HEADER HYDROLASE 16-MAY-08 2RPI TITLE THE NMR STRUCTURE OF THE SUBMILLISECOND FOLDING INTERMEDIATE OF THE TITLE 2 THERMUS THERMOPHILUS RIBONUCLEASE H COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE H; COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS HB8; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 GENE: RNHA, TTHA1556; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET42B(+) KEYWDS SUBMILLISECOND FOLDING INTERMEDIATE, THERMUS THERMOPHILUS KEYWDS 2 RIBONUCLEASE H, HIGH-RESOLUTION STRUCTURE, ENDONUCLEASE, HYDROLASE, KEYWDS 3 MAGNESIUM, METAL-BINDING, NUCLEASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Z.ZHOU,H.FENG,Y.BAI REVDAT 3 29-MAY-24 2RPI 1 REMARK REVDAT 2 16-MAR-22 2RPI 1 REMARK SEQADV REVDAT 1 31-MAR-09 2RPI 0 JRNL AUTH Z.ZHOU,H.FENG,R.GHIRLANDO,Y.BAI JRNL TITL THE HIGH-RESOLUTION NMR STRUCTURE OF THE EARLY FOLDING JRNL TITL 2 INTERMEDIATE OF THE THERMUS THERMOPHILUS RIBONUCLEASE H JRNL REF J.MOL.BIOL. V. 384 531 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18848567 JRNL DOI 10.1016/J.JMB.2008.09.044 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, X-PLOR NIH REMARK 3 AUTHORS : DELAGLIO, ZHENGRONG AND BAX (NMRPIPE), SCHWIETERS, REMARK 3 KUSZEWSKI, TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RPI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000150128. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 5.2 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0-1.2MM [U-100% 13C; U-100% REMARK 210 15N] PROTEIN, 100% D2O; 1.0- REMARK 210 1.2MM PROTEIN, 100% D2O; 1.0- REMARK 210 1.2MM [U-100% 13C] PROTEIN, 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-1H NOESY; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HNCO; 3D HN(CO)CA; 3D H(CCO)NH; REMARK 210 3D HNHA; 3D HCCH-TOCSY; 3D REMARK 210 HBHA(CO)NH; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY; 3D HN(CA)NNH; 3D REMARK 210 HN(CA)CO REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW, TALOS, X-PLOR REMARK 210 NIH, PROCHECKNMR, MOLMOL REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING, TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 HIS A 107 REMARK 465 HIS A 108 REMARK 465 HIS A 109 REMARK 465 HIS A 110 REMARK 465 HIS A 111 REMARK 465 HIS A 112 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 THR A 26 H MET A 30 1.56 REMARK 500 O TRP A 88 H LEU A 92 1.58 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 ASN A 2 170.25 79.93 REMARK 500 1 PRO A 3 157.03 -46.28 REMARK 500 1 PRO A 5 -77.01 -52.43 REMARK 500 1 ARG A 6 -62.50 -148.01 REMARK 500 1 LYS A 7 104.41 -177.49 REMARK 500 1 THR A 13 84.15 -65.05 REMARK 500 1 ASP A 14 53.46 -115.05 REMARK 500 1 ALA A 16 -55.66 -175.52 REMARK 500 1 ALA A 17 86.90 77.40 REMARK 500 1 LEU A 18 11.64 -178.45 REMARK 500 1 THR A 25 -6.01 160.31 REMARK 500 1 LEU A 42 -60.09 -121.25 REMARK 500 1 PRO A 45 105.33 -41.23 REMARK 500 1 ASP A 53 40.99 -94.91 REMARK 500 1 TRP A 74 87.07 72.61 REMARK 500 1 PRO A 81 158.73 -43.24 REMARK 500 1 VAL A 100 111.93 -2.28 REMARK 500 1 PHE A 104 97.72 -67.84 REMARK 500 2 ASN A 2 160.79 162.13 REMARK 500 2 PRO A 3 160.21 -48.31 REMARK 500 2 PRO A 5 -71.54 -49.56 REMARK 500 2 ARG A 6 -64.47 -157.44 REMARK 500 2 LYS A 7 102.96 -174.65 REMARK 500 2 THR A 13 84.98 -64.88 REMARK 500 2 ASP A 14 50.84 -114.14 REMARK 500 2 ALA A 16 -54.26 -173.26 REMARK 500 2 ALA A 17 84.86 78.21 REMARK 500 2 LEU A 18 13.66 -176.99 REMARK 500 2 THR A 25 2.42 168.08 REMARK 500 2 PRO A 45 98.32 -41.53 REMARK 500 2 ASP A 53 42.41 -98.58 REMARK 500 2 TRP A 74 86.05 77.65 REMARK 500 2 PRO A 81 159.56 -39.97 REMARK 500 2 VAL A 100 116.38 -4.30 REMARK 500 3 ASN A 2 162.40 164.86 REMARK 500 3 PRO A 3 172.87 -45.15 REMARK 500 3 ARG A 6 -60.39 -159.63 REMARK 500 3 LYS A 7 100.56 -176.75 REMARK 500 3 THR A 13 81.09 -66.16 REMARK 500 3 ASP A 14 54.98 -114.27 REMARK 500 3 ALA A 16 -53.57 -176.34 REMARK 500 3 ALA A 17 86.51 77.33 REMARK 500 3 LEU A 18 13.50 -178.32 REMARK 500 3 THR A 25 0.80 160.24 REMARK 500 3 PRO A 45 105.43 -42.65 REMARK 500 3 ASP A 53 40.60 -95.35 REMARK 500 3 TRP A 74 87.95 73.05 REMARK 500 3 PRO A 81 153.95 -49.22 REMARK 500 3 VAL A 100 113.68 -3.02 REMARK 500 3 PHE A 104 96.79 -68.24 REMARK 500 REMARK 500 THIS ENTRY HAS 175 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QF8 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE RESIDUES 25-45 IN THE DATABASE SEQUENCE REMARK 999 (RNH_THET8 P29253) WERE DELETED REMARK 999 SINCE THIS IS THE INTERMEDIATE STATE OF THE PROTEIN. REMARK 999 IN THIS INTERMEDIATE STATE, IT EXCLUDES THE RESIDUES 25-45, REMARK 999 BUT STILL FOLDS WELL. REMARK 999 ABOUT RESIDUE 17, 67, THESE CONFLICTS ARE BASED ON REMARK 999 FOLDING, THERMAL STABILITY AND EXPRESSION. DBREF 2RPI A 1 24 UNP P29253 RNH_THET8 1 24 DBREF 2RPI A 25 106 UNP P29253 RNH_THET8 46 127 SEQADV 2RPI ALA A 17 UNP P29253 CYS 17 SEE REMARK 999 SEQADV 2RPI ALA A 46 UNP P29253 CYS 67 SEE REMARK 999 SEQADV 2RPI HIS A 107 UNP P29253 EXPRESSION TAG SEQADV 2RPI HIS A 108 UNP P29253 EXPRESSION TAG SEQADV 2RPI HIS A 109 UNP P29253 EXPRESSION TAG SEQADV 2RPI HIS A 110 UNP P29253 EXPRESSION TAG SEQADV 2RPI HIS A 111 UNP P29253 EXPRESSION TAG SEQADV 2RPI HIS A 112 UNP P29253 EXPRESSION TAG SEQRES 1 A 112 MET ASN PRO SER PRO ARG LYS ARG VAL ALA LEU PHE THR SEQRES 2 A 112 ASP GLY ALA ALA LEU GLY ASN PRO GLY PRO GLY THR THR SEQRES 3 A 112 ASN ASN ARG MET GLU LEU LYS ALA ALA ILE GLU GLY LEU SEQRES 4 A 112 LYS ALA LEU LYS GLU PRO ALA GLU VAL ASP LEU TYR THR SEQRES 5 A 112 ASP SER HIS TYR LEU LYS LYS ALA PHE THR GLU GLY TRP SEQRES 6 A 112 LEU GLU GLY TRP ARG LYS ARG GLY TRP ARG THR ALA GLU SEQRES 7 A 112 GLY LYS PRO VAL LYS ASN ARG ASP LEU TRP GLU ALA LEU SEQRES 8 A 112 LEU LEU ALA MET ALA PRO HIS ARG VAL ARG PHE HIS PHE SEQRES 9 A 112 VAL LYS HIS HIS HIS HIS HIS HIS HELIX 1 1 THR A 25 ALA A 41 1 17 HELIX 2 2 TYR A 56 GLU A 63 1 8 HELIX 3 3 TRP A 65 ARG A 72 1 8 HELIX 4 4 ASN A 84 MET A 95 1 12 SHEET 1 A 2 ASP A 49 TYR A 51 0 SHEET 2 A 2 ARG A 101 HIS A 103 1 O HIS A 103 N LEU A 50 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