PDB Short entry for 2L9N HEADER RNA BINDING PROTEIN 21-FEB-11 2L9N TITLE STRUCTURE OF THE HUMAN SHWACHMAN-BODIAN-DIAMOND SYNDROME (SBDS) TITLE 2 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME MATURATION PROTEIN SBDS; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SHWACHMAN-BODIAN-DIAMOND SYNDROME PROTEIN; COMPND 5 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: CGI-97, SBDS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C41 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PSBDS KEYWDS RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.HILCENKO,S.M.V.FREUND,A.J.WARREN REVDAT 2 14-JUN-23 2L9N 1 REMARK SEQADV REVDAT 1 11-MAY-11 2L9N 0 JRNL AUTH A.J.FINCH,C.HILCENKO,N.BASSE,L.F.DRYNAN,B.GOYENECHEA, JRNL AUTH 2 T.F.MENNE,A.GONZALEZ FERNANDEZ,P.SIMPSON,C.S.D'SANTOS, JRNL AUTH 3 M.J.ARENDS,J.DONADIEU,C.BELLANNE-CHANTELOT,M.COSTANZO, JRNL AUTH 4 C.BOONE,A.N.MCKENZIE,S.M.FREUND,A.J.WARREN JRNL TITL UNCOUPLING OF GTP HYDROLYSIS FROM EIF6 RELEASE ON THE JRNL TITL 2 RIBOSOME CAUSES SHWACHMAN-DIAMOND SYNDROME. JRNL REF GENES DEV. V. 25 917 2011 JRNL REFN ISSN 0890-9369 JRNL PMID 21536732 JRNL DOI 10.1101/GAD.623011 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SPARKY 3, CNS REMARK 3 AUTHORS : GODDARD (SPARKY), REMARK 3 BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI, REMARK 3 NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L9N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000102130. 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 : 0.163 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 25 MM POTASSIUM PHOSPHATE, 150 REMARK 210 MM SODIUM CHLORIDE, 1 MM DTT, REMARK 210 0.05 % SODIUM AZIDE, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D HNCO; 3D HN(CO)CA; REMARK 210 3D HBHA(CO)NH; 3D HNCACB; 3D REMARK 210 HNCACO; 2D 1H-15N HSQC; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY; 2D REMARK 210 1H-13C HSQC; 3D HCCH-TOCSY; 3D REMARK 210 HCCH-COSY; 3D HN(CAN)NH; 3D (H) REMARK 210 CC(CO)NH; 3D H(CCCO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3, TOPSPIN 2.1, CNS REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A -1 REMARK 465 SER A 0 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 ILE A 3 -54.66 77.74 REMARK 500 1 PHE A 4 102.11 64.34 REMARK 500 1 THR A 7 31.90 -165.32 REMARK 500 1 ASN A 8 -61.42 -153.21 REMARK 500 1 GLN A 9 -76.59 -107.08 REMARK 500 1 LEU A 12 92.37 59.91 REMARK 500 1 GLU A 44 88.28 -59.67 REMARK 500 1 VAL A 58 -54.14 -132.41 REMARK 500 1 ASP A 79 94.14 -61.83 REMARK 500 1 CYS A 119 155.08 178.29 REMARK 500 1 PRO A 122 63.86 -68.54 REMARK 500 1 GLU A 123 76.88 -156.77 REMARK 500 1 MET A 172 139.09 -174.09 REMARK 500 1 PRO A 179 -162.58 -57.38 REMARK 500 1 PRO A 214 -166.59 -67.73 REMARK 500 1 ASN A 238 -69.16 -95.84 REMARK 500 1 GLU A 243 84.05 -67.73 REMARK 500 1 GLU A 244 33.47 -148.58 REMARK 500 1 PHE A 249 37.75 -153.24 REMARK 500 2 ILE A 3 105.22 63.27 REMARK 500 2 PRO A 6 91.66 -69.10 REMARK 500 2 ASN A 8 45.20 -92.58 REMARK 500 2 GLN A 9 -45.13 -161.06 REMARK 500 2 ARG A 11 -66.54 -105.24 REMARK 500 2 LEU A 12 92.63 -166.55 REMARK 500 2 ASN A 14 -52.09 -176.78 REMARK 500 2 GLU A 44 -78.19 -65.92 REMARK 500 2 LYS A 45 146.71 62.22 REMARK 500 2 VAL A 58 -53.24 -131.81 REMARK 500 2 THR A 77 -42.71 -148.88 REMARK 500 2 ASP A 117 -68.93 -101.62 REMARK 500 2 HIS A 141 75.07 60.39 REMARK 500 2 PRO A 179 -178.93 -58.83 REMARK 500 2 GLU A 198 81.91 52.81 REMARK 500 2 GLN A 204 53.28 -109.48 REMARK 500 2 ASP A 213 80.75 64.29 REMARK 500 2 GLU A 244 -67.56 -176.43 REMARK 500 2 GLU A 247 -168.71 -174.26 REMARK 500 3 SER A 2 -61.28 -129.08 REMARK 500 3 ILE A 3 -50.79 -135.92 REMARK 500 3 ASN A 8 51.01 179.46 REMARK 500 3 GLN A 9 -66.89 -169.29 REMARK 500 3 VAL A 58 -46.02 -130.71 REMARK 500 3 ASP A 79 86.07 -59.12 REMARK 500 3 LYS A 118 46.11 -92.71 REMARK 500 3 GLU A 123 -56.13 -142.34 REMARK 500 3 ASN A 147 31.00 -98.13 REMARK 500 3 LYS A 164 -66.98 -98.41 REMARK 500 3 PRO A 179 -162.72 -77.20 REMARK 500 3 ILE A 197 142.91 -178.55 REMARK 500 REMARK 500 THIS ENTRY HAS 404 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17479 RELATED DB: BMRB DBREF 2L9N A 1 250 UNP Q9Y3A5 SBDS_HUMAN 1 250 SEQADV 2L9N GLY A -1 UNP Q9Y3A5 EXPRESSION TAG SEQADV 2L9N SER A 0 UNP Q9Y3A5 EXPRESSION TAG SEQRES 1 A 252 GLY SER MET SER ILE PHE THR PRO THR ASN GLN ILE ARG SEQRES 2 A 252 LEU THR ASN VAL ALA VAL VAL ARG MET LYS ARG ALA GLY SEQRES 3 A 252 LYS ARG PHE GLU ILE ALA CYS TYR LYS ASN LYS VAL VAL SEQRES 4 A 252 GLY TRP ARG SER GLY VAL GLU LYS ASP LEU ASP GLU VAL SEQRES 5 A 252 LEU GLN THR HIS SER VAL PHE VAL ASN VAL SER LYS GLY SEQRES 6 A 252 GLN VAL ALA LYS LYS GLU ASP LEU ILE SER ALA PHE GLY SEQRES 7 A 252 THR ASP ASP GLN THR GLU ILE CYS LYS GLN ILE LEU THR SEQRES 8 A 252 LYS GLY GLU VAL GLN VAL SER ASP LYS GLU ARG HIS THR SEQRES 9 A 252 GLN LEU GLU GLN MET PHE ARG ASP ILE ALA THR ILE VAL SEQRES 10 A 252 ALA ASP LYS CYS VAL ASN PRO GLU THR LYS ARG PRO TYR SEQRES 11 A 252 THR VAL ILE LEU ILE GLU ARG ALA MET LYS ASP ILE HIS SEQRES 12 A 252 TYR SER VAL LYS THR ASN LYS SER THR LYS GLN GLN ALA SEQRES 13 A 252 LEU GLU VAL ILE LYS GLN LEU LYS GLU LYS MET LYS ILE SEQRES 14 A 252 GLU ARG ALA HIS MET ARG LEU ARG PHE ILE LEU PRO VAL SEQRES 15 A 252 ASN GLU GLY LYS LYS LEU LYS GLU LYS LEU LYS PRO LEU SEQRES 16 A 252 ILE LYS VAL ILE GLU SER GLU ASP TYR GLY GLN GLN LEU SEQRES 17 A 252 GLU ILE VAL CYS LEU ILE ASP PRO GLY CYS PHE ARG GLU SEQRES 18 A 252 ILE ASP GLU LEU ILE LYS LYS GLU THR LYS GLY LYS GLY SEQRES 19 A 252 SER LEU GLU VAL LEU ASN LEU LYS ASP VAL GLU GLU GLY SEQRES 20 A 252 ASP GLU LYS PHE GLU HELIX 1 1 TYR A 32 GLY A 42 1 11 HELIX 2 2 ASP A 46 LEU A 51 1 6 HELIX 3 3 LYS A 67 GLY A 76 1 10 HELIX 4 4 ASP A 79 LYS A 90 1 12 HELIX 5 5 SER A 96 LYS A 118 1 23 HELIX 6 6 THR A 129 ILE A 140 1 12 HELIX 7 7 SER A 149 MET A 165 1 17 HELIX 8 8 ASN A 181 ILE A 194 1 14 HELIX 9 9 PHE A 217 GLY A 230 1 14 SHEET 1 A 3 LYS A 25 CYS A 31 0 SHEET 2 A 3 ALA A 16 ARG A 22 -1 N ALA A 16 O CYS A 31 SHEET 3 A 3 GLU A 92 GLN A 94 -1 O GLU A 92 N ARG A 19 SHEET 1 B 4 LYS A 195 ASP A 201 0 SHEET 2 B 4 GLU A 207 PRO A 214 -1 O ILE A 208 N GLU A 200 SHEET 3 B 4 HIS A 171 LEU A 178 -1 N PHE A 176 O VAL A 209 SHEET 4 B 4 LEU A 234 LEU A 237 -1 O LEU A 234 N ILE A 177 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