HEADER HYDROLASE 24-OCT-09 2KQ2 TITLE SOLUTION NMR STRUCTURE OF THE APO FORM OF A RIBONUCLEASE H DOMAIN OF TITLE 2 PROTEIN DSY1790 FROM DESULFITOBACTERIUM HAFNIENSE, NORTHEAST TITLE 3 STRUCTURAL GENOMICS TARGET DHR1A COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H-RELATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 69-206; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFITOBACTERIUM HAFNIENSE DCB-2; SOURCE 3 ORGANISM_TAXID: 272564; SOURCE 4 STRAIN: DCB-2 / DSM 10664; SOURCE 5 GENE: DHAF_2944; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+ MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET 21-23C KEYWDS PSI, NESG, PROTEIN STRUCTURE, RIBONUCLEASE H, APO ENZYME, STRUCTURAL KEYWDS 2 GENOMICS, PROTEIN STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL KEYWDS 3 GENOMICS CONSORTIUM, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.L.MILLS,A.ELETSKY,J.HUA,R.L.BELOTE,W.A.BUCHWALD,C.CICCOSANTI, AUTHOR 2 H.JANJUA,R.NAIR,B.ROST,T.B.ACTON,R.XIAO,J.K.EVERETT,G.T.MONTELIONE, AUTHOR 3 T.SZYPERSKI,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 2 26-FEB-20 2KQ2 1 REMARK SEQADV REVDAT 1 16-MAR-10 2KQ2 0 JRNL AUTH J.L.MILLS,A.ELETSKY,J.HUA,R.L.BELOTE,W.A.BUCHWALD, JRNL AUTH 2 C.CICCOSANTI,H.JANJUA,R.NAIR,B.ROST,T.B.ACTON,R.XIAO, JRNL AUTH 3 J.K.EVERETT,G.T.MONTELIONE,T.SZYPERSKI JRNL TITL SOLUTION NMR STRUCTURE OF THE APO FORM OF A RIBONUCLEASE H JRNL TITL 2 DOMAIN OF PROTEIN DSY1790 FROM DESULFITOBACTERIUM HAFNIENSE, JRNL TITL 3 NORTHEAST STRUCTURAL GENOMICS TARGET DHR1A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMRJ, CNS, MOLMOL, PSVS REMARK 3 AUTHORS : VARIAN (VNMRJ), BRUNGER, ADAMS, CLORE, GROS, REMARK 3 NILGES AND READ (CNS), KORADI, BILLETER AND REMARK 3 WUTHRICH (MOLMOL), BHATTACHARYA AND MONTELIONE REMARK 3 (PSVS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KQ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000101431. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 430 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.89 MM [U-99% 13C; U-99% 15N] REMARK 210 DHR1A, 10 V/V [U-2H] D2O, 90 V/V REMARK 210 H2O, 20 MM MES, 200 MM SODIUM REMARK 210 CHLORIDE, 5 MM CALCIUM CHLORIDE, REMARK 210 10 MM DTT, 50 UM DSS, 0.02 W/V REMARK 210 SODIUM AZIDE, 90% H2O/10% D2O; REMARK 210 0.943 MM [U-5% 13C; U-99% 15N] REMARK 210 DHR1A, 10 V/V [U-2H] D2O, 90 V/V REMARK 210 H2O, 20 MM MES, 200 MM SODIUM REMARK 210 CHLORIDE, 5 MM CALCIUM CHLORIDE, REMARK 210 10 MM DTT, 50 UM DSS, 0.02 W/V REMARK 210 SODIUM AZIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCO; 3D REMARK 210 HNCACB; 3D HBHA(CO)NH; 3D HCCH- REMARK 210 COSY; 3D SIMULTANEOUS NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRDRAW, XEASY, SPSCAN, REMARK 210 AUTOASSIGN, CSI, TALOS, CYANA, REMARK 210 MOLMOL REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 HZ3 LYS A 41 OD2 ASP A 77 1.55 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 GLU A 6 173.88 57.21 REMARK 500 1 THR A 11 12.16 -152.10 REMARK 500 1 HIS A 76 -80.27 -142.22 REMARK 500 1 TRP A 89 -164.61 -174.29 REMARK 500 1 ASN A 93 157.88 71.47 REMARK 500 1 LYS A 101 -54.02 69.79 REMARK 500 1 SER A 119 36.53 -87.99 REMARK 500 2 SER A 14 -82.45 -77.66 REMARK 500 2 TYR A 78 19.47 -158.41 REMARK 500 2 GLU A 88 -60.05 -97.95 REMARK 500 2 ASN A 93 -73.21 -147.73 REMARK 500 2 GLU A 94 -57.82 -165.67 REMARK 500 2 HIS A 142 99.64 -68.46 REMARK 500 2 HIS A 144 106.62 -170.40 REMARK 500 3 ASP A 3 80.28 56.89 REMARK 500 3 TYR A 78 82.89 59.38 REMARK 500 3 THR A 86 -31.42 -130.66 REMARK 500 3 ASN A 93 -72.08 68.14 REMARK 500 3 GLU A 94 -18.31 -168.01 REMARK 500 3 SER A 119 14.20 -149.62 REMARK 500 3 HIS A 144 41.65 -166.29 REMARK 500 4 ARG A 49 -63.81 71.16 REMARK 500 4 ASN A 50 -88.51 60.62 REMARK 500 4 HIS A 76 85.07 69.54 REMARK 500 4 TYR A 78 -30.92 -160.60 REMARK 500 4 SER A 119 -31.29 -146.57 REMARK 500 4 ARG A 138 -164.35 -100.95 REMARK 500 4 HIS A 144 -78.18 61.25 REMARK 500 4 HIS A 145 -26.93 -168.62 REMARK 500 4 HIS A 146 -169.14 49.28 REMARK 500 5 GLU A 6 107.82 62.43 REMARK 500 5 ASP A 12 -78.71 -95.15 REMARK 500 5 ASN A 93 -73.71 -142.62 REMARK 500 5 GLU A 94 -56.96 -149.15 REMARK 500 5 SER A 119 -31.75 -149.07 REMARK 500 6 ASP A 3 26.06 -141.40 REMARK 500 6 GLU A 6 125.79 65.24 REMARK 500 6 THR A 11 103.71 67.71 REMARK 500 6 THR A 47 -60.99 -95.43 REMARK 500 6 MET A 48 -58.84 66.86 REMARK 500 6 ARG A 49 -71.42 -126.51 REMARK 500 6 ASN A 50 -9.13 -158.13 REMARK 500 6 LYS A 92 -57.56 -152.06 REMARK 500 6 ASN A 93 -19.00 -142.43 REMARK 500 6 HIS A 118 41.86 -142.79 REMARK 500 7 GLU A 6 -163.96 44.42 REMARK 500 7 THR A 11 86.80 74.42 REMARK 500 7 LYS A 41 -168.42 -102.58 REMARK 500 7 MET A 48 75.84 -111.94 REMARK 500 7 HIS A 76 7.27 -154.58 REMARK 500 REMARK 500 THIS ENTRY HAS 181 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: DHR1A RELATED DB: TARGETDB REMARK 900 RELATED ID: 16578 RELATED DB: BMRB DBREF 2KQ2 A 2 139 UNP B8FYP4 B8FYP4_DESHD 69 206 SEQADV 2KQ2 MET A 1 UNP B8FYP4 INITIATING METHIONINE SEQADV 2KQ2 LEU A 140 UNP B8FYP4 EXPRESSION TAG SEQADV 2KQ2 GLU A 141 UNP B8FYP4 EXPRESSION TAG SEQADV 2KQ2 HIS A 142 UNP B8FYP4 EXPRESSION TAG SEQADV 2KQ2 HIS A 143 UNP B8FYP4 EXPRESSION TAG SEQADV 2KQ2 HIS A 144 UNP B8FYP4 EXPRESSION TAG SEQADV 2KQ2 HIS A 145 UNP B8FYP4 EXPRESSION TAG SEQADV 2KQ2 HIS A 146 UNP B8FYP4 EXPRESSION TAG SEQADV 2KQ2 HIS A 147 UNP B8FYP4 EXPRESSION TAG SEQRES 1 A 147 MET ASP ASP ARG THR GLU TYR ASP VAL TYR THR ASP GLY SEQRES 2 A 147 SER TYR VAL ASN GLY GLN TYR ALA TRP ALA TYR ALA PHE SEQRES 3 A 147 VAL LYS ASP GLY LYS VAL HIS TYR GLU ASP ALA ASP VAL SEQRES 4 A 147 GLY LYS ASN PRO ALA ALA ALA THR MET ARG ASN VAL ALA SEQRES 5 A 147 GLY GLU ILE ALA ALA ALA LEU TYR ALA VAL LYS LYS ALA SEQRES 6 A 147 SER GLN LEU GLY VAL LYS ILE ARG ILE LEU HIS ASP TYR SEQRES 7 A 147 ALA GLY ILE ALA PHE TRP ALA THR GLY GLU TRP LYS ALA SEQRES 8 A 147 LYS ASN GLU PHE THR GLN ALA TYR ALA LYS LEU MET ASN SEQRES 9 A 147 GLN TYR ARG GLY ILE TYR SER PHE GLU LYS VAL LYS ALA SEQRES 10 A 147 HIS SER GLY ASN GLU PHE ASN ASP TYR VAL ASP MET LYS SEQRES 11 A 147 ALA LYS SER ALA LEU GLY ILE ARG ASP LEU GLU HIS HIS SEQRES 12 A 147 HIS HIS HIS HIS HELIX 1 1 ASN A 42 MET A 48 5 7 HELIX 2 2 ARG A 49 ASN A 50 5 2 HELIX 3 3 VAL A 51 GLY A 69 1 19 HELIX 4 4 ALA A 79 GLY A 87 5 9 HELIX 5 5 LYS A 92 LYS A 101 1 10 HELIX 6 6 LEU A 102 ARG A 107 5 6 HELIX 7 7 ASN A 121 GLY A 136 1 16 SHEET 1 A 3 ASP A 8 TYR A 10 0 SHEET 2 A 3 TRP A 22 LYS A 28 -1 O ALA A 25 N TYR A 10 SHEET 3 A 3 LYS A 31 ASP A 38 -1 O LYS A 31 N LYS A 28 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