PDB Short entry for 1XKE HEADER PROTEIN TRANSPORT 28-SEP-04 1XKE TITLE SOLUTION STRUCTURE OF THE SECOND RAN-BINDING DOMAIN FROM HUMAN RANBP2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAN-BINDING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RAN-BINDING DOMAIN 2 (RANBD2); COMPND 5 SYNONYM: RANBP2, NUCLEAR PORE COMPLEX PROTEIN NUP358, NUCLEOPORIN COMPND 6 NUP358, 358 KDA NUCLEOPORIN, P270; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS BETA BARREL, PLECKSTRIN-HOMOLOGY (PH) DOMAIN, PHOSPHOTYROSINE-BINDING KEYWDS 2 (PTB) DOMAIN, PROTEIN TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.P.GEYER,R.DOEKER,W.KREMER,X.ZHAO,J.KUHLMANN,H.R.KALBITZER REVDAT 3 02-MAR-22 1XKE 1 REMARK SEQADV REVDAT 2 24-FEB-09 1XKE 1 VERSN REVDAT 1 19-APR-05 1XKE 0 JRNL AUTH J.P.GEYER,R.DOKER,W.KREMER,X.ZHAO,J.KUHLMANN,H.R.KALBITZER JRNL TITL SOLUTION STRUCTURE OF THE RAN-BINDING DOMAIN 2 OF RANBP2 AND JRNL TITL 2 ITS INTERACTION WITH THE C TERMINUS OF RAN. JRNL REF J.MOL.BIOL. V. 348 711 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 15826666 JRNL DOI 10.1016/J.JMB.2005.02.033 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.DOEKER,X.ZHAO,W.KREMER,B.VILLA,J.KUHLMANN,H.R.KALBITZER REMARK 1 TITL SEQUENCE-SPECIFIC RESONANCE ASSIGNMENT OF THE SECOND REMARK 1 TITL 2 RAN-BINDING DOMAIN OF HUMAN RANBP2 REMARK 1 REF J.BIOMOL.NMR V. 22 185 2002 REMARK 1 REFN ISSN 0925-2738 REMARK 1 PMID 11883781 REMARK 1 DOI 10.1023/A:1014275704491 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CNS 1.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), 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: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 1492 RESTRAINTS (1281 NOE- REMARK 3 DERIVED DISTANCE RESTRAINTS, 182 DIHEDRAL ANGLE RESTRAINTS AND 29 REMARK 3 HYDROGEN BOND RESTRAINTS). REMARK 3 THE STRUCTURES WERE ALSO REFINED IN WATER USING XPLOR-NIH 2.9.6 REMARK 3 USING THE PROTOCOL OF LINGE ET AL. (LINGE, J. P., WILLIAMS, M. A., REMARK 3 SPRONK, C. A., BONVIN, A. M., & NILGES, M. ,2003. REFINEMENT OF REMARK 3 PROTEIN STRUCTURES IN EXPLICIT SOLVENT. PROTEINS 50, 496-506). REMARK 4 REMARK 4 1XKE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000030454. 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 : 150 MM NA2SO4 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.4MM RANBD2 U-13C; U-15N; 150MM REMARK 210 NA2SO4; 10MM DTE; 0.5 MM EDTA; REMARK 210 1MM NAN3; 0.1MM DSS; 10MM REMARK 210 POTASSIUM PHOSPHATE BUFFER AT PH REMARK 210 6.5;; 0.7MM RANBD2 U-13C; U-15N; REMARK 210 150MM NA2SO4; 10MM DTE; 0.5MM REMARK 210 EDTA; 1MM NAN3; 0.1MM DSS; 10MM REMARK 210 POTASSIUM PHOSPHATE BUFFER AT PH REMARK 210 6.5;; 1.0MM RANBD2 U-15N; 150MM REMARK 210 NA2SO4; 10MM DTE; 0.5MM EDTA; REMARK 210 1MM NAN3; 0.1 MM DSS; 10MM REMARK 210 POTASSIUM PHOSPHATE BUFFER AT PH REMARK 210 6.5;; 1.0MM RANBD2 U-15N; 150MM REMARK 210 NA2SO4; 10MM DTE; 0.5MM EDTA; REMARK 210 1MM NAN3; 0.1MM DSS; 10MM REMARK 210 POTASSIUM PHOSPHATE BUFFER AT PH REMARK 210 6.5; REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, AUREMOL 2.0.3, CNS REMARK 210 1.1, XPLOR-NIH 2.9.6 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 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 HZ1 LYS A 111 OE2 GLU A 115 1.57 REMARK 500 O GLN A 13 H LEU A 35 1.57 REMARK 500 O LEU A 17 H ARG A 30 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 MET A 50 N MET A 50 CA -0.132 REMARK 500 1 MET A 50 C ARG A 51 N -0.150 REMARK 500 1 GLN A 96 N GLN A 96 CA -0.125 REMARK 500 2 MET A 50 N MET A 50 CA -0.137 REMARK 500 2 MET A 50 C ARG A 51 N -0.157 REMARK 500 2 GLN A 96 N GLN A 96 CA -0.139 REMARK 500 3 ARG A 19 C PHE A 20 N -0.139 REMARK 500 3 MET A 50 N MET A 50 CA -0.144 REMARK 500 3 MET A 50 C ARG A 51 N -0.154 REMARK 500 3 GLN A 96 N GLN A 96 CA -0.135 REMARK 500 4 MET A 50 N MET A 50 CA -0.142 REMARK 500 4 MET A 50 C ARG A 51 N -0.150 REMARK 500 4 MET A 81 C TRP A 82 N -0.141 REMARK 500 4 GLN A 96 N GLN A 96 CA -0.135 REMARK 500 5 MET A 50 N MET A 50 CA -0.144 REMARK 500 5 MET A 50 C ARG A 51 N -0.160 REMARK 500 5 ASP A 86 N ASP A 86 CA -0.125 REMARK 500 5 GLN A 96 N GLN A 96 CA -0.125 REMARK 500 5 PRO A 104 C PRO A 104 O -0.121 REMARK 500 6 MET A 50 N MET A 50 CA -0.131 REMARK 500 6 MET A 50 C ARG A 51 N -0.143 REMARK 500 6 GLN A 96 N GLN A 96 CA -0.126 REMARK 500 7 MET A 50 N MET A 50 CA -0.143 REMARK 500 7 MET A 50 C ARG A 51 N -0.161 REMARK 500 7 GLN A 96 N GLN A 96 CA -0.123 REMARK 500 8 MET A 50 C ARG A 51 N -0.153 REMARK 500 9 MET A 50 N MET A 50 CA -0.129 REMARK 500 9 MET A 50 C ARG A 51 N -0.150 REMARK 500 9 GLY A 90 N GLY A 90 CA -0.090 REMARK 500 9 GLN A 96 N GLN A 96 CA -0.124 REMARK 500 9 LYS A 100 C PHE A 101 N -0.139 REMARK 500 10 LEU A 35 N LEU A 35 CA -0.128 REMARK 500 10 MET A 50 N MET A 50 CA -0.146 REMARK 500 10 MET A 50 C ARG A 51 N -0.151 REMARK 500 10 GLY A 90 N GLY A 90 CA -0.092 REMARK 500 10 GLN A 96 N GLN A 96 CA -0.128 REMARK 500 11 MET A 50 N MET A 50 CA -0.128 REMARK 500 11 MET A 50 C ARG A 51 N -0.141 REMARK 500 12 MET A 50 N MET A 50 CA -0.141 REMARK 500 12 MET A 50 C ARG A 51 N -0.162 REMARK 500 12 ASP A 91 C ALA A 92 N -0.144 REMARK 500 12 GLN A 96 N GLN A 96 CA -0.120 REMARK 500 13 MET A 50 N MET A 50 CA -0.158 REMARK 500 13 MET A 50 C ARG A 51 N -0.162 REMARK 500 13 MET A 81 C TRP A 82 N -0.142 REMARK 500 13 GLY A 90 N GLY A 90 CA -0.097 REMARK 500 13 GLN A 96 N GLN A 96 CA -0.135 REMARK 500 14 MET A 50 N MET A 50 CA -0.142 REMARK 500 14 MET A 50 C ARG A 51 N -0.163 REMARK 500 14 GLN A 96 N GLN A 96 CA -0.121 REMARK 500 REMARK 500 THIS ENTRY HAS 68 BOND DEVIATIONS. 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 5 -157.92 -140.83 REMARK 500 1 LEU A 56 10.82 52.48 REMARK 500 1 VAL A 58 124.87 -37.64 REMARK 500 1 PHE A 87 61.66 -158.45 REMARK 500 1 ASP A 89 33.87 177.93 REMARK 500 1 ASP A 91 125.97 80.51 REMARK 500 1 PRO A 104 -8.07 -55.95 REMARK 500 2 SER A 2 -79.89 64.58 REMARK 500 2 GLU A 4 43.36 -102.33 REMARK 500 2 ASP A 6 -0.41 88.26 REMARK 500 2 LEU A 10 -65.53 -92.12 REMARK 500 2 GLU A 53 -76.46 -45.45 REMARK 500 2 LEU A 56 10.40 51.31 REMARK 500 2 VAL A 58 122.11 -28.91 REMARK 500 2 ARG A 78 39.12 -152.64 REMARK 500 2 PHE A 87 109.51 158.54 REMARK 500 2 ASP A 91 132.50 86.29 REMARK 500 3 ASP A 6 3.39 81.62 REMARK 500 3 LEU A 56 10.91 52.59 REMARK 500 3 VAL A 58 116.39 -28.95 REMARK 500 3 ARG A 78 37.03 -149.95 REMARK 500 3 PHE A 87 21.03 -141.17 REMARK 500 3 ASP A 89 10.63 -152.75 REMARK 500 3 ASP A 91 159.80 70.92 REMARK 500 4 GLU A 5 -143.18 -129.19 REMARK 500 4 ASP A 6 -1.64 104.19 REMARK 500 4 LEU A 10 -68.41 -94.77 REMARK 500 4 LEU A 56 10.90 50.31 REMARK 500 4 VAL A 58 123.85 -29.97 REMARK 500 4 ARG A 78 48.79 -167.79 REMARK 500 4 PHE A 87 79.78 -152.25 REMARK 500 4 ASP A 89 36.25 162.53 REMARK 500 4 ASP A 91 144.69 178.75 REMARK 500 5 ASP A 6 -12.88 146.68 REMARK 500 5 GLU A 53 -73.31 -48.09 REMARK 500 5 LEU A 56 9.56 52.16 REMARK 500 5 VAL A 58 125.85 -30.39 REMARK 500 5 ARG A 78 43.98 177.45 REMARK 500 5 PHE A 87 108.74 -168.83 REMARK 500 5 ASP A 89 45.05 159.95 REMARK 500 6 SER A 2 86.92 -153.15 REMARK 500 6 GLU A 4 70.26 49.57 REMARK 500 6 GLU A 5 -167.38 -120.27 REMARK 500 6 ASN A 43 -14.23 153.58 REMARK 500 6 GLU A 53 -73.74 -48.50 REMARK 500 6 LEU A 56 9.42 50.58 REMARK 500 6 VAL A 58 126.11 -33.52 REMARK 500 6 ARG A 78 40.74 -167.64 REMARK 500 6 PHE A 87 79.81 176.94 REMARK 500 6 ASP A 89 31.93 171.79 REMARK 500 REMARK 500 THIS ENTRY HAS 150 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 51 0.09 SIDE CHAIN REMARK 500 3 ARG A 30 0.07 SIDE CHAIN REMARK 500 3 ARG A 51 0.08 SIDE CHAIN REMARK 500 5 ARG A 30 0.10 SIDE CHAIN REMARK 500 5 ARG A 51 0.08 SIDE CHAIN REMARK 500 5 ARG A 78 0.08 SIDE CHAIN REMARK 500 8 ARG A 19 0.07 SIDE CHAIN REMARK 500 11 ARG A 30 0.09 SIDE CHAIN REMARK 500 12 ARG A 30 0.09 SIDE CHAIN REMARK 500 12 ARG A 78 0.09 SIDE CHAIN REMARK 500 15 ARG A 51 0.10 SIDE CHAIN REMARK 500 16 ARG A 51 0.08 SIDE CHAIN REMARK 500 19 ARG A 119 0.11 SIDE CHAIN REMARK 500 20 ARG A 51 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5159 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFT ASSIGNMENT DBREF 1XKE A 3 129 UNP P49792 RBP2_HUMAN 2028 2154 SEQADV 1XKE GLY A 1 UNP P49792 CLONING ARTIFACT SEQADV 1XKE SER A 2 UNP P49792 CLONING ARTIFACT SEQADV 1XKE LYS A 130 UNP P49792 CLONING ARTIFACT SEQRES 1 A 130 GLY SER GLY GLU GLU ASP GLU LYS VAL LEU TYR SER GLN SEQRES 2 A 130 ARG VAL LYS LEU PHE ARG PHE ASP ALA GLU VAL SER GLN SEQRES 3 A 130 TRP LYS GLU ARG GLY LEU GLY ASN LEU LYS ILE LEU LYS SEQRES 4 A 130 ASN GLU VAL ASN GLY LYS LEU ARG MET LEU MET ARG ARG SEQRES 5 A 130 GLU GLN VAL LEU LYS VAL CYS ALA ASN HIS TRP ILE THR SEQRES 6 A 130 THR THR MET ASN LEU LYS PRO LEU SER GLY SER ASP ARG SEQRES 7 A 130 ALA TRP MET TRP LEU ALA SER ASP PHE SER ASP GLY ASP SEQRES 8 A 130 ALA LYS LEU GLU GLN LEU ALA ALA LYS PHE LYS THR PRO SEQRES 9 A 130 GLU LEU ALA GLU GLU PHE LYS GLN LYS PHE GLU GLU CYS SEQRES 10 A 130 GLN ARG LEU LEU LEU ASP ILE PRO LEU GLN THR PRO LYS HELIX 1 1 THR A 103 LEU A 121 1 19 SHEET 1 A 4 GLU A 7 VAL A 9 0 SHEET 2 A 4 GLN A 26 ASN A 40 -1 O LYS A 39 N LYS A 8 SHEET 3 A 4 LEU A 46 ARG A 52 -1 O LEU A 49 N LYS A 36 SHEET 4 A 4 LYS A 57 TRP A 63 -1 O HIS A 62 N MET A 48 SHEET 1 B 6 GLU A 7 VAL A 9 0 SHEET 2 B 6 GLN A 26 ASN A 40 -1 O LYS A 39 N LYS A 8 SHEET 3 B 6 GLN A 13 ASP A 21 -1 N ARG A 19 O LYS A 28 SHEET 4 B 6 LYS A 93 LYS A 100 -1 O ALA A 98 N PHE A 18 SHEET 5 B 6 TRP A 80 ASP A 86 -1 N ALA A 84 O GLU A 95 SHEET 6 B 6 LEU A 70 PRO A 72 -1 N LYS A 71 O MET A 81 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