HEADER TRANSFERASE 11-FEB-15 2MZB TITLE SOLUTION STRUCTURAL STUDIES OF GTP:ADENOSYLCOBINAMIDE-PHOSPHATE TITLE 2 GUANYLYLTRANSFERASE (COBY) FROM METHANOCALDOCOCCUS JANNASCHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENOSYLCOBINAMIDE-PHOSPHATE GUANYLYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADOCBI-P GUANYLYLTRANSFERASE; COMPND 5 EC: 2.7.7.62; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 243232; SOURCE 4 STRAIN: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440; SOURCE 5 GENE: COBY, MJ1117; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PCOBY14 KEYWDS TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.SINGARAPU,M.OTTE,M.TONELLI,W.M.WESTLER,J.C.ESCALANTE-SEMERENA, AUTHOR 2 J.L.MARKLEY REVDAT 3 15-MAY-24 2MZB 1 REMARK REVDAT 2 14-JUN-23 2MZB 1 REMARK REVDAT 1 11-NOV-15 2MZB 0 JRNL AUTH K.K.SINGARAPU,M.M.OTTE,M.TONELLI,W.M.WESTLER, JRNL AUTH 2 J.C.ESCALANTE-SEMERENA,J.L.MARKLEY JRNL TITL SOLUTION STRUCTURAL STUDIES OF JRNL TITL 2 GTP:ADENOSYLCOBINAMIDE-PHOSPHATEGUANYLYL TRANSFERASE (COBY) JRNL TITL 3 FROM METHANOCALDOCOCCUS JANNASCHII. JRNL REF PLOS ONE V. 10 41297 2015 JRNL REFN ESSN 1932-6203 JRNL PMID 26513744 JRNL DOI 10.1371/JOURNAL.PONE.0141297 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, CYANA REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), GUNTERT, MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MZB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000104224. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.0 MM [U-100% 15N] COBY, 2.0 MM REMARK 210 [U-100% 15N] COBY, 2.0 MM [U-100% REMARK 210 15N] COBY, 2.0 MM [U-100% 15N] REMARK 210 COBY, 2.0 MM [U-100% 15N] COBY, REMARK 210 2.0 MM [U-100% 15N] COBY, 90% REMARK 210 H2O/10% D2O; 2.0 MM [U-100% 13C; REMARK 210 U-100% 15N] COBY, 2.0 MM [U-100% REMARK 210 13C; U-100% 15N] COBY, 2.0 MM [U- REMARK 210 100% 13C; U-100% 15N] COBY, 2.0 REMARK 210 MM [U-100% 13C; U-100% 15N] COBY, REMARK 210 2.0 MM [U-100% 13C; U-100% 15N] REMARK 210 COBY, 2.0 MM [U-100% 13C; U-100% REMARK 210 15N] COBY, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HNCO; 3D H(CCO)NH; 3D HCCH-TOCSY; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMRJ, NMRPIPE, XEASY, TALOS, REMARK 210 SPARKY, CYANA, MOLMOL, PROCHECK REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING, SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O SER A 76 H GLY A 79 1.59 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 1 ARG A 13 -80.00 -142.87 REMARK 500 1 MET A 14 -53.47 -130.42 REMARK 500 1 LYS A 55 -44.58 -151.01 REMARK 500 1 TYR A 67 113.50 -35.69 REMARK 500 1 SER A 76 1.48 -69.06 REMARK 500 1 ASN A 104 153.15 170.04 REMARK 500 1 ILE A 144 -55.75 -123.53 REMARK 500 1 ASN A 179 -30.98 -130.12 REMARK 500 2 MET A 14 168.85 76.03 REMARK 500 2 ASN A 43 -75.58 -85.03 REMARK 500 2 LYS A 55 -47.24 -154.63 REMARK 500 2 THR A 75 -167.29 -167.06 REMARK 500 2 SER A 76 1.17 -64.08 REMARK 500 2 SER A 143 -161.19 63.30 REMARK 500 2 ASP A 145 -134.66 56.20 REMARK 500 2 PRO A 159 75.20 -67.13 REMARK 500 3 MET A 14 133.81 70.08 REMARK 500 3 ASN A 43 -76.31 -83.38 REMARK 500 3 LYS A 55 -50.43 -147.83 REMARK 500 3 ILE A 144 148.57 71.72 REMARK 500 3 ALA A 152 -30.19 -135.25 REMARK 500 4 MET A 14 -37.40 71.71 REMARK 500 4 CYS A 25 -75.65 63.33 REMARK 500 4 ASN A 43 -75.44 -80.12 REMARK 500 4 LYS A 55 -45.78 -151.43 REMARK 500 4 TYR A 67 132.96 -39.51 REMARK 500 4 THR A 75 -169.22 -160.57 REMARK 500 4 SER A 76 2.35 -64.32 REMARK 500 4 ASN A 104 176.95 173.58 REMARK 500 4 PRO A 140 -76.92 -65.84 REMARK 500 4 ILE A 144 -68.29 -138.09 REMARK 500 4 ASP A 145 148.25 -176.52 REMARK 500 5 THR A 12 102.39 70.75 REMARK 500 5 CYS A 25 -74.32 65.66 REMARK 500 5 LYS A 55 -45.63 -146.45 REMARK 500 5 SER A 76 2.08 -66.69 REMARK 500 5 ASN A 104 -178.08 -176.91 REMARK 500 5 PRO A 140 -73.65 -54.59 REMARK 500 5 ILE A 144 -38.49 71.86 REMARK 500 5 ASN A 147 132.07 -171.81 REMARK 500 5 PRO A 159 93.93 -62.98 REMARK 500 5 HIS A 161 -68.81 -124.08 REMARK 500 5 TYR A 163 148.90 74.90 REMARK 500 6 LYS A 10 105.33 72.74 REMARK 500 6 GLU A 18 -162.45 49.69 REMARK 500 6 LYS A 19 176.25 67.26 REMARK 500 6 PRO A 20 -8.96 -59.16 REMARK 500 6 LYS A 55 -46.78 -147.63 REMARK 500 6 SER A 76 3.81 -66.73 REMARK 500 6 ASN A 104 167.61 173.28 REMARK 500 REMARK 500 THIS ENTRY HAS 181 RAMACHANDRAN OUTLIERS. 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 1 PRO A 54 -10.34 REMARK 500 2 PRO A 54 -11.04 REMARK 500 3 PRO A 54 -10.24 REMARK 500 4 PRO A 54 -10.39 REMARK 500 5 PRO A 54 -10.30 REMARK 500 6 PRO A 54 -10.61 REMARK 500 7 PRO A 54 -10.18 REMARK 500 8 PRO A 54 -10.68 REMARK 500 9 PRO A 54 -10.38 REMARK 500 10 PRO A 54 -10.98 REMARK 500 15 PRO A 54 -10.74 REMARK 500 16 PRO A 54 -10.39 REMARK 500 17 PRO A 54 -10.81 REMARK 500 18 PRO A 54 -10.09 REMARK 500 19 PRO A 54 -10.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25482 RELATED DB: BMRB DBREF 2MZB A 1 196 UNP Q58517 COBY_METJA 1 196 SEQRES 1 A 196 MET ASP ALA LEU ILE MET ALA GLY GLY LYS GLY THR ARG SEQRES 2 A 196 MET GLY GLY VAL GLU LYS PRO LEU ILE LYS LEU CYS GLY SEQRES 3 A 196 ARG CYS LEU ILE ASP TYR VAL VAL SER PRO LEU LEU LYS SEQRES 4 A 196 SER LYS VAL ASN ASN ILE PHE ILE ALA THR SER PRO ASN SEQRES 5 A 196 THR PRO LYS THR LYS GLU TYR ILE ASN SER ALA TYR LYS SEQRES 6 A 196 ASP TYR LYS ASN ILE VAL VAL ILE ASP THR SER GLY LYS SEQRES 7 A 196 GLY TYR ILE GLU ASP LEU ASN GLU CYS ILE GLY TYR PHE SEQRES 8 A 196 SER GLU PRO PHE LEU VAL VAL SER SER ASP LEU ILE ASN SEQRES 9 A 196 LEU LYS SER LYS ILE ILE ASN SER ILE VAL ASP TYR PHE SEQRES 10 A 196 TYR CYS ILE LYS ALA LYS THR PRO ASP VAL GLU ALA LEU SEQRES 11 A 196 ALA VAL MET ILE PRO LYS GLU LYS TYR PRO ASN PRO SER SEQRES 12 A 196 ILE ASP PHE ASN GLY LEU VAL PRO ALA GLY ILE ASN VAL SEQRES 13 A 196 VAL SER PRO LYS HIS GLY TYR GLN LYS GLU GLU ILE MET SEQRES 14 A 196 VAL ILE ASP GLU LEU ILE PHE ASN ILE ASN THR LYS ASP SEQRES 15 A 196 ASP LEU LYS LEU ALA GLU MET LEU LEU LYS LYS ASP GLY SEQRES 16 A 196 LEU HELIX 1 1 LEU A 29 SER A 40 1 12 HELIX 2 2 LYS A 55 TYR A 64 1 10 HELIX 3 3 GLY A 79 PHE A 91 1 13 HELIX 4 4 LYS A 106 THR A 124 1 19 HELIX 5 5 THR A 180 LEU A 196 1 17 SHEET 1 A 7 ILE A 70 ASP A 74 0 SHEET 2 A 7 ILE A 45 THR A 49 1 N ILE A 45 O VAL A 71 SHEET 3 A 7 ASP A 2 MET A 6 1 N ALA A 3 O PHE A 46 SHEET 4 A 7 PHE A 95 SER A 99 1 O LEU A 96 N ASP A 2 SHEET 5 A 7 LEU A 149 VAL A 157 -1 O ASN A 155 N VAL A 97 SHEET 6 A 7 ALA A 129 PRO A 135 -1 N LEU A 130 O VAL A 156 SHEET 7 A 7 GLU A 166 VAL A 170 1 O GLU A 167 N ALA A 129 SHEET 1 B 2 LYS A 23 LEU A 24 0 SHEET 2 B 2 ARG A 27 CYS A 28 -1 O ARG A 27 N LEU A 24 SHEET 1 C 2 LEU A 102 ILE A 103 0 SHEET 2 C 2 PHE A 176 ASN A 177 -1 O PHE A 176 N ILE A 103 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1