10 20 30 40 50 60 70 80 2RPI - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 16-MAY-08 2RPI
TITLE THE NMR STRUCTURE OF THE SUBMILLISECOND FOLDING TITLE 2 INTERMEDIATE OF THE 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, KEYWDS 3 HYDROLASE, MAGNESIUM, METAL-BINDING, NUCLEASE
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR Z.ZHOU,H.FENG,Y.BAI
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 JRNL TITL 2 FOLDING INTERMEDIATE OF THE THERMUS THERMOPHILUS JRNL TITL 3 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 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2RPI COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-MAY-08. REMARK 100 THE RCSB ID CODE IS RCSB150128.
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, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC, 2D 1H-1H REMARK 210 NOESY, 3D CBCA(CO)NH, 3D REMARK 210 HNCACB, 3D HNCO, 3D HN(CO)CA, REMARK 210 3D H(CCO)NH, 3D HNHA, 3D HCCH- REMARK 210 TOCSY, 3D HBHA(CO)NH, 3D 1H- REMARK 210 15N NOESY, 3D 1H-13C NOESY, 3D REMARK 210 HN(CA)NNH, 3D 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- REMARK 210 PLOR_NIH, PROCHECKNMR, MOLMOL REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY REMARK 210 SIMULATED ANNEALING, TORSION REMARK 210 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 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: 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 4 ASN A 2 -179.68 76.05 REMARK 500 4 PRO A 5 -83.75 -46.63 REMARK 500 4 ARG A 6 -59.22 -145.35 REMARK 500 4 LYS A 7 103.42 -177.35 REMARK 500 4 THR A 13 84.21 -63.56 REMARK 500 4 ASP A 14 52.45 -114.55 REMARK 500 4 ALA A 16 -54.44 -173.92 REMARK 500 4 ALA A 17 89.29 78.20 REMARK 500 4 LEU A 18 15.78 -179.64 REMARK 500 4 THR A 25 -1.39 164.69 REMARK 500 4 LEU A 42 -56.51 -120.32 REMARK 500 4 LYS A 43 16.07 59.97 REMARK 500 4 PRO A 45 102.43 -43.37 REMARK 500 4 ASP A 53 42.19 -95.79 REMARK 500 4 TRP A 74 87.45 74.11 REMARK 500 4 PRO A 81 157.86 -42.21 REMARK 500 4 VAL A 100 114.27 -3.54 REMARK 500 4 PHE A 104 97.99 -68.44 REMARK 500 5 ASN A 2 164.59 166.17 REMARK 500 5 PRO A 3 171.88 -44.43 REMARK 500 5 PRO A 5 -80.02 -50.86 REMARK 500 5 ARG A 6 -61.69 -146.61 REMARK 500 5 LYS A 7 103.82 -174.88 REMARK 500 5 THR A 13 83.53 -64.72 REMARK 500 5 ASP A 14 58.52 -114.81 REMARK 500 5 ALA A 16 -57.52 -175.84 REMARK 500 5 ALA A 17 84.80 77.78 REMARK 500 5 LEU A 18 11.50 -178.80 REMARK 500 5 THR A 25 -5.44 164.60 REMARK 500 5 LEU A 42 -57.22 -120.27 REMARK 500 5 PRO A 45 97.89 -40.24 REMARK 500 5 TRP A 74 86.13 78.54 REMARK 500 5 PRO A 81 159.09 -42.56 REMARK 500 5 VAL A 100 115.17 -3.80 REMARK 500 5 PHE A 104 97.94 -62.48 REMARK 500 6 ASN A 2 163.45 165.77 REMARK 500 6 PRO A 3 173.65 -45.16 REMARK 500 6 ARG A 6 -59.98 -163.98 REMARK 500 6 LYS A 7 115.67 -178.84 REMARK 500 6 THR A 13 82.16 -66.66 REMARK 500 6 ASP A 14 55.51 -113.84 REMARK 500 6 ALA A 16 -55.16 -173.98 REMARK 500 6 ALA A 17 86.75 78.16 REMARK 500 6 LEU A 18 13.57 -178.39 REMARK 500 6 THR A 25 1.28 162.88 REMARK 500 6 LEU A 42 -58.68 -122.25 REMARK 500 6 PRO A 45 102.92 -47.07 REMARK 500 6 ASP A 53 40.76 -100.65 REMARK 500 6 TRP A 74 88.03 74.47 REMARK 500 6 PRO A 81 160.23 -38.94 REMARK 500 6 VAL A 100 113.78 -1.33 REMARK 500 6 PHE A 104 98.02 -67.53 REMARK 500 7 ASN A 2 165.00 166.95 REMARK 500 7 PRO A 3 173.46 -46.03 REMARK 500 7 ARG A 6 -60.80 -164.89 REMARK 500 7 LYS A 7 117.11 -179.05 REMARK 500 7 THR A 13 84.27 -63.13 REMARK 500 7 ASP A 14 53.15 -114.42 REMARK 500 7 ALA A 16 -55.49 -176.24 REMARK 500 7 ALA A 17 83.58 77.57 REMARK 500 7 LEU A 18 13.62 -177.39 REMARK 500 7 THR A 25 -0.99 161.39 REMARK 500 7 LEU A 42 -61.47 -122.78 REMARK 500 7 PRO A 45 103.78 -42.50 REMARK 500 7 ASP A 53 39.45 -97.71 REMARK 500 7 TRP A 74 86.63 73.12 REMARK 500 7 ALA A 77 -9.90 -58.28 REMARK 500 7 PRO A 81 158.22 -45.20 REMARK 500 7 VAL A 100 112.60 -1.71 REMARK 500 7 PHE A 104 99.16 -67.65 REMARK 500 8 ASN A 2 163.71 165.41 REMARK 500 8 PRO A 3 173.62 -44.66 REMARK 500 8 PRO A 5 -82.59 -46.86 REMARK 500 8 ARG A 6 -59.52 -146.28 REMARK 500 8 LYS A 7 101.05 -176.80 REMARK 500 8 THR A 13 82.29 -62.62 REMARK 500 8 ASP A 14 54.68 -113.97 REMARK 500 8 ALA A 16 -54.26 -174.67 REMARK 500 8 ALA A 17 86.97 77.42 REMARK 500 8 LEU A 18 12.68 -178.22 REMARK 500 8 THR A 25 -2.36 163.78 REMARK 500 8 PRO A 45 100.22 -41.83 REMARK 500 8 ASP A 53 40.98 -96.59 REMARK 500 8 ALA A 60 -77.15 -68.03 REMARK 500 8 TRP A 74 84.75 71.44 REMARK 500 8 PRO A 81 158.42 -40.45 REMARK 500 8 VAL A 100 116.49 -1.39 REMARK 500 8 PHE A 104 97.28 -68.74 REMARK 500 9 ASN A 2 160.84 162.70 REMARK 500 9 PRO A 3 169.34 -46.06 REMARK 500 9 PRO A 5 -78.33 -48.96 REMARK 500 9 ARG A 6 -61.66 -148.38 REMARK 500 9 LYS A 7 101.10 -178.05 REMARK 500 9 THR A 13 82.30 -62.53 REMARK 500 9 ASP A 14 52.08 -113.73 REMARK 500 9 ALA A 16 -56.05 -177.83 REMARK 500 9 ALA A 17 87.14 77.39 REMARK 500 9 LEU A 18 9.16 -178.00 REMARK 500 9 THR A 25 -0.17 162.80 REMARK 500 9 LEU A 42 -61.39 -120.30 REMARK 500 9 PRO A 45 102.36 -42.05 REMARK 500 9 ASP A 53 41.33 -99.70 REMARK 500 9 TRP A 74 86.76 75.31 REMARK 500 9 PRO A 81 158.30 -43.70 REMARK 500 9 VAL A 100 113.24 -3.99 REMARK 500 9 PHE A 104 101.57 -58.81 REMARK 500 10 ASN A 2 162.88 165.70 REMARK 500 10 PRO A 3 173.84 -44.67 REMARK 500 10 PRO A 5 -70.70 -46.29 REMARK 500 10 ARG A 6 -67.56 -156.79 REMARK 500 10 LYS A 7 102.09 -172.18 REMARK 500 10 THR A 13 83.29 -67.12 REMARK 500 10 ASP A 14 52.90 -112.90 REMARK 500 10 ALA A 16 -54.56 -174.79 REMARK 500 10 ALA A 17 85.05 77.85 REMARK 500 10 LEU A 18 15.64 -177.95 REMARK 500 10 THR A 25 -2.10 162.13 REMARK 500 10 LEU A 42 -58.75 -122.66 REMARK 500 10 LYS A 43 16.13 58.91 REMARK 500 10 PRO A 45 105.73 -41.39 REMARK 500 10 ASP A 53 42.36 -98.45 REMARK 500 10 TRP A 74 91.79 73.95 REMARK 500 10 PRO A 81 158.31 -45.23 REMARK 500 10 VAL A 100 111.20 -1.67 REMARK 500 10 PHE A 104 102.19 -59.07 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