HEADER DNA BINDING PROTEIN 07-APR-19 6RAS TITLE PMAR-LIG_PRE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*TP*TP*CP*CP*GP*AP*CP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)- COMPND 4 3'); COMPND 5 CHAIN: B; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA/RNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC))- COMPND 9 D(P*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: THERE IS A BREAK IN THE CHAIN BETWEEN NT31 AND NT32.; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA; COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: ATP-DEPENDENT DNA LIGASE; COMPND 19 CHAIN: I; COMPND 20 ENGINEERED: YES; COMPND 21 OTHER_DETAILS: THIS IS A R120 A MUTANT SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: DNA LAUNCH VECTOR PDE-GFP2; SOURCE 4 ORGANISM_TAXID: 415098; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: DNA LAUNCH VECTOR PDE-GFP2; SOURCE 8 ORGANISM_TAXID: 415098; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: DNA LAUNCH VECTOR PDE-GFP2; SOURCE 12 ORGANISM_TAXID: 415098; SOURCE 13 MOL_ID: 4; SOURCE 14 ORGANISM_SCIENTIFIC: PROCHLOROCOCCUS MARINUS STR. MIT 9302; SOURCE 15 ORGANISM_TAXID: 74545; SOURCE 16 GENE: EU96_0746; SOURCE 17 EXPRESSION_SYSTEM: PROCHLOROCOCCUS MARINUS; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 1219 KEYWDS DNA LIGASE, ATP-DEPENDENT, LIGASE-DNA CO-CRYSTAL STRUCTURE, KEYWDS 2 DETERMINANTS IN DNA BINDING, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.K.S.LEIROS,A.WILLIAMSON REVDAT 3 01-MAY-24 6RAS 1 REMARK REVDAT 2 29-JAN-20 6RAS 1 JRNL REVDAT 1 10-JUL-19 6RAS 0 JRNL AUTH A.WILLIAMSON,H.S.LEIROS JRNL TITL STRUCTURAL INTERMEDIATES OF A DNA-LIGASE COMPLEX ILLUMINATE JRNL TITL 2 THE ROLE OF THE CATALYTIC METAL ION AND MECHANISM OF JRNL TITL 3 PHOSPHODIESTER BOND FORMATION. JRNL REF NUCLEIC ACIDS RES. V. 47 7147 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 31312841 JRNL DOI 10.1093/NAR/GKZ596 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 24493 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1227 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 24.3671 - 5.6985 0.99 2609 160 0.1828 0.2077 REMARK 3 2 5.6985 - 4.5326 0.99 2593 142 0.1525 0.2011 REMARK 3 3 4.5326 - 3.9624 0.99 2582 136 0.1516 0.2167 REMARK 3 4 3.9624 - 3.6014 1.00 2595 141 0.1696 0.2268 REMARK 3 5 3.6014 - 3.3439 0.99 2580 117 0.1888 0.2804 REMARK 3 6 3.3439 - 3.1472 0.99 2568 143 0.2174 0.2602 REMARK 3 7 3.1472 - 2.9899 1.00 2637 90 0.2355 0.3139 REMARK 3 8 2.9899 - 2.8600 1.00 2549 159 0.2760 0.3623 REMARK 3 9 2.8600 - 2.7500 0.99 2553 139 0.2968 0.3558 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.017 4588 REMARK 3 ANGLE : 1.329 6337 REMARK 3 CHIRALITY : 0.067 685 REMARK 3 PLANARITY : 0.006 658 REMARK 3 DIHEDRAL : 13.523 2606 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 6RAS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1292101700. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-18 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 : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24531 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.690 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.16000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: HOME-MADE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, BUFFER, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 51.70400 REMARK 290 SMTRY3 2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, D, I 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 GLY I 1 REMARK 465 ARG I 2 REMARK 465 GLN I 3 REMARK 465 LYS I 4 REMARK 465 ALA I 438 REMARK 465 GLY I 439 REMARK 465 GLU I 440 REMARK 465 LYS I 441 REMARK 465 VAL I 442 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 GLU I 72 CD OE1 OE2 REMARK 470 GLU I 155 CD OE1 OE2 REMARK 470 LYS I 239 CD CE NZ REMARK 470 LYS I 259 CG CD CE NZ REMARK 470 LYS I 285 CE NZ REMARK 470 LYS I 398 CD CE NZ REMARK 470 LYS I 437 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 HD1 HIS I 149 O1 SO4 I 503 1.30 REMARK 500 HH11 ARG I 364 OE2 GLU I 393 1.40 REMARK 500 O TRP I 396 HE ARG I 399 1.58 REMARK 500 HH22 ARG I 21 O GLY I 122 1.58 REMARK 500 O3 SO4 I 502 O HOH I 601 1.61 REMARK 500 OP2 DA B 8 O HOH B 101 1.90 REMARK 500 O HOH I 737 O HOH I 740 1.97 REMARK 500 NH1 ARG I 364 OE2 GLU I 393 2.01 REMARK 500 O1 SO4 I 502 O HOH I 602 2.08 REMARK 500 ND1 HIS I 149 O1 SO4 I 503 2.14 REMARK 500 NZ LYS I 161 O HOH I 603 2.15 REMARK 500 NH2 ARG I 178 O HOH I 604 2.16 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 OH TYR I 213 O PHE I 436 1554 2.04 REMARK 500 OE1 GLN I 179 NZ LYS I 400 1554 2.18 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 DG B 11 O3' DG B 11 C3' -0.042 REMARK 500 DC D 32 P DC D 32 OP3 -0.105 REMARK 500 ASN I 129 C ASN I 129 O 0.147 REMARK 500 GLN I 179 CD GLN I 179 NE2 0.284 REMARK 500 LYS I 400 CG LYS I 400 CD -0.287 REMARK 500 LYS I 400 CE LYS I 400 NZ 0.798 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 DC B 3 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA B 6 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 11 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT C 24 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG C 25 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA C 28 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC C 29 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG D 39 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG D 40 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA D 41 O4' - C4' - C3' ANGL. DEV. = -3.4 DEGREES REMARK 500 DA D 41 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 LYS I 130 C - N - CA ANGL. DEV. = -20.0 DEGREES REMARK 500 GLN I 179 CA - CB - CG ANGL. DEV. = -18.9 DEGREES REMARK 500 GLN I 179 CB - CG - CD ANGL. DEV. = -24.3 DEGREES REMARK 500 GLN I 179 CG - CD - OE1 ANGL. DEV. = -13.7 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 LYS I 8 -60.84 -29.04 REMARK 500 GLN I 67 -136.97 -84.97 REMARK 500 PHE I 110 -70.55 -155.52 REMARK 500 SER I 124 -157.65 -125.59 REMARK 500 PHE I 135 68.69 -156.73 REMARK 500 HIS I 154 44.58 -154.81 REMARK 500 SER I 223 -153.33 -133.82 REMARK 500 ASP I 237 -0.95 -57.19 REMARK 500 ASN I 263 51.93 -100.57 REMARK 500 LYS I 279 -9.82 -55.71 REMARK 500 HIS I 280 37.49 -153.46 REMARK 500 LEU I 284 63.38 -106.67 REMARK 500 LEU I 297 5.30 -68.80 REMARK 500 LYS I 333 162.84 175.79 REMARK 500 PHE I 436 57.19 80.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN I 129 -12.33 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 I 751 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH I 752 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH I 753 DISTANCE = 8.08 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP D 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE I 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 I 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 I 503 DBREF 6RAS B 1 21 PDB 6RAS 6RAS 1 21 DBREF 6RAS C 22 31 PDB 6RAS 6RAS 22 31 DBREF 6RAS D 32 42 PDB 6RAS 6RAS 32 42 DBREF1 6RAS I 2 442 UNP A0A0A2ACP7_PROMR DBREF2 6RAS I A0A0A2ACP7 2 442 SEQADV 6RAS GLY I 1 UNP A0A0A2ACP EXPRESSION TAG SEQADV 6RAS ALA I 120 UNP A0A0A2ACP ARG 120 ENGINEERED MUTATION SEQRES 1 B 21 DT DT DC DC DG DA DC DA DG DT DG DG DG SEQRES 2 B 21 DG DT DC DG DC DA DA DT SEQRES 1 C 10 DA DT DT DG DC DG DA DC OMC DC SEQRES 1 D 11 DC DA DC DT DA DT DC DG DG DA DA SEQRES 1 I 442 GLY ARG GLN LYS GLU LEU PHE LYS GLU GLU ILE ILE HIS SEQRES 2 I 442 GLN LEU GLU LEU HIS PRO SER ARG LEU ASP LYS GLU LYS SEQRES 3 I 442 ILE ILE SER GLU ALA MET GLU ASP GLY ILE ASP ASP PHE SEQRES 4 I 442 PHE GLU GLY ILE ARG MET ALA LEU ASP PRO LEU VAL THR SEQRES 5 I 442 PHE GLY VAL LYS ILE VAL PRO GLU LYS GLU SER GLU LYS SEQRES 6 I 442 SER GLN ASN PHE LEU TRP GLU ASP PHE ARG LYS LEU ALA SEQRES 7 I 442 ASN LYS LEU MET GLN ARG GLU LEU THR GLY HIS ALA ALA SEQRES 8 I 442 ARG ASP ALA ILE LEU THR ALA MET GLU SER ALA THR LYS SEQRES 9 I 442 GLU GLU TRP ASN GLY PHE TYR ARG ARG VAL LEU ILE LYS SEQRES 10 I 442 ASP LEU ALA CYS GLY VAL SER GLU LYS THR ILE ASN LYS SEQRES 11 I 442 ILE ALA LYS LYS PHE PRO LYS TYR ALA ILE PRO ILE PHE SEQRES 12 I 442 SER CYS PRO LEU ALA HIS ASP SER ALA ASN HIS GLU LYS SEQRES 13 I 442 LYS MET ILE GLY LYS LYS GLN ILE GLU ILE LYS LEU ASP SEQRES 14 I 442 GLY VAL ARG VAL LEU THR ILE ILE ARG GLN ASN LYS VAL SEQRES 15 I 442 GLU MET PHE SER ARG ASN GLY LYS GLN PHE HIS ASN PHE SEQRES 16 I 442 GLY HIS ILE ILE LEU GLU ILE GLU ASN VAL LEU LYS GLU SEQRES 17 I 442 ASP PRO ALA PRO TYR ASP LEU VAL LEU ASP GLY GLU VAL SEQRES 18 I 442 MET SER ALA ASN PHE GLN ASP LEU MET LYS GLN VAL HIS SEQRES 19 I 442 ARG LYS ASP GLY LYS GLN THR LYS ASP ALA VAL LEU HIS SEQRES 20 I 442 LEU PHE ASP LEU CYS PRO LEU GLU ASN PHE GLN LYS GLY SEQRES 21 I 442 ARG TRP ASN THR LYS GLN THR ALA ARG SER LEU LEU VAL SEQRES 22 I 442 LYS LYS TRP VAL ALA LYS HIS SER LEU LEU LEU LYS HIS SEQRES 23 I 442 ILE GLN THR LEU GLU TRP GLU ASN VAL ASP LEU ASP THR SEQRES 24 I 442 ILE GLN GLY GLN LYS ARG PHE VAL GLU LEU ASN LYS SER SEQRES 25 I 442 ALA VAL GLU GLY GLY TYR GLU GLY VAL MET ILE LYS ASP SEQRES 26 I 442 PRO ASP GLY MET TYR GLU CYS LYS ARG THR HIS SER TRP SEQRES 27 I 442 LEU LYS ALA LYS PRO PHE ILE GLU VAL THR LEU LYS VAL SEQRES 28 I 442 VAL SER VAL GLU GLU GLY THR GLY ARG ASN LYS GLY ARG SEQRES 29 I 442 LEU GLY ALA ILE LEU VAL GLU GLY GLU ASP ASP GLY TYR SEQRES 30 I 442 GLU TYR SER LEU SER CYS GLY SER GLY PHE SER ASP ILE SEQRES 31 I 442 GLN ARG GLU GLU TYR TRP SER LYS ARG LYS HIS LEU LEU SEQRES 32 I 442 GLY GLN LEU VAL GLU ILE ARG ALA ASP ALA LYS THR LYS SEQRES 33 I 442 SER LYS ASP GLY VAL ALA PHE SER LEU ARG PHE PRO ARG SEQRES 34 I 442 PHE LYS CYS PHE ARG GLY PHE LYS ALA GLY GLU LYS VAL HET OMC C 30 34 HET PGE C 101 24 HET AMP D 300 34 HET PGE I 501 24 HET SO4 I 502 5 HET SO4 I 503 5 HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM PGE TRIETHYLENE GLYCOL HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 2 OMC C10 H16 N3 O8 P FORMUL 5 PGE 2(C6 H14 O4) FORMUL 6 AMP C10 H14 N5 O7 P FORMUL 8 SO4 2(O4 S 2-) FORMUL 10 HOH *196(H2 O) HELIX 1 AA1 PHE I 7 HIS I 18 1 12 HELIX 2 AA2 SER I 20 ASP I 34 1 15 HELIX 3 AA3 ILE I 36 ASP I 48 1 13 HELIX 4 AA4 LEU I 70 GLN I 83 1 14 HELIX 5 AA5 THR I 87 ALA I 102 1 16 HELIX 6 AA6 THR I 103 PHE I 110 1 8 HELIX 7 AA7 PHE I 110 ILE I 116 1 7 HELIX 8 AA8 SER I 124 LYS I 133 1 10 HELIX 9 AA9 LYS I 134 ALA I 139 5 6 HELIX 10 AB1 ALA I 152 MET I 158 5 7 HELIX 11 AB2 PHE I 195 ASP I 209 1 15 HELIX 12 AB3 ASN I 225 HIS I 234 1 10 HELIX 13 AB4 LEU I 254 GLY I 260 1 7 HELIX 14 AB5 LYS I 265 LYS I 279 1 15 HELIX 15 AB6 THR I 299 GLY I 316 1 18 HELIX 16 AB7 THR I 358 LYS I 362 5 5 HELIX 17 AB8 SER I 388 LYS I 398 1 11 SHEET 1 AA1 5 LEU I 147 ASP I 150 0 SHEET 2 AA1 5 ARG I 334 ALA I 341 1 O LYS I 340 N HIS I 149 SHEET 3 AA1 5 GLY I 320 LYS I 324 -1 N ILE I 323 O LEU I 339 SHEET 4 AA1 5 LYS I 161 LYS I 167 -1 N GLU I 165 O MET I 322 SHEET 5 AA1 5 GLU I 293 ASP I 296 -1 O GLU I 293 N ILE I 164 SHEET 1 AA2 6 GLN I 191 PHE I 192 0 SHEET 2 AA2 6 LYS I 181 PHE I 185 -1 N MET I 184 O PHE I 192 SHEET 3 AA2 6 VAL I 171 ARG I 178 -1 N ILE I 176 O GLU I 183 SHEET 4 AA2 6 LEU I 215 MET I 222 -1 O LEU I 215 N ILE I 177 SHEET 5 AA2 6 VAL I 245 PRO I 253 -1 O CYS I 252 N VAL I 216 SHEET 6 AA2 6 ILE I 287 THR I 289 1 O GLN I 288 N LEU I 248 SHEET 1 AA3 2 ARG I 261 TRP I 262 0 SHEET 2 AA3 2 TYR I 330 GLU I 331 -1 O TYR I 330 N TRP I 262 SHEET 1 AA4 5 TYR I 377 CYS I 383 0 SHEET 2 AA4 5 LEU I 365 ASP I 374 -1 N GLY I 372 O TYR I 379 SHEET 3 AA4 5 ILE I 345 GLU I 356 -1 N VAL I 352 O LEU I 369 SHEET 4 AA4 5 LEU I 406 ALA I 411 -1 O ALA I 411 N ILE I 345 SHEET 5 AA4 5 ARG I 429 PHE I 433 -1 O CYS I 432 N GLU I 408 SHEET 1 AA5 2 ALA I 413 LYS I 416 0 SHEET 2 AA5 2 PHE I 423 ARG I 426 -1 O SER I 424 N THR I 415 LINK O3' DC C 29 P OMC C 30 1555 1555 1.61 LINK O3' OMC C 30 P DC C 31 1555 1555 1.61 LINK OP1 DC D 32 P AMP D 300 1555 1555 1.59 SITE 1 AC1 3 DC C 31 DC D 32 ARG I 334 SITE 1 AC2 12 DC D 32 GLU I 165 ILE I 166 LYS I 167 SITE 2 AC2 12 LEU I 168 ARG I 172 GLU I 220 PHE I 249 SITE 3 AC2 12 LEU I 290 MET I 322 LYS I 324 LYS I 340 SITE 1 AC3 6 ILE I 176 ARG I 178 GLU I 183 PHE I 185 SITE 2 AC3 6 GLN I 258 HOH I 636 SITE 1 AC4 5 LYS I 274 GLU I 291 TRP I 292 HOH I 601 SITE 2 AC4 5 HOH I 602 SITE 1 AC5 4 HIS I 149 ASP I 150 ASN I 153 HIS I 154 CRYST1 67.469 103.408 68.906 90.00 90.91 90.00 P 1 21 1 2 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 0.014822 0.000000 0.000236 0.00000 SCALE2 0.000000 0.009670 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014514 0.00000