HEADER TRANSFERASE 16-APR-09 3H37 TITLE THE STRUCTURE OF CCA-ADDING ENZYME APO FORM I COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA NUCLEOTIDYL TRANSFERASE-RELATED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 437-863; COMPND 5 SYNONYM: TRNA NUCLEOTIDYLTRANSFERASE, TRNA ADENYL-/CYTIDYL- COMPND 6 TRANSFERASE, TRNA CCA-PYROPHOSPHORYLASE, TRNA-NT; COMPND 7 EC: 2.7.7.25; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-22B KEYWDS TRANSFERASE/RNA, NUCLEOTIDE-BINDING, NUCLEOTIDYLTRANSFERASE, RNA- KEYWDS 2 BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.TOH,K.TOMITA REVDAT 2 05-FEB-14 3H37 1 JRNL VERSN REVDAT 1 13-OCT-09 3H37 0 JRNL AUTH Y.TOH,D.TAKESHITA,T.NUMATA,S.FUKAI,O.NUREKI,K.TOMITA JRNL TITL MECHANISM FOR THE DEFINITION OF ELONGATION AND TERMINATION JRNL TITL 2 BY THE CLASS II CCA-ADDING ENZYME JRNL REF EMBO J. V. 28 3353 2009 JRNL REFN ISSN 0261-4189 JRNL PMID 19745807 JRNL DOI 10.1038/EMBOJ.2009.260 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.130 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 40424 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 3802 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.6506 - 8.5325 0.87 2407 176 0.2054 0.2106 REMARK 3 2 8.5325 - 6.7783 0.99 2788 146 0.2062 0.2454 REMARK 3 3 6.7783 - 5.9232 1.00 2826 133 0.2241 0.2455 REMARK 3 4 5.9232 - 5.3824 0.99 2838 138 0.2026 0.2538 REMARK 3 5 5.3824 - 4.9970 0.99 2758 137 0.1825 0.1893 REMARK 3 6 4.9970 - 4.7027 0.99 2822 139 0.1795 0.2480 REMARK 3 7 4.7027 - 4.4673 0.98 2690 164 0.1708 0.2231 REMARK 3 8 4.4673 - 4.2730 0.98 2810 145 0.1900 0.2211 REMARK 3 9 4.2730 - 4.1086 0.98 2736 156 0.2016 0.2868 REMARK 3 10 4.1086 - 3.9669 0.98 2787 131 0.2218 0.2817 REMARK 3 11 3.9669 - 3.8429 0.98 2723 127 0.2262 0.2461 REMARK 3 12 3.8429 - 3.7331 0.97 2760 146 0.2439 0.2670 REMARK 3 13 3.7331 - 3.6348 0.97 2772 151 0.2461 0.2711 REMARK 3 14 3.6348 - 3.5462 0.97 2684 147 0.2429 0.2857 REMARK 3 15 3.5462 - 3.4656 0.98 2723 121 0.2514 0.2970 REMARK 3 16 3.4656 - 3.3919 0.96 2776 158 0.2562 0.3248 REMARK 3 17 3.3919 - 3.3240 0.96 2681 125 0.2646 0.3666 REMARK 3 18 3.3240 - 3.2613 0.95 2741 137 0.2657 0.3037 REMARK 3 19 3.2613 - 3.2031 0.95 2701 138 0.2822 0.3308 REMARK 3 20 3.2031 - 3.1488 0.94 2569 145 0.2909 0.3510 REMARK 3 21 3.1488 - 3.0980 0.94 2705 142 0.3012 0.3239 REMARK 3 22 3.0980 - 3.0503 0.92 2508 121 0.2940 0.3119 REMARK 3 23 3.0503 - 3.0055 0.91 2571 165 0.3170 0.3434 REMARK 3 24 3.0055 - 2.9632 0.90 2527 120 0.3133 0.3541 REMARK 3 25 2.9632 - 2.9231 0.88 2542 119 0.3152 0.4283 REMARK 3 26 2.9231 - 2.8852 0.85 2330 150 0.3261 0.3712 REMARK 3 27 2.8852 - 2.8491 0.79 2170 125 0.3436 0.3639 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 : 0.33 REMARK 3 B_SOL : 83.12 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.960 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 79.60 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 : 0.009 NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : 20.000 NULL 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 3H37 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-APR-09. REMARK 100 THE RCSB ID CODE IS RCSB052634. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97940, 0.97952, 0.98200 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40434 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07500 REMARK 200 FOR THE DATA SET : 40.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.23200 REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% ETHYLENE GLYCOL, 0.05M TRIS-CL REMARK 280 PH8.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 95.28450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.36900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 95.28450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.36900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 ARG A 104 REMARK 465 LEU A 105 REMARK 465 GLU A 106 REMARK 465 TYR A 107 REMARK 465 TYR A 108 REMARK 465 GLU A 109 REMARK 465 SER A 110 REMARK 465 PRO A 111 REMARK 465 ALA A 112 REMARK 465 LYS A 113 REMARK 465 LEU A 114 REMARK 465 PRO A 115 REMARK 465 ASP A 116 REMARK 465 VAL A 117 REMARK 465 LEU A 430 REMARK 465 ALA A 431 REMARK 465 ALA A 432 REMARK 465 ALA A 433 REMARK 465 LEU A 434 REMARK 465 GLU A 435 REMARK 465 HIS A 436 REMARK 465 HIS A 437 REMARK 465 HIS A 438 REMARK 465 HIS A 439 REMARK 465 HIS A 440 REMARK 465 HIS A 441 REMARK 465 MSE B 1 REMARK 465 GLU B 106 REMARK 465 TYR B 107 REMARK 465 TYR B 108 REMARK 465 GLU B 109 REMARK 465 SER B 110 REMARK 465 PRO B 111 REMARK 465 ALA B 112 REMARK 465 LYS B 113 REMARK 465 LEU B 114 REMARK 465 ALA B 432 REMARK 465 ALA B 433 REMARK 465 LEU B 434 REMARK 465 GLU B 435 REMARK 465 HIS B 436 REMARK 465 HIS B 437 REMARK 465 HIS B 438 REMARK 465 HIS B 439 REMARK 465 HIS B 440 REMARK 465 HIS B 441 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 A 281 OH TYR A 382 4546 1.44 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 GLU A 381 CB - CA - C ANGL. DEV. = -15.9 DEGREES REMARK 500 GLU A 381 N - CA - C ANGL. DEV. = 18.0 DEGREES REMARK 500 LYS B 369 N - CA - C ANGL. DEV. = -17.5 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 PHE A 290 62.96 61.68 REMARK 500 GLU A 329 -11.79 81.52 REMARK 500 ARG A 330 48.33 33.32 REMARK 500 ILE A 378 140.14 5.26 REMARK 500 ASN A 379 6.08 115.47 REMARK 500 GLU A 381 -25.91 58.01 REMARK 500 ILE A 388 0.81 121.20 REMARK 500 THR A 410 -157.43 -87.34 REMARK 500 GLU B 118 -79.93 16.77 REMARK 500 MSE B 119 20.63 -74.05 REMARK 500 ALA B 135 42.70 -108.12 REMARK 500 ASP B 189 93.10 -67.94 REMARK 500 ASN B 229 57.38 39.58 REMARK 500 VAL B 286 -64.10 -109.91 REMARK 500 PHE B 287 -35.56 -37.98 REMARK 500 GLU B 329 -14.92 84.00 REMARK 500 PRO B 332 177.20 -44.61 REMARK 500 LYS B 341 -91.97 7.66 REMARK 500 LYS B 369 -58.50 152.02 REMARK 500 ASN B 372 -79.23 -91.61 REMARK 500 ILE B 384 -9.06 107.91 REMARK 500 LYS B 386 37.88 -96.44 REMARK 500 ASP B 407 0.59 -157.41 REMARK 500 ARG B 411 76.49 90.10 REMARK 500 THR B 426 -146.97 62.07 REMARK 500 LYS B 429 -158.71 63.57 REMARK 500 LEU B 430 -157.13 62.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASN B 34 22.7 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3H38 RELATED DB: PDB REMARK 900 RELATED ID: 3H39 RELATED DB: PDB REMARK 900 RELATED ID: 3H3A RELATED DB: PDB DBREF 3H37 A 2 428 UNP Q9WZH4 Q9WZH4_THEMA 437 863 DBREF 3H37 B 2 428 UNP Q9WZH4 Q9WZH4_THEMA 437 863 SEQADV 3H37 MSE A 1 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 LYS A 429 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 LEU A 430 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 ALA A 431 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 ALA A 432 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 ALA A 433 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 LEU A 434 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 GLU A 435 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 HIS A 436 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 HIS A 437 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 HIS A 438 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 HIS A 439 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 HIS A 440 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 HIS A 441 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 MSE B 1 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 LYS B 429 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 LEU B 430 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 ALA B 431 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 ALA B 432 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 ALA B 433 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 LEU B 434 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 GLU B 435 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 HIS B 436 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 HIS B 437 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 HIS B 438 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 HIS B 439 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 HIS B 440 UNP Q9WZH4 EXPRESSION TAG SEQADV 3H37 HIS B 441 UNP Q9WZH4 EXPRESSION TAG SEQRES 1 A 441 MSE GLN ILE PHE ARG ASP VAL SER LYS LEU LEU VAL GLU SEQRES 2 A 441 ARG VAL ASP PRO LYS ILE LEU ASN LEU PHE ARG LEU LEU SEQRES 3 A 441 GLY LYS PHE GLY ASP GLU VAL ASN MSE PRO VAL TYR VAL SEQRES 4 A 441 VAL GLY GLY PHE VAL ARG ASP LEU LEU LEU GLY ILE LYS SEQRES 5 A 441 ASN LEU ASP ILE ASP ILE VAL VAL GLU GLY ASN ALA LEU SEQRES 6 A 441 GLU PHE ALA GLU TYR ALA LYS ARG PHE LEU PRO GLY LYS SEQRES 7 A 441 LEU VAL LYS HIS ASP LYS PHE MSE THR ALA SER LEU PHE SEQRES 8 A 441 LEU LYS GLY GLY LEU ARG ILE ASP ILE ALA THR ALA ARG SEQRES 9 A 441 LEU GLU TYR TYR GLU SER PRO ALA LYS LEU PRO ASP VAL SEQRES 10 A 441 GLU MSE SER THR ILE LYS LYS ASP LEU TYR ARG ARG ASP SEQRES 11 A 441 PHE THR ILE ASN ALA MSE ALA ILE LYS LEU ASN PRO LYS SEQRES 12 A 441 ASP PHE GLY LEU LEU ILE ASP PHE PHE GLY GLY TYR ARG SEQRES 13 A 441 ASP LEU LYS GLU GLY VAL ILE ARG VAL LEU HIS THR LEU SEQRES 14 A 441 SER PHE VAL ASP ASP PRO THR ARG ILE LEU ARG ALA ILE SEQRES 15 A 441 ARG PHE GLU GLN ARG PHE ASP PHE ARG ILE GLU GLU THR SEQRES 16 A 441 THR GLU ARG LEU LEU LYS GLN ALA VAL GLU GLU GLY TYR SEQRES 17 A 441 LEU GLU ARG THR THR GLY PRO ARG LEU ARG GLN GLU LEU SEQRES 18 A 441 GLU LYS ILE LEU GLU GLU LYS ASN PRO LEU LYS SER ILE SEQRES 19 A 441 ARG ARG MSE ALA GLN PHE ASP VAL ILE LYS HIS LEU PHE SEQRES 20 A 441 PRO LYS THR TYR TYR THR PRO SER MSE ASP GLU LYS MSE SEQRES 21 A 441 GLU ASN LEU PHE ARG ASN ILE PRO TRP VAL GLU GLU ASN SEQRES 22 A 441 PHE GLY GLU VAL ASP ARG PHE TYR ALA VAL LEU HIS VAL SEQRES 23 A 441 PHE LEU GLU PHE TYR ASP ASP GLU SER TRP LYS GLU VAL SEQRES 24 A 441 ARG ASP ARG TYR SER LEU ARG ARG ASN LEU ILE ASN GLU SEQRES 25 A 441 ILE ARG HIS VAL GLU LYS SER ALA PRO ALA LEU LEU GLU SEQRES 26 A 441 MSE LEU SER GLU ARG VAL PRO ALA SER PHE VAL TYR PRO SEQRES 27 A 441 LEU VAL LYS GLY VAL SER ASN GLU THR ILE CYS HIS PHE SEQRES 28 A 441 LEU ALA TYR LEU SER GLY GLU LYS GLU GLY LEU PHE LYS SEQRES 29 A 441 SER TYR LEU LEU LYS ILE LYS ASN THR LYS LEU GLU LYS SEQRES 30 A 441 ILE ASN GLY GLU TYR LEU ILE ARG LYS GLY ILE THR SER SEQRES 31 A 441 GLY LYS ILE ILE GLY GLU VAL LEU GLU LYS ILE LEU MSE SEQRES 32 A 441 LYS LYS LEU ASP GLY ASP THR ARG ASP GLU GLU GLU ILE SEQRES 33 A 441 LEU GLU GLU VAL LEU ALA SER LEU GLU THR GLU GLY LYS SEQRES 34 A 441 LEU ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 441 MSE GLN ILE PHE ARG ASP VAL SER LYS LEU LEU VAL GLU SEQRES 2 B 441 ARG VAL ASP PRO LYS ILE LEU ASN LEU PHE ARG LEU LEU SEQRES 3 B 441 GLY LYS PHE GLY ASP GLU VAL ASN MSE PRO VAL TYR VAL SEQRES 4 B 441 VAL GLY GLY PHE VAL ARG ASP LEU LEU LEU GLY ILE LYS SEQRES 5 B 441 ASN LEU ASP ILE ASP ILE VAL VAL GLU GLY ASN ALA LEU SEQRES 6 B 441 GLU PHE ALA GLU TYR ALA LYS ARG PHE LEU PRO GLY LYS SEQRES 7 B 441 LEU VAL LYS HIS ASP LYS PHE MSE THR ALA SER LEU PHE SEQRES 8 B 441 LEU LYS GLY GLY LEU ARG ILE ASP ILE ALA THR ALA ARG SEQRES 9 B 441 LEU GLU TYR TYR GLU SER PRO ALA LYS LEU PRO ASP VAL SEQRES 10 B 441 GLU MSE SER THR ILE LYS LYS ASP LEU TYR ARG ARG ASP SEQRES 11 B 441 PHE THR ILE ASN ALA MSE ALA ILE LYS LEU ASN PRO LYS SEQRES 12 B 441 ASP PHE GLY LEU LEU ILE ASP PHE PHE GLY GLY TYR ARG SEQRES 13 B 441 ASP LEU LYS GLU GLY VAL ILE ARG VAL LEU HIS THR LEU SEQRES 14 B 441 SER PHE VAL ASP ASP PRO THR ARG ILE LEU ARG ALA ILE SEQRES 15 B 441 ARG PHE GLU GLN ARG PHE ASP PHE ARG ILE GLU GLU THR SEQRES 16 B 441 THR GLU ARG LEU LEU LYS GLN ALA VAL GLU GLU GLY TYR SEQRES 17 B 441 LEU GLU ARG THR THR GLY PRO ARG LEU ARG GLN GLU LEU SEQRES 18 B 441 GLU LYS ILE LEU GLU GLU LYS ASN PRO LEU LYS SER ILE SEQRES 19 B 441 ARG ARG MSE ALA GLN PHE ASP VAL ILE LYS HIS LEU PHE SEQRES 20 B 441 PRO LYS THR TYR TYR THR PRO SER MSE ASP GLU LYS MSE SEQRES 21 B 441 GLU ASN LEU PHE ARG ASN ILE PRO TRP VAL GLU GLU ASN SEQRES 22 B 441 PHE GLY GLU VAL ASP ARG PHE TYR ALA VAL LEU HIS VAL SEQRES 23 B 441 PHE LEU GLU PHE TYR ASP ASP GLU SER TRP LYS GLU VAL SEQRES 24 B 441 ARG ASP ARG TYR SER LEU ARG ARG ASN LEU ILE ASN GLU SEQRES 25 B 441 ILE ARG HIS VAL GLU LYS SER ALA PRO ALA LEU LEU GLU SEQRES 26 B 441 MSE LEU SER GLU ARG VAL PRO ALA SER PHE VAL TYR PRO SEQRES 27 B 441 LEU VAL LYS GLY VAL SER ASN GLU THR ILE CYS HIS PHE SEQRES 28 B 441 LEU ALA TYR LEU SER GLY GLU LYS GLU GLY LEU PHE LYS SEQRES 29 B 441 SER TYR LEU LEU LYS ILE LYS ASN THR LYS LEU GLU LYS SEQRES 30 B 441 ILE ASN GLY GLU TYR LEU ILE ARG LYS GLY ILE THR SER SEQRES 31 B 441 GLY LYS ILE ILE GLY GLU VAL LEU GLU LYS ILE LEU MSE SEQRES 32 B 441 LYS LYS LEU ASP GLY ASP THR ARG ASP GLU GLU GLU ILE SEQRES 33 B 441 LEU GLU GLU VAL LEU ALA SER LEU GLU THR GLU GLY LYS SEQRES 34 B 441 LEU ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS MODRES 3H37 MSE A 1 MET SELENOMETHIONINE MODRES 3H37 MSE A 35 MET SELENOMETHIONINE MODRES 3H37 MSE A 86 MET SELENOMETHIONINE MODRES 3H37 MSE A 119 MET SELENOMETHIONINE MODRES 3H37 MSE A 136 MET SELENOMETHIONINE MODRES 3H37 MSE A 237 MET SELENOMETHIONINE MODRES 3H37 MSE A 256 MET SELENOMETHIONINE MODRES 3H37 MSE A 260 MET SELENOMETHIONINE MODRES 3H37 MSE A 326 MET SELENOMETHIONINE MODRES 3H37 MSE A 403 MET SELENOMETHIONINE MODRES 3H37 MSE B 35 MET SELENOMETHIONINE MODRES 3H37 MSE B 86 MET SELENOMETHIONINE MODRES 3H37 MSE B 119 MET SELENOMETHIONINE MODRES 3H37 MSE B 136 MET SELENOMETHIONINE MODRES 3H37 MSE B 237 MET SELENOMETHIONINE MODRES 3H37 MSE B 256 MET SELENOMETHIONINE MODRES 3H37 MSE B 260 MET SELENOMETHIONINE MODRES 3H37 MSE B 326 MET SELENOMETHIONINE MODRES 3H37 MSE B 403 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 35 8 HET MSE A 86 8 HET MSE A 119 8 HET MSE A 136 8 HET MSE A 237 8 HET MSE A 256 8 HET MSE A 260 8 HET MSE A 326 8 HET MSE A 403 8 HET MSE B 35 8 HET MSE B 86 8 HET MSE B 119 8 HET MSE B 136 8 HET MSE B 237 8 HET MSE B 256 8 HET MSE B 260 8 HET MSE B 326 8 HET MSE B 403 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 19(C5 H11 N O2 SE) FORMUL 3 HOH *36(H2 O) HELIX 1 1 VAL A 7 VAL A 15 1 9 HELIX 2 2 ASP A 16 VAL A 33 1 18 HELIX 3 3 GLY A 41 GLY A 50 1 10 HELIX 4 4 ASN A 63 ARG A 73 1 11 HELIX 5 5 THR A 121 TYR A 127 1 7 HELIX 6 6 PHE A 131 ALA A 135 5 5 HELIX 7 7 GLY A 153 GLU A 160 1 8 HELIX 8 8 LEU A 169 ASP A 174 1 6 HELIX 9 9 THR A 176 ASP A 189 1 14 HELIX 10 10 GLU A 193 GLU A 206 1 14 HELIX 11 11 TYR A 208 THR A 212 5 5 HELIX 12 12 THR A 213 GLU A 227 1 15 HELIX 13 13 ASN A 229 PHE A 240 1 12 HELIX 14 14 THR A 253 GLY A 275 1 23 HELIX 15 15 ASP A 278 LEU A 288 1 11 HELIX 16 16 ASP A 292 TYR A 303 1 12 HELIX 17 17 ASN A 308 SER A 328 1 21 HELIX 18 18 PRO A 332 TYR A 337 1 6 HELIX 19 19 PRO A 338 LYS A 341 5 4 HELIX 20 20 SER A 344 ALA A 353 1 10 HELIX 21 21 SER A 356 ASN A 372 1 17 HELIX 22 22 GLU A 381 ILE A 388 1 8 HELIX 23 23 LYS A 392 LEU A 406 1 15 HELIX 24 24 ARG A 411 GLU A 427 1 17 HELIX 25 25 VAL B 7 VAL B 15 1 9 HELIX 26 26 ASP B 16 VAL B 33 1 18 HELIX 27 27 GLY B 41 GLY B 50 1 10 HELIX 28 28 ASN B 63 PHE B 74 1 12 HELIX 29 29 VAL B 117 SER B 120 5 4 HELIX 30 30 THR B 121 ARG B 128 1 8 HELIX 31 31 PHE B 131 ALA B 135 5 5 HELIX 32 32 ASN B 141 PHE B 145 5 5 HELIX 33 33 GLY B 153 GLU B 160 1 8 HELIX 34 34 LEU B 169 ASP B 174 1 6 HELIX 35 35 PRO B 175 PHE B 188 1 14 HELIX 36 36 GLU B 193 GLY B 207 1 15 HELIX 37 37 TYR B 208 THR B 212 5 5 HELIX 38 38 THR B 213 GLU B 227 1 15 HELIX 39 39 ASN B 229 PHE B 240 1 12 HELIX 40 40 ASP B 241 PHE B 247 1 7 HELIX 41 41 THR B 253 GLY B 275 1 23 HELIX 42 42 ASP B 278 LEU B 288 1 11 HELIX 43 43 ASP B 292 SER B 304 1 13 HELIX 44 44 ASN B 308 SER B 328 1 21 HELIX 45 45 ALA B 333 PHE B 335 5 3 HELIX 46 46 VAL B 336 LYS B 341 1 6 HELIX 47 47 SER B 344 ALA B 353 1 10 HELIX 48 48 SER B 356 LYS B 371 1 16 HELIX 49 49 LYS B 392 LYS B 405 1 14 HELIX 50 50 GLU B 413 GLU B 419 1 7 HELIX 51 51 VAL B 420 SER B 423 5 4 SHEET 1 A 8 PHE A 4 ASP A 6 0 SHEET 2 A 8 LEU A 147 ILE A 149 -1 O LEU A 148 N ARG A 5 SHEET 3 A 8 ALA A 137 LYS A 139 -1 N ALA A 137 O ILE A 149 SHEET 4 A 8 VAL A 37 VAL A 40 -1 N VAL A 39 O ILE A 138 SHEET 5 A 8 ILE A 56 VAL A 60 -1 O VAL A 59 N TYR A 38 SHEET 6 A 8 ARG A 97 THR A 102 1 O ASP A 99 N ILE A 58 SHEET 7 A 8 ALA A 88 LEU A 92 -1 N LEU A 90 O ILE A 98 SHEET 8 A 8 GLY A 77 VAL A 80 -1 N LYS A 78 O PHE A 91 SHEET 1 B 2 VAL A 162 ILE A 163 0 SHEET 2 B 2 ARG A 191 ILE A 192 1 O ARG A 191 N ILE A 163 SHEET 1 C 8 PHE B 4 ASP B 6 0 SHEET 2 C 8 LEU B 147 ILE B 149 -1 O LEU B 148 N ARG B 5 SHEET 3 C 8 ALA B 137 LYS B 139 -1 N ALA B 137 O ILE B 149 SHEET 4 C 8 VAL B 37 VAL B 40 -1 N VAL B 39 O ILE B 138 SHEET 5 C 8 ILE B 56 VAL B 60 -1 O VAL B 59 N TYR B 38 SHEET 6 C 8 ARG B 97 THR B 102 1 O ASP B 99 N ILE B 58 SHEET 7 C 8 THR B 87 LEU B 92 -1 N LEU B 90 O ILE B 98 SHEET 8 C 8 GLY B 77 HIS B 82 -1 N VAL B 80 O SER B 89 SHEET 1 D 2 VAL B 162 ILE B 163 0 SHEET 2 D 2 ARG B 191 ILE B 192 1 O ARG B 191 N ILE B 163 LINK C MSE A 1 N GLN A 2 1555 1555 1.32 LINK C ASN A 34 N MSE A 35 1555 1555 1.33 LINK C MSE A 35 N PRO A 36 1555 1555 1.33 LINK C PHE A 85 N MSE A 86 1555 1555 1.33 LINK C MSE A 86 N THR A 87 1555 1555 1.33 LINK C GLU A 118 N MSE A 119 1555 1555 1.33 LINK C MSE A 119 N SER A 120 1555 1555 1.32 LINK C ALA A 135 N MSE A 136 1555 1555 1.33 LINK C MSE A 136 N ALA A 137 1555 1555 1.33 LINK C ARG A 236 N MSE A 237 1555 1555 1.33 LINK C MSE A 237 N ALA A 238 1555 1555 1.33 LINK C SER A 255 N MSE A 256 1555 1555 1.33 LINK C MSE A 256 N ASP A 257 1555 1555 1.33 LINK C LYS A 259 N MSE A 260 1555 1555 1.33 LINK C MSE A 260 N GLU A 261 1555 1555 1.33 LINK C GLU A 325 N MSE A 326 1555 1555 1.33 LINK C MSE A 326 N LEU A 327 1555 1555 1.33 LINK C LEU A 402 N MSE A 403 1555 1555 1.33 LINK C MSE A 403 N LYS A 404 1555 1555 1.33 LINK C ASN B 34 N MSE B 35 1555 1555 1.33 LINK C MSE B 35 N PRO B 36 1555 1555 1.33 LINK C PHE B 85 N MSE B 86 1555 1555 1.33 LINK C MSE B 86 N THR B 87 1555 1555 1.33 LINK C GLU B 118 N MSE B 119 1555 1555 1.32 LINK C MSE B 119 N SER B 120 1555 1555 1.32 LINK C ALA B 135 N MSE B 136 1555 1555 1.31 LINK C MSE B 136 N ALA B 137 1555 1555 1.33 LINK C ARG B 236 N MSE B 237 1555 1555 1.31 LINK C MSE B 237 N ALA B 238 1555 1555 1.31 LINK C SER B 255 N MSE B 256 1555 1555 1.33 LINK C MSE B 256 N ASP B 257 1555 1555 1.33 LINK C LYS B 259 N MSE B 260 1555 1555 1.32 LINK C MSE B 260 N GLU B 261 1555 1555 1.34 LINK C GLU B 325 N MSE B 326 1555 1555 1.34 LINK C MSE B 326 N LEU B 327 1555 1555 1.33 LINK C LEU B 402 N MSE B 403 1555 1555 1.33 LINK C MSE B 403 N LYS B 404 1555 1555 1.33 CISPEP 1 PRO B 115 ASP B 116 0 -10.10 CISPEP 2 LYS B 386 GLY B 387 0 0.56 CRYST1 190.569 62.738 152.390 90.00 103.96 90.00 C 1 2 1 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 0.005247 0.000000 0.001304 0.00000 SCALE2 0.000000 0.015939 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006762 0.00000 HETATM 1 N MSE A 1 15.712 -2.233 20.748 1.00 83.15 N HETATM 2 CA MSE A 1 16.793 -3.206 20.860 1.00 87.49 C HETATM 3 C MSE A 1 17.968 -2.732 20.006 1.00 75.52 C HETATM 4 O MSE A 1 18.876 -3.496 19.670 1.00 81.14 O HETATM 5 CB MSE A 1 16.315 -4.606 20.450 1.00 97.74 C HETATM 6 CG MSE A 1 17.230 -5.766 20.871 1.00 99.14 C HETATM 7 SE MSE A 1 18.486 -6.384 19.522 1.00391.35 SE HETATM 8 CE MSE A 1 19.754 -7.265 20.697 1.00104.93 C