PDB Short entry for 1N38 HEADER TRANSFERASE/RNA 25-OCT-02 1N38 TITLE REOVIRUS POLYMERASE LAMBDA3 ELONGATION COMPLEX WITH ONE PHOSPHODIESTER TITLE 2 BOND FORMED COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(P*GP*C)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-R(*AP*UP*UP*AP*GP*C)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: MINOR CORE PROTEIN LAMBDA 3; COMPND 11 CHAIN: A; COMPND 12 SYNONYM: LAMBDA3; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 OTHER_DETAILS: AUUAGC, ORDERED FROM DHARMACON; SOURCE 6 MOL_ID: 3; SOURCE 7 ORGANISM_SCIENTIFIC: MAMMALIAN ORTHOREOVIRUS 3; SOURCE 8 ORGANISM_TAXID: 10886; SOURCE 9 STRAIN: DEARING; SOURCE 10 GENE: L1; SOURCE 11 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 12 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: SF21; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS ACNPV; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PFASTBAC KEYWDS RNA POLYMERASE, RIGHT HAND CONFIGURATION, BRACELET, TRANSFERASE-RNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.TAO,D.L.FARSETTA,M.L.NIBERT,S.C.HARRISON REVDAT 4 03-APR-24 1N38 1 REMARK REVDAT 3 14-FEB-24 1N38 1 REMARK LINK REVDAT 2 24-FEB-09 1N38 1 VERSN REVDAT 1 25-DEC-02 1N38 0 JRNL AUTH Y.TAO,D.L.FARSETTA,M.L.NIBERT,S.C.HARRISON JRNL TITL RNA SYNTHESIS IN A CAGE--STRUCTURAL STUDIES OF REOVIRUS JRNL TITL 2 POLYMERASE [LAMBDA] 3 JRNL REF CELL(CAMBRIDGE,MASS.) V. 111 733 2002 JRNL REFN ISSN 0092-8674 JRNL PMID 12464184 JRNL DOI 10.1016/S0092-8674(02)01110-8 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.6 REMARK 3 NUMBER OF REFLECTIONS : 33194 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2003 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.95 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3243 REMARK 3 BIN FREE R VALUE : 0.2514 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 264 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 9986 REMARK 3 NUCLEIC ACID ATOMS : 148 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 265 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -9.70000 REMARK 3 B22 (A**2) : 6.47000 REMARK 3 B33 (A**2) : 3.23000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.41 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.080 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 12.18 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NTP_DEOXY_XPLOR REMARK 3 PARAMETER FILE 5 : ION.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NTP_DEOXY_XPLOR REMARK 3 TOPOLOGY FILE 5 : ION.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1N38 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-OCT-02. REMARK 100 THE DEPOSITION ID IS D_1000017462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.948 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33254 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.4 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.13900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.52200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: LAMBDA3 NATIVE STRUCTURE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, NACL, HEPES, GLYCEROL, PH REMARK 280 7.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 35.35950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 124.23650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.60350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 124.23650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.35950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.60350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 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 A C 1281 REMARK 465 MET A 1 REMARK 465 SER A 1266 REMARK 465 ALA A 1267 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 C B1276 O3' 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 G B1275 P G B1275 OP3 -0.076 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 TYR A 86 -40.04 -136.70 REMARK 500 ASP A 91 65.29 -56.86 REMARK 500 TYR A 93 -164.60 -73.30 REMARK 500 ILE A 99 -20.71 -151.12 REMARK 500 THR A 108 -52.99 123.14 REMARK 500 LEU A 109 58.74 -95.97 REMARK 500 THR A 110 -28.40 -38.36 REMARK 500 GLN A 146 32.52 -67.98 REMARK 500 LEU A 210 -164.95 -123.02 REMARK 500 MET A 218 59.64 -66.52 REMARK 500 SER A 263 -168.66 -74.14 REMARK 500 SER A 265 91.25 -163.46 REMARK 500 THR A 281 -80.86 -138.56 REMARK 500 SER A 284 18.43 -144.04 REMARK 500 PRO A 325 154.10 -49.90 REMARK 500 TYR A 389 42.58 -101.16 REMARK 500 THR A 390 -59.14 -124.43 REMARK 500 PRO A 484 15.67 -69.82 REMARK 500 GLN A 522 17.54 53.33 REMARK 500 SER A 559 -174.57 167.03 REMARK 500 SER A 561 -124.85 174.13 REMARK 500 ALA A 562 106.82 77.09 REMARK 500 VAL A 563 149.94 -28.55 REMARK 500 ILE A 564 -42.33 72.38 REMARK 500 GLU A 565 31.31 -97.34 REMARK 500 PHE A 598 -72.09 -76.41 REMARK 500 SER A 625 -158.71 -159.63 REMARK 500 VAL A 635 106.37 -48.38 REMARK 500 THR A 687 -80.98 -21.17 REMARK 500 VAL A 705 -77.79 -113.55 REMARK 500 TRP A 814 -86.25 -9.97 REMARK 500 PRO A 815 -53.66 -20.27 REMARK 500 ILE A 856 18.85 -142.99 REMARK 500 GLU A 858 -5.09 73.00 REMARK 500 LYS A 879 122.16 -178.13 REMARK 500 PRO A 893 172.02 -56.57 REMARK 500 ALA A 916 -7.85 -57.71 REMARK 500 ASN A 930 32.00 -90.44 REMARK 500 SER A 963 108.41 -58.96 REMARK 500 MET A 979 33.48 -91.13 REMARK 500 ILE A1002 -70.72 -66.84 REMARK 500 GLU A1022 -7.78 -59.61 REMARK 500 HIS A1044 157.37 -49.36 REMARK 500 CYS A1064 -143.07 -124.29 REMARK 500 PRO A1083 -4.75 -57.48 REMARK 500 ALA A1173 -15.77 -49.10 REMARK 500 ASP A1203 40.93 -104.68 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 MN A1301 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 585 OD1 REMARK 620 2 ILE A 586 O 90.6 REMARK 620 3 ASP A 734 OD2 119.2 81.0 REMARK 620 4 U3H A1291 O2B 143.3 113.5 92.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 734 OD1 REMARK 620 2 U3H A1291 O1A 133.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U3H A 1291 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CH1 A 1294 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CH1 A 1295 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MUK RELATED DB: PDB REMARK 900 LAMBDA3 NATIVE STRUCTURE REMARK 900 RELATED ID: 1MWH RELATED DB: PDB REMARK 900 LAMBDA3 IN COMPLEX WITH A MRNA CAP ANALOG REMARK 900 RELATED ID: 1N1H RELATED DB: PDB REMARK 900 LAMBDA3 INITIATION COMPLEX REMARK 900 RELATED ID: 1N35 RELATED DB: PDB REMARK 900 LAMBDA3 ELONGATION COMPLEX WITH FOUR PHOSPHODIESTER BOND FORMED DBREF 1N38 A 1 1267 UNP P17378 VL3_REOVD 1 1267 DBREF 1N38 B 1275 1276 PDB 1N38 1N38 1275 1276 DBREF 1N38 C 1281 1286 PDB 1N38 1N38 1281 1286 SEQRES 1 B 2 G C SEQRES 1 C 6 A U U A G C SEQRES 1 A 1267 MET SER SER MET ILE LEU THR GLN PHE GLY PRO PHE ILE SEQRES 2 A 1267 GLU SER ILE SER GLY ILE THR ASP GLN SER ASN ASP VAL SEQRES 3 A 1267 PHE GLU ASP ALA ALA LYS ALA PHE SER MET PHE THR ARG SEQRES 4 A 1267 SER ASP VAL TYR LYS ALA LEU ASP GLU ILE PRO PHE SER SEQRES 5 A 1267 ASP ASP ALA MET LEU PRO ILE PRO PRO THR ILE TYR THR SEQRES 6 A 1267 LYS PRO SER HIS ASP SER TYR TYR TYR ILE ASP ALA LEU SEQRES 7 A 1267 ASN ARG VAL ARG ARG LYS THR TYR GLN GLY PRO ASP ASP SEQRES 8 A 1267 VAL TYR VAL PRO ASN CYS SER ILE VAL GLU LEU LEU GLU SEQRES 9 A 1267 PRO HIS GLU THR LEU THR SER TYR GLY ARG LEU SER GLU SEQRES 10 A 1267 ALA ILE GLU ASN ARG ALA LYS ASP GLY ASP SER GLN ALA SEQRES 11 A 1267 ARG ILE ALA THR THR TYR GLY ARG ILE ALA GLU SER GLN SEQRES 12 A 1267 ALA ARG GLN ILE LYS ALA PRO LEU GLU LYS PHE VAL LEU SEQRES 13 A 1267 ALA LEU LEU VAL ALA GLU ALA GLY GLY SER LEU TYR ASP SEQRES 14 A 1267 PRO VAL LEU GLN LYS TYR ASP GLU ILE PRO ASP LEU SER SEQRES 15 A 1267 HIS ASN CYS PRO LEU TRP CYS PHE ARG GLU ILE CYS ARG SEQRES 16 A 1267 HIS ILE SER GLY PRO LEU PRO ASP ARG ALA PRO TYR LEU SEQRES 17 A 1267 TYR LEU SER ALA GLY VAL PHE TRP LEU MET SER PRO ARG SEQRES 18 A 1267 MET THR SER ALA ILE PRO PRO LEU LEU SER ASP LEU VAL SEQRES 19 A 1267 ASN LEU ALA ILE LEU GLN GLN THR ALA GLY LEU ASP PRO SEQRES 20 A 1267 SER LEU VAL LYS LEU GLY VAL GLN ILE CYS LEU HIS ALA SEQRES 21 A 1267 ALA ALA SER SER SER TYR SER TRP PHE ILE LEU LYS THR SEQRES 22 A 1267 LYS SER ILE PHE PRO GLN ASN THR LEU HIS SER MET TYR SEQRES 23 A 1267 GLU SER LEU GLU GLY GLY TYR CYS PRO ASN LEU GLU TRP SEQRES 24 A 1267 LEU GLU PRO ARG SER ASP TYR LYS PHE MET TYR MET GLY SEQRES 25 A 1267 VAL MET PRO LEU SER ALA LYS TYR ALA ARG SER ALA PRO SEQRES 26 A 1267 SER ASN ASP LYS LYS ALA ARG GLU LEU GLY GLU LYS TYR SEQRES 27 A 1267 GLY LEU SER SER VAL VAL GLY GLU LEU ARG LYS ARG THR SEQRES 28 A 1267 LYS THR TYR VAL LYS HIS ASP PHE ALA SER VAL ARG TYR SEQRES 29 A 1267 ILE ARG ASP ALA MET ALA CYS THR SER GLY ILE PHE LEU SEQRES 30 A 1267 VAL ARG THR PRO THR GLU THR VAL LEU GLN GLU TYR THR SEQRES 31 A 1267 GLN SER PRO GLU ILE LYS VAL PRO ILE PRO GLN LYS ASP SEQRES 32 A 1267 TRP THR GLY PRO ILE GLY GLU ILE ARG ILE LEU LYS ASP SEQRES 33 A 1267 THR THR SER SER ILE ALA ARG TYR LEU TYR ARG THR TRP SEQRES 34 A 1267 TYR LEU ALA ALA ALA ARG MET ALA ALA GLN PRO ARG THR SEQRES 35 A 1267 TRP ASP PRO LEU PHE GLN ALA ILE MET ARG SER GLN TYR SEQRES 36 A 1267 VAL THR ALA ARG GLY GLY SER GLY ALA ALA LEU ARG GLU SEQRES 37 A 1267 SER LEU TYR ALA ILE ASN VAL SER LEU PRO ASP PHE LYS SEQRES 38 A 1267 GLY LEU PRO VAL LYS ALA ALA THR LYS ILE PHE GLN ALA SEQRES 39 A 1267 ALA GLN LEU ALA ASN LEU PRO PHE SER HIS THR SER VAL SEQRES 40 A 1267 ALA ILE LEU ALA ASP THR SER MET GLY LEU ARG ASN GLN SEQRES 41 A 1267 VAL GLN ARG ARG PRO ARG SER ILE MET PRO LEU ASN VAL SEQRES 42 A 1267 PRO GLN GLN GLN VAL SER ALA PRO HIS THR LEU THR ALA SEQRES 43 A 1267 ASP TYR ILE ASN TYR HIS MET ASN LEU SER PRO THR SER SEQRES 44 A 1267 GLY SER ALA VAL ILE GLU LYS VAL ILE PRO LEU GLY VAL SEQRES 45 A 1267 TYR ALA SER SER PRO PRO ASN GLN SER ILE ASN ILE ASP SEQRES 46 A 1267 ILE SER ALA CYS ASP ALA SER ILE THR TRP ASP PHE PHE SEQRES 47 A 1267 LEU SER VAL ILE MET ALA ALA ILE HIS GLU GLY VAL ALA SEQRES 48 A 1267 SER SER SER ILE GLY LYS PRO PHE MET GLY VAL PRO ALA SEQRES 49 A 1267 SER ILE VAL ASN ASP GLU SER VAL VAL GLY VAL ARG ALA SEQRES 50 A 1267 ALA ARG PRO ILE SER GLY MET GLN ASN MET ILE GLN HIS SEQRES 51 A 1267 LEU SER LYS LEU TYR LYS ARG GLY PHE SER TYR ARG VAL SEQRES 52 A 1267 ASN ASP SER PHE SER PRO GLY ASN ASP PHE THR HIS MET SEQRES 53 A 1267 THR THR THR PHE PRO SER GLY SER THR ALA THR SER THR SEQRES 54 A 1267 GLU HIS THR ALA ASN ASN SER THR MET MET GLU THR PHE SEQRES 55 A 1267 LEU THR VAL TRP GLY PRO GLU HIS THR ASP ASP PRO ASP SEQRES 56 A 1267 VAL LEU ARG LEU MET LYS SER LEU THR ILE GLN ARG ASN SEQRES 57 A 1267 TYR VAL CYS GLN GLY ASP ASP GLY LEU MET ILE ILE ASP SEQRES 58 A 1267 GLY THR THR ALA GLY LYS VAL ASN SER GLU THR ILE GLN SEQRES 59 A 1267 ASN ASP LEU GLU LEU ILE SER LYS TYR GLY GLU GLU PHE SEQRES 60 A 1267 GLY TRP LYS TYR ASP ILE ALA TYR ASP GLY THR ALA GLU SEQRES 61 A 1267 TYR LEU LYS LEU TYR PHE ILE PHE GLY CYS ARG ILE PRO SEQRES 62 A 1267 ASN LEU SER ARG HIS PRO ILE VAL GLY LYS GLU ARG ALA SEQRES 63 A 1267 ASN SER SER ALA GLU GLU PRO TRP PRO ALA ILE LEU ASP SEQRES 64 A 1267 GLN ILE MET GLY VAL PHE PHE ASN GLY VAL HIS ASP GLY SEQRES 65 A 1267 LEU GLN TRP GLN ARG TRP ILE ARG TYR SER TRP ALA LEU SEQRES 66 A 1267 CYS CYS ALA PHE SER ARG GLN ARG THR MET ILE GLY GLU SEQRES 67 A 1267 SER VAL GLY TYR LEU GLN TYR PRO MET TRP SER PHE VAL SEQRES 68 A 1267 TYR TRP GLY LEU PRO LEU VAL LYS ALA PHE GLY SER ASP SEQRES 69 A 1267 PRO TRP ILE PHE SER TRP TYR MET PRO THR GLY ASP LEU SEQRES 70 A 1267 GLY MET TYR SER TRP ILE SER LEU ILE ARG PRO LEU MET SEQRES 71 A 1267 THR ARG TRP MET VAL ALA ASN GLY TYR VAL THR ASP ARG SEQRES 72 A 1267 CYS SER THR VAL PHE GLY ASN ALA ASP TYR ARG ARG CYS SEQRES 73 A 1267 PHE ASN GLU LEU LYS LEU TYR GLN GLY TYR TYR MET ALA SEQRES 74 A 1267 GLN LEU PRO ARG ASN PRO LYS LYS SER GLY ARG ALA ALA SEQRES 75 A 1267 SER ARG GLU VAL ARG GLU GLN PHE THR GLN ALA LEU SER SEQRES 76 A 1267 ASP TYR LEU MET GLN ASN PRO GLU LEU LYS SER ARG VAL SEQRES 77 A 1267 LEU ARG GLY ARG SER GLU TRP GLU LYS TYR GLY ALA GLY SEQRES 78 A 1267 ILE ILE HIS ASN PRO PRO SER LEU PHE ASP VAL PRO HIS SEQRES 79 A 1267 LYS TRP TYR GLN GLY ALA GLN GLU ALA ALA ILE ALA THR SEQRES 80 A 1267 ARG GLU GLU LEU ALA GLU MET ASP GLU THR LEU MET ARG SEQRES 81 A 1267 ALA ARG ARG HIS SER TYR SER SER PHE SER LYS LEU LEU SEQRES 82 A 1267 GLU ALA TYR LEU LEU VAL LYS TRP ARG MET CYS GLU ALA SEQRES 83 A 1267 ARG GLU PRO SER VAL ASP LEU ARG LEU PRO LEU CYS ALA SEQRES 84 A 1267 GLY ILE ASP PRO LEU ASN SER ASP PRO PHE LEU LYS MET SEQRES 85 A 1267 VAL SER VAL GLY PRO MET LEU GLN SER THR ARG LYS TYR SEQRES 86 A 1267 PHE ALA GLN THR LEU PHE MET ALA LYS THR VAL SER GLY SEQRES 87 A 1267 LEU ASP VAL ASN ALA ILE ASP SER ALA LEU LEU ARG LEU SEQRES 88 A 1267 ARG THR LEU GLY ALA ASP LYS LYS ALA LEU THR ALA GLN SEQRES 89 A 1267 LEU LEU MET VAL GLY LEU GLN GLU SER GLU ALA ASP ALA SEQRES 90 A 1267 LEU ALA GLY LYS ILE MET LEU GLN ASP VAL ASN THR VAL SEQRES 91 A 1267 GLN LEU ALA ARG VAL VAL ASN LEU ALA VAL PRO ASP THR SEQRES 92 A 1267 TRP MET SER LEU ASP PHE ASP SER MET PHE LYS HIS HIS SEQRES 93 A 1267 VAL LYS LEU LEU PRO LYS ASP GLY ARG HIS LEU ASN THR SEQRES 94 A 1267 ASP ILE PRO PRO ARG MET GLY TRP LEU ARG ALA ILE LEU SEQRES 95 A 1267 ARG PHE LEU GLY ALA GLY MET VAL MET THR ALA THR GLY SEQRES 96 A 1267 VAL ALA VAL ASP ILE TYR LEU GLU ASP ILE HIS GLY GLY SEQRES 97 A 1267 GLY ARG SER LEU GLY GLN ARG PHE MET THR TRP MET ARG SEQRES 98 A 1267 GLN GLU GLY ARG SER ALA HET MN A1301 1 HET MN A1302 1 HET U3H A1291 28 HET CH1 A1294 28 HET CH1 A1295 28 HETNAM MN MANGANESE (II) ION HETNAM U3H 3'-DEOXY-URIDINE 5'-TRIPHOSPHATE HETNAM CH1 3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE FORMUL 4 MN 2(MN 2+) FORMUL 6 U3H C9 H17 N2 O14 P3 FORMUL 7 CH1 2(C9 H16 N3 O13 P3) FORMUL 9 HOH *265(H2 O) HELIX 1 1 SER A 2 ILE A 16 1 15 HELIX 2 2 SER A 23 PHE A 37 1 15 HELIX 3 3 THR A 38 GLU A 48 1 11 HELIX 4 4 SER A 52 MET A 56 5 5 HELIX 5 5 PRO A 60 TYR A 64 5 5 HELIX 6 6 SER A 68 SER A 71 5 4 HELIX 7 7 ILE A 99 GLU A 101 5 3 HELIX 8 8 SER A 116 GLY A 126 1 11 HELIX 9 9 ASP A 127 ARG A 145 1 19 HELIX 10 10 PRO A 150 ALA A 163 1 14 HELIX 11 11 ASP A 180 HIS A 183 5 4 HELIX 12 12 ASN A 184 GLY A 199 1 16 HELIX 13 13 ALA A 225 ALA A 243 1 19 HELIX 14 14 ASP A 246 SER A 263 1 18 HELIX 15 15 SER A 265 LYS A 274 1 10 HELIX 16 16 SER A 275 ASN A 280 1 6 HELIX 17 17 THR A 281 MET A 285 5 5 HELIX 18 18 PRO A 302 TYR A 306 5 5 HELIX 19 19 SER A 317 ALA A 321 5 5 HELIX 20 20 ASN A 327 TYR A 338 1 12 HELIX 21 21 LEU A 340 TYR A 354 1 15 HELIX 22 22 ASP A 358 ALA A 370 1 13 HELIX 23 23 THR A 380 TYR A 389 1 10 HELIX 24 24 PRO A 400 LYS A 402 5 3 HELIX 25 25 ILE A 421 GLN A 439 1 19 HELIX 26 26 PRO A 440 TRP A 443 5 4 HELIX 27 27 ASP A 444 TYR A 455 1 12 HELIX 28 28 SER A 462 ALA A 472 1 11 HELIX 29 29 THR A 489 ALA A 498 1 10 HELIX 30 30 PRO A 501 SER A 506 1 6 HELIX 31 31 VAL A 507 ALA A 511 5 5 HELIX 32 32 ASN A 532 SER A 539 1 8 HELIX 33 33 SER A 539 MET A 553 1 15 HELIX 34 34 VAL A 567 SER A 576 1 10 HELIX 35 35 ALA A 588 ILE A 593 1 6 HELIX 36 36 PHE A 597 VAL A 610 1 14 HELIX 37 37 VAL A 610 ILE A 615 1 6 HELIX 38 38 SER A 642 GLY A 658 1 17 HELIX 39 39 ALA A 686 VAL A 705 1 20 HELIX 40 40 VAL A 705 HIS A 710 1 6 HELIX 41 41 ASP A 713 SER A 722 1 10 HELIX 42 42 ASN A 749 GLU A 766 1 18 HELIX 43 43 ASN A 794 HIS A 798 5 5 HELIX 44 44 PRO A 815 ASP A 831 1 17 HELIX 45 45 GLN A 834 ALA A 848 1 15 HELIX 46 46 PRO A 866 GLY A 874 1 9 HELIX 47 47 THR A 894 ILE A 906 1 13 HELIX 48 48 ILE A 906 ASN A 917 1 12 HELIX 49 49 ASP A 932 LEU A 940 1 9 HELIX 50 50 LYS A 941 ALA A 949 1 9 HELIX 51 51 SER A 963 MET A 979 1 17 HELIX 52 52 ASN A 981 GLY A 999 1 19 HELIX 53 53 SER A 1008 PHE A 1010 5 3 HELIX 54 54 ASP A 1011 ALA A 1024 1 14 HELIX 55 55 THR A 1027 HIS A 1044 1 18 HELIX 56 56 SER A 1050 LEU A 1057 1 8 HELIX 57 57 ASN A 1085 GLY A 1096 1 12 HELIX 58 58 SER A 1101 GLN A 1108 1 8 HELIX 59 59 ASP A 1120 LEU A 1134 1 15 HELIX 60 60 ASP A 1137 MET A 1147 1 11 HELIX 61 61 GLN A 1151 LEU A 1164 1 14 HELIX 62 62 ASN A 1168 ARG A 1174 1 7 HELIX 63 63 VAL A 1175 ASN A 1177 5 3 HELIX 64 64 PRO A 1181 MET A 1185 5 5 HELIX 65 65 ASP A 1188 HIS A 1196 1 9 HELIX 66 66 PRO A 1212 GLY A 1216 5 5 HELIX 67 67 TRP A 1217 ALA A 1233 1 17 HELIX 68 68 GLY A 1247 GLU A 1263 1 17 SHEET 1 A 2 TYR A 73 ILE A 75 0 SHEET 2 A 2 VAL A 81 ARG A 83 -1 O ARG A 82 N TYR A 74 SHEET 1 B 4 LEU A 103 PRO A 105 0 SHEET 2 B 4 TYR A 112 LEU A 115 -1 O ARG A 114 N GLU A 104 SHEET 3 B 4 VAL A 214 LEU A 217 -1 O TRP A 216 N GLY A 113 SHEET 4 B 4 TYR A 207 TYR A 209 -1 N LEU A 208 O PHE A 215 SHEET 1 C 2 TYR A 168 ASP A 169 0 SHEET 2 C 2 LYS A 174 TYR A 175 -1 O LYS A 174 N ASP A 169 SHEET 1 D 3 PHE A 308 PRO A 315 0 SHEET 2 D 3 GLY A 291 TRP A 299 -1 N CYS A 294 O MET A 314 SHEET 3 D 3 LYS A 356 HIS A 357 1 O HIS A 357 N GLY A 291 SHEET 1 E 2 TRP A 404 ILE A 408 0 SHEET 2 E 2 ILE A 411 LEU A 414 -1 O ILE A 411 N ILE A 408 SHEET 1 F 2 GLY A 516 GLN A 520 0 SHEET 2 F 2 ARG A 523 ILE A 528 -1 O ILE A 528 N GLY A 516 SHEET 1 G 4 TYR A 729 GLN A 732 0 SHEET 2 G 4 ASP A 735 ILE A 740 -1 O ASP A 735 N GLN A 732 SHEET 3 G 4 GLN A 580 SER A 587 -1 N ILE A 584 O GLY A 736 SHEET 4 G 4 LYS A 770 TYR A 771 -1 O LYS A 770 N SER A 587 SHEET 1 H 2 SER A 625 ASP A 629 0 SHEET 2 H 2 ALA A 637 ILE A 641 -1 O ARG A 639 N VAL A 627 SHEET 1 I 2 PHE A 659 ASN A 664 0 SHEET 2 I 2 ASP A 672 THR A 677 -1 O HIS A 675 N TYR A 661 SHEET 1 J 3 THR A 778 TYR A 781 0 SHEET 2 J 3 LEU A 784 ILE A 787 -1 O PHE A 786 N ALA A 779 SHEET 3 J 3 CYS A 790 ARG A 791 -1 O CYS A 790 N ILE A 787 SHEET 1 K 2 ARG A 851 THR A 854 0 SHEET 2 K 2 GLY A 861 GLN A 864 -1 O LEU A 863 N GLN A 852 SHEET 1 L 2 VAL A 920 SER A 925 0 SHEET 2 L 2 GLY A 929 ALA A 931 -1 O GLY A 929 N SER A 925 SHEET 1 M 3 VAL A1059 ALA A1066 0 SHEET 2 M 3 VAL A1238 ILE A1245 -1 O ASP A1244 N LYS A1060 SHEET 3 M 3 VAL A1197 LYS A1198 1 N LYS A1198 O LEU A1242 LINK OD1 ASP A 585 MN MN A1301 1555 1555 2.68 LINK O ILE A 586 MN MN A1301 1555 1555 2.43 LINK OD2 ASP A 734 MN MN A1301 1555 1555 2.17 LINK OD1 ASP A 734 MN MN A1302 1555 1555 2.30 LINK O2B U3H A1291 MN MN A1301 1555 1555 2.14 LINK O1A U3H A1291 MN MN A1302 1555 1555 2.27 CISPEP 1 GLU A 301 PRO A 302 0 -0.43 CISPEP 2 PRO A 577 PRO A 578 0 1.87 SITE 1 AC1 5 ASP A 585 ILE A 586 ASP A 734 U3H A1291 SITE 2 AC1 5 MN A1302 SITE 1 AC2 5 ASP A 585 ASP A 734 ASP A 735 U3H A1291 SITE 2 AC2 5 MN A1301 SITE 1 AC3 13 ARG A 523 ARG A 524 ARG A 526 SER A 587 SITE 2 AC3 13 ASP A 590 THR A 687 ASP A 734 MN A1301 SITE 3 AC3 13 MN A1302 HOH A1406 C B1276 A C1284 SITE 4 AC3 13 G C1285 SITE 1 AC4 5 LYS A 32 SER A 35 MET A 36 ARG A 851 SITE 2 AC4 5 TYR A 862 SITE 1 AC5 9 PRO A 815 GLN A 852 ARG A 853 THR A 854 SITE 2 AC5 9 MET A 855 ASP A1035 HOH A1367 HOH A1396 SITE 3 AC5 9 HOH A1557 CRYST1 70.719 85.207 248.473 90.00 90.00 90.00 P 21 21 21 4 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 0.014140 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011736 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004025 0.00000