HEADER HYDROLASE 12-APR-12 2LRR TITLE SOLUTION STRUCTURE OF THE R3H DOMAIN FROM HUMAN SMUBP-2 IN COMPLEX TITLE 2 WITH 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-BINDING PROTEIN SMUBP-2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: R3H DOMAIN RESIDUES 711-786; COMPND 5 SYNONYM: ATP-DEPENDENT HELICASE IGHMBP2, GLIAL FACTOR 1, GF-1, COMPND 6 IMMUNOGLOBULIN MU-BINDING PROTEIN 2; COMPND 7 EC: 3.6.4.12, 3.6.4.13; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: IGHMBP2, SMBP2, SMUBP-2, SMUBP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PQE60 KEYWDS DNA BINDING PROTEIN, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.JAUDZEMS,D.ZHULENKOVS,G.OTTING,E.LIEPINSH REVDAT 2 14-JUN-23 2LRR 1 REMARK SEQADV REVDAT 1 24-OCT-12 2LRR 0 JRNL AUTH K.JAUDZEMS,X.JIA,H.YAGI,D.ZHULENKOVS,B.GRAHAM,G.OTTING, JRNL AUTH 2 E.LIEPINSH JRNL TITL STRUCTURAL BASIS FOR 5'-END-SPECIFIC RECOGNITION OF JRNL TITL 2 SINGLE-STRANDED DNA BY THE R3H DOMAIN FROM HUMAN SMUBP-2 JRNL REF J.MOL.BIOL. V. 12 760 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22999958 JRNL DOI 10.1016/J.JMB.2012.09.010 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMRJ 2.1B, CNS, CYANA 2.1 REMARK 3 AUTHORS : VARIAN (VNMRJ), BRUNGER, ADAMS, CLORE, GROS, REMARK 3 NILGES AND READ (CNS), GUNTERT, MUMENTHALER AND REMARK 3 WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LRR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000102751. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.3 REMARK 210 IONIC STRENGTH : 0.12 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.9 MM [U-99% 15N] SMUBP2_R3H, REMARK 210 5.5 MM 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE, 5 % [U-100% 2H] D2O, REMARK 210 10 MM SODIUM PHOSPHATE, 100 MM SODIUM CHLORIDE, 0.03 % SODIUM REMARK 210 AZIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H NOESY; 3D 1H-15N NOESY; REMARK 210 3D HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, XEASY, CYANA 2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING 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 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 709 REMARK 465 GLY A 710 REMARK 465 SER A 711 REMARK 465 LEU A 712 REMARK 465 ASN A 713 REMARK 465 GLY A 714 REMARK 465 GLY A 715 REMARK 465 SER A 716 REMARK 465 GLY A 787 REMARK 465 SER A 788 REMARK 465 HIS A 789 REMARK 465 HIS A 790 REMARK 465 HIS A 791 REMARK 465 HIS A 792 REMARK 465 HIS A 793 REMARK 465 HIS A 794 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 OE1 GLU A 774 HZ3 LYS A 776 1.56 REMARK 500 OE1 GLU A 745 HG1 THR A 781 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 GLU A 774 -100.58 -134.22 REMARK 500 3 ASP A 724 43.93 -93.99 REMARK 500 3 ARG A 785 -76.98 -118.91 REMARK 500 4 GLU A 718 -75.78 -105.39 REMARK 500 4 GLN A 723 -72.17 -73.77 REMARK 500 4 ASP A 724 -86.89 -82.53 REMARK 500 5 GLU A 718 95.63 62.83 REMARK 500 7 SER A 722 97.49 -69.33 REMARK 500 7 GLN A 723 -52.38 -129.99 REMARK 500 8 ASP A 724 -70.29 -74.79 REMARK 500 8 VAL A 726 119.97 -163.89 REMARK 500 8 GLU A 774 -77.48 -87.73 REMARK 500 9 GLU A 718 -77.79 -105.20 REMARK 500 11 VAL A 720 78.76 -107.06 REMARK 500 12 GLU A 718 99.16 60.65 REMARK 500 12 ASP A 724 -156.92 -97.13 REMARK 500 13 LYS A 784 -85.35 -68.20 REMARK 500 15 GLU A 774 -84.39 -101.05 REMARK 500 17 GLU A 774 -88.79 -94.76 REMARK 500 18 ARG A 785 -81.42 -115.40 REMARK 500 20 ASP A 724 -156.26 -104.09 REMARK 500 20 VAL A 726 137.90 -170.29 REMARK 500 20 GLU A 774 -92.64 -84.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGP A 801 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MSZ RELATED DB: PDB REMARK 900 STRUCTURE OF LIGAND FREE FORM REMARK 900 RELATED ID: 18391 RELATED DB: BMRB DBREF 2LRR A 711 786 UNP P38935 SMBP2_HUMAN 711 786 SEQADV 2LRR MET A 709 UNP P38935 EXPRESSION TAG SEQADV 2LRR GLY A 710 UNP P38935 EXPRESSION TAG SEQADV 2LRR GLY A 787 UNP P38935 EXPRESSION TAG SEQADV 2LRR SER A 788 UNP P38935 EXPRESSION TAG SEQADV 2LRR HIS A 789 UNP P38935 EXPRESSION TAG SEQADV 2LRR HIS A 790 UNP P38935 EXPRESSION TAG SEQADV 2LRR HIS A 791 UNP P38935 EXPRESSION TAG SEQADV 2LRR HIS A 792 UNP P38935 EXPRESSION TAG SEQADV 2LRR HIS A 793 UNP P38935 EXPRESSION TAG SEQADV 2LRR HIS A 794 UNP P38935 EXPRESSION TAG SEQRES 1 A 86 MET GLY SER LEU ASN GLY GLY SER PRO GLU GLY VAL GLU SEQRES 2 A 86 SER GLN ASP GLY VAL ASP HIS PHE ARG ALA MET ILE VAL SEQRES 3 A 86 GLU PHE MET ALA SER LYS LYS MET GLN LEU GLU PHE PRO SEQRES 4 A 86 PRO SER LEU ASN SER HIS ASP ARG LEU ARG VAL HIS GLN SEQRES 5 A 86 ILE ALA GLU GLU HIS GLY LEU ARG HIS ASP SER SER GLY SEQRES 6 A 86 GLU GLY LYS ARG ARG PHE ILE THR VAL SER LYS ARG ALA SEQRES 7 A 86 GLY SER HIS HIS HIS HIS HIS HIS HET DGP A 801 34 HETNAM DGP 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE FORMUL 2 DGP C10 H14 N5 O7 P HELIX 1 1 ASP A 727 SER A 739 1 13 HELIX 2 2 ASN A 751 GLY A 766 1 16 SHEET 1 A 3 GLN A 743 GLU A 745 0 SHEET 2 A 3 PHE A 779 SER A 783 -1 O VAL A 782 N LEU A 744 SHEET 3 A 3 ARG A 768 SER A 772 -1 N ASP A 770 O THR A 781 SITE 1 AC1 8 SER A 752 ARG A 755 LEU A 756 HIS A 759 SITE 2 AC1 8 GLU A 763 HIS A 769 SER A 771 ARG A 778 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