A 21 CG CD OE1 OE2 REMARK 470 ASN A 25 CG OD1 ND2 REMARK 470 LYS A 26 CG CD CE NZ REMARK 470 VAL A 30 CG1 REMARK 470 ASP A 44 CB CG OD1 OD2 REMARK 470 SER A 45 CB OG REMARK 470 ARG A 47 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 58 CB CG CD OE1 OE2 REMARK 470 HIS A 59 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 68 CD1 REMARK 470 ARG A 80 NH2 REMARK 470 LYS A 83 CD CE NZ REMARK 470 LYS A 85 CD CE NZ REMARK 470 GLU A 105 CD OE1 OE2 REMARK 470 LEU A 130 CB CG CD1 CD2 REMARK 470 MET A 139 CE REMARK 470 LYS A 161 CG CD CE NZ REMARK 470 LYS A 175 CG CD CE NZ REMARK 470 ARG A 178 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 183 CG CD OE1 OE2 REMARK 470 GLU A 184 CG CD OE1 OE2 REMARK 470 GLU A 190 CG CD OE1 OE2 REMARK 470 ASP A 209 OD2 REMARK 470 LYS A 220 CE NZ REMARK 470 LYS A 234 CE NZ REMARK 470 LYS A 235 CG CD CE NZ REMARK 470 GLU A 283 CG CD OE1 OE2 REMARK 470 ARG A 290 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 294 CG CD CE NZ REMARK 470 ASP A 311 CG OD1 OD2 REMARK 470 LYS A 323 CD CE NZ REMARK 470 LYS A 324 CG CD CE NZ REMARK 470 GLU A 326 CG CD OE1 OE2 REMARK 470 ARG A 337 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG A 339 CB CG CD NE CZ NH1 NH2 REMARK 470 LYS A 341 CG CD CE NZ 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 MG MG A 409 O HOH A 511 1.65 REMARK 500 O HOH A 608 O HOH A 674 1.96 REMARK 500 O HOH A 542 O HOH A 551 2.06 REMARK 500 O HOH A 516 O HOH A 551 2.07 REMARK 500 OH TYR A 288 O HOH A 501 2.08 REMARK 500 NH2 ARG A 70 O HOH A 502 2.09 REMARK 500 O HOH A 576 O HOH A 674 2.11 REMARK 500 O HOH A 556 O HOH A 697 2.12 REMARK 500 O HOH A 517 O HOH A 577 2.12 REMARK 500 O1A ATP A 401 O HOH A 502 2.15 REMARK 500 O HOH A 504 O HOH A 511 2.16 REMARK 500 O HOH A 502 O HOH A 503 2.16 REMARK 500 O1A ATP A 401 O HOH A 503 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 ARG A 47 -127.37 53.77 REMARK 500 ASP A 57 -168.56 -167.12 REMARK 500 LYS A 83 -126.59 54.28 REMARK 500 GLU A 149 69.22 -119.02 REMARK 500 ASP A 163 -127.82 58.04 REMARK 500 LYS A 175 -50.07 72.25 REMARK 500 PHE A 256 -57.25 61.35 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 408 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 94 OD2 REMARK 620 2 GLU A 155 OE2 86.4 REMARK 620 3 ASP A 248 OD1 177.3 94.9 REMARK 620 4 HOH A 524 O 89.3 91.5 93.1 REMARK 620 5 HOH A 556 O 88.1 83.2 89.7 174.2 REMARK 620 6 HOH A 599 O 90.6 173.5 87.9 94.2 90.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 410 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 148 O REMARK 620 2 HOH A 516 O 82.9 REMARK 620 3 HOH A 551 O 71.3 46.1 REMARK 620 4 HOH A 614 O 85.6 65.5 108.9 REMARK 620 5 HOH A 664 O 80.8 134.4 88.3 153.4 REMARK 620 6 HOH A 672 O 135.8 136.2 117.4 124.8 57.6 REMARK 620 7 HOH A 685 O 73.5 155.7 127.2 106.2 47.9 67.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 409 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 306 O REMARK 620 2 SER A 309 O 88.4 REMARK 620 3 ASP A 312 OD1 110.6 132.7 REMARK 620 4 ASP A 312 OD2 129.2 87.2 46.9 REMARK 620 5 HOH A 504 O 100.9 149.4 71.1 108.0 REMARK 620 6 HOH A 505 O 78.2 61.1 80.3 55.8 149.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 412 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 349 O REMARK 620 2 HOH A 528 O 80.8 REMARK 620 3 HOH A 711 O 163.0 88.7 REMARK 620 N 1 2 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 ATP A 401 O2A REMARK 620 2 HOH A 536 O 91.7 REMARK 620 3 HOH A 544 O 172.2 88.4 REMARK 620 4 HOH A 557 O 90.0 177.8 90.1 REMARK 620 5 HOH A 558 O 83.0 94.3 89.2 87.2 REMARK 620 6 HOH A 581 O 94.7 88.4 93.1 90.1 176.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 411 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 401 O2G REMARK 620 2 ATP A 401 O1B 95.1 REMARK 620 3 HOH A 510 O 101.8 92.4 REMARK 620 4 HOH A 523 O 141.1 107.2 108.4 REMARK 620 N 1 2 3 DBREF1 8UCH A 1 381 UNP A0A075LQ94_9EURY DBREF2 8UCH A A0A075LQ94 1 381 SEQADV 8UCH MET A -20 UNP A0A075LQ9 INITIATING METHIONINE SEQADV 8UCH GLY A -19 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH SER A -18 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH SER A -17 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH HIS A -16 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH HIS A -15 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH HIS A -14 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH HIS A -13 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH HIS A -12 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH HIS A -11 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH SER A -10 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH SER A -9 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH GLY A -8 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH LEU A -7 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH VAL A -6 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH PRO A -5 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH ARG A -4 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH GLY A -3 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH SER A -2 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH HIS A -1 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH MET A 0 UNP A0A075LQ9 EXPRESSION TAG SEQADV 8UCH ALA A 92 UNP A0A075LQ9 LYS 92 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 ALA 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 LYS 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 ATP A 401 31 HET GOL A 402 6 HET GOL A 403 6 HET SPD A 404 10 HET GOL A 405 6 HET GOL A 406 6 HET MG A 407 1 HET MG A 408 1 HET MG A 409 1 HET NA A 410 1 HET NA A 411 1 HET NA A 412 1 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM GOL GLYCEROL HETNAM SPD SPERMIDINE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 GOL 4(C3 H8 O3) FORMUL 5 SPD C7 H19 N3 FORMUL 8 MG 3(MG 2+) FORMUL 11 NA 3(NA 1+) FORMUL 14 HOH *212(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 GLY A 282 SER A 308 1 27 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 LYS 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 ALA 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 THR A 111 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 PHE A 359 N PHE A 318 SHEET 3 AA4 3 LYS A 341 VAL A 349 -1 N ASP A 346 O THR A 358 LINK OD2 ASP A 94 MG MG A 408 1555 1555 2.11 LINK O PRO A 148 NA NA A 410 1555 1555 2.49 LINK OE2 GLU A 155 MG MG A 408 1555 1555 1.89 LINK OD1 ASP A 248 MG MG A 408 1555 1555 2.05 LINK O ASP A 306 MG MG A 409 1555 1555 2.37 LINK O SER A 309 MG MG A 409 1555 1555 2.37 LINK OD1 ASP A 312 MG MG A 409 1555 1555 2.66 LINK OD2 ASP A 312 MG MG A 409 1555 1555 2.84 LINK O VAL A 349 NA NA A 412 1555 1555 2.54 LINK O2A ATP A 401 MG MG A 407 1555 1555 2.09 LINK O2G ATP A 401 NA NA A 411 1555 1555 2.73 LINK O1B ATP A 401 NA NA A 411 1555 1555 1.99 LINK MG MG A 407 O HOH A 536 1555 1555 1.99 LINK MG MG A 407 O HOH A 544 1555 1555 2.20 LINK MG MG A 407 O HOH A 557 1555 1555 1.96 LINK MG MG A 407 O HOH A 558 1555 1555 2.05 LINK MG MG A 407 O HOH A 581 1555 1555 2.19 LINK MG MG A 408 O HOH A 524 1555 1555 2.06 LINK MG MG A 408 O HOH A 556 1555 1555 2.11 LINK MG MG A 408 O HOH A 599 1555 1555 1.97 LINK MG MG A 409 O HOH A 504 1555 1555 1.73 LINK MG MG A 409 O HOH A 505 1555 1555 2.08 LINK NA NA A 410 O HOH A 516 1555 1555 2.79 LINK NA NA A 410 O HOH A 551 1555 1555 2.43 LINK NA NA A 410 O HOH A 614 1555 1555 1.95 LINK NA NA A 410 O HOH A 664 1555 1555 2.36 LINK NA NA A 410 O HOH A 672 1555 1555 2.87 LINK NA NA A 410 O HOH A 685 1555 1555 2.98 LINK NA NA A 411 O HOH A 510 1555 1555 2.00 LINK NA NA A 411 O HOH A 523 1555 1555 1.93 LINK NA NA A 412 O HOH A 528 1555 3755 3.19 LINK NA NA A 412 O HOH A 711 1555 1555 2.67 CRYST1 82.020 97.251 140.101 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 0.012192 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010283 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007138 0.00000