HEADER TRANSPORT PROTEIN 24-JUL-12 4GA1 TITLE STRUCTURE OF THE N-TERMINAL DOMAIN OF NUP358 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 SUMO-PROTEIN LIGASE RANBP2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-145; COMPND 5 SYNONYM: 358 KDA NUCLEOPORIN, NUCLEAR PORE COMPLEX PROTEIN NUP358, COMPND 6 NUCLEOPORIN NUP358, RAN-BINDING PROTEIN 2, RANBP2, P270, PUTATIVE COMPND 7 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE, PPIASE, ROTAMASE; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PAN TROGLODYTES; SOURCE 3 ORGANISM_COMMON: CHIMPANZEE; SOURCE 4 ORGANISM_TAXID: 9598; SOURCE 5 GENE: ENSG00000153201; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PGEX-6P1 KEYWDS TPR MOTIF, NUCLEAR PORE COMPLEX COMPONENT NUCLEOCYTOPLASMIC KEYWDS 2 TRANSPORT, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.HOELZ,S.A.KASSUBE,D.H.LIN,T.STUWE REVDAT 3 20-NOV-24 4GA1 1 SEQADV LINK REVDAT 2 02-JAN-13 4GA1 1 JRNL REVDAT 1 26-SEP-12 4GA1 0 JRNL AUTH S.A.KASSUBE,T.STUWE,D.H.LIN,C.D.ANTONUK,J.NAPETSCHNIG, JRNL AUTH 2 G.BLOBEL,A.HOELZ JRNL TITL CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF NUP358/RANBP2. JRNL REF J.MOL.BIOL. V. 423 752 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22959972 JRNL DOI 10.1016/J.JMB.2012.08.026 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 99449 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 5019 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.9175 - 3.5704 0.97 3112 174 0.2161 0.2225 REMARK 3 2 3.5704 - 2.8340 0.97 3095 161 0.1832 0.2272 REMARK 3 3 2.8340 - 2.4758 1.00 3196 156 0.1930 0.2381 REMARK 3 4 2.4758 - 2.2494 1.00 3225 158 0.1847 0.1833 REMARK 3 5 2.2494 - 2.0882 1.00 3154 192 0.1734 0.2077 REMARK 3 6 2.0882 - 1.9651 1.00 3178 167 0.1870 0.2241 REMARK 3 7 1.9651 - 1.8667 1.00 3222 134 0.1822 0.2116 REMARK 3 8 1.8667 - 1.7854 0.99 3164 180 0.1788 0.2404 REMARK 3 9 1.7854 - 1.7167 1.00 3180 190 0.1803 0.1814 REMARK 3 10 1.7167 - 1.6574 1.00 3168 194 0.1811 0.2196 REMARK 3 11 1.6574 - 1.6056 1.00 3202 158 0.1780 0.2305 REMARK 3 12 1.6056 - 1.5597 1.00 3155 178 0.1780 0.1706 REMARK 3 13 1.5597 - 1.5186 1.00 3205 170 0.1789 0.2234 REMARK 3 14 1.5186 - 1.4816 0.99 3184 172 0.1899 0.2586 REMARK 3 15 1.4816 - 1.4479 0.99 3125 217 0.1991 0.2310 REMARK 3 16 1.4479 - 1.4171 0.99 3148 153 0.2012 0.2434 REMARK 3 17 1.4171 - 1.3887 0.99 3257 131 0.1950 0.2371 REMARK 3 18 1.3887 - 1.3625 0.99 3121 157 0.1987 0.2432 REMARK 3 19 1.3625 - 1.3382 0.99 3254 175 0.2031 0.2374 REMARK 3 20 1.3382 - 1.3155 0.99 3182 155 0.2011 0.2598 REMARK 3 21 1.3155 - 1.2943 0.99 3098 175 0.2048 0.2424 REMARK 3 22 1.2943 - 1.2744 0.99 3185 186 0.2104 0.2214 REMARK 3 23 1.2744 - 1.2556 0.99 3131 165 0.2030 0.2742 REMARK 3 24 1.2556 - 1.2380 0.99 3159 178 0.2195 0.2471 REMARK 3 25 1.2380 - 1.2212 0.99 3214 144 0.2258 0.2658 REMARK 3 26 1.2212 - 1.2054 0.99 3130 182 0.2335 0.2674 REMARK 3 27 1.2054 - 1.1903 0.99 3177 149 0.2448 0.2960 REMARK 3 28 1.1903 - 1.1759 0.98 3212 145 0.2425 0.2659 REMARK 3 29 1.1759 - 1.1623 0.94 2952 161 0.2631 0.2489 REMARK 3 30 1.1623 - 1.1492 0.84 2645 162 0.2769 0.3820 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 1232 REMARK 3 ANGLE : 1.396 1667 REMARK 3 CHIRALITY : 0.075 177 REMARK 3 PLANARITY : 0.009 217 REMARK 3 DIHEDRAL : 13.186 491 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4GA1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073926. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 99452 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 47.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.52700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18 % (W/V) PEG 3350 200 MM LITHIUM REMARK 280 ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 29.19350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.82050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.19350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.82050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 323 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MSE A 1 REMARK 465 ARG A 2 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 GLU A 41 78.84 -105.35 REMARK 500 ASP A 108 95.48 -166.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GA0 RELATED DB: PDB REMARK 900 RELATED ID: 4GA2 RELATED DB: PDB DBREF 4GA1 A 1 145 UNP H2QII6 H2QII6_PANTR 1 145 SEQADV 4GA1 GLY A -4 UNP H2QII6 EXPRESSION TAG SEQADV 4GA1 PRO A -3 UNP H2QII6 EXPRESSION TAG SEQADV 4GA1 LEU A -2 UNP H2QII6 EXPRESSION TAG SEQADV 4GA1 GLY A -1 UNP H2QII6 EXPRESSION TAG SEQADV 4GA1 SER A 0 UNP H2QII6 EXPRESSION TAG SEQADV 4GA1 MSE A 27 UNP H2QII6 ILE 27 ENGINEERED MUTATION SEQADV 4GA1 MSE A 37 UNP H2QII6 TYR 37 ENGINEERED MUTATION SEQADV 4GA1 MSE A 92 UNP H2QII6 THR 92 ENGINEERED MUTATION SEQRES 1 A 150 GLY PRO LEU GLY SER MSE ARG ARG SER LYS ALA ASP VAL SEQRES 2 A 150 GLU ARG TYR ILE ALA SER VAL GLN GLY SER THR PRO SER SEQRES 3 A 150 PRO ARG GLN LYS SER MSE LYS GLY PHE TYR PHE ALA LYS SEQRES 4 A 150 LEU TYR MSE GLU ALA LYS GLU TYR ASP LEU ALA LYS LYS SEQRES 5 A 150 TYR ILE CYS THR TYR ILE ASN VAL GLN GLU ARG ASP PRO SEQRES 6 A 150 LYS ALA HIS ARG PHE LEU GLY LEU LEU TYR GLU LEU GLU SEQRES 7 A 150 GLU ASN THR ASP LYS ALA VAL GLU CYS TYR ARG ARG SER SEQRES 8 A 150 VAL GLU LEU ASN PRO MSE GLN LYS ASP LEU VAL LEU LYS SEQRES 9 A 150 ILE ALA GLU LEU LEU CYS LYS ASN ASP VAL THR ASP GLY SEQRES 10 A 150 ARG ALA LYS TYR TRP VAL GLU ARG ALA ALA LYS LEU PHE SEQRES 11 A 150 PRO GLY SER PRO ALA VAL TYR LYS LEU LYS GLU GLN LEU SEQRES 12 A 150 LEU ASP CYS GLU GLY GLU ASP MODRES 4GA1 MSE A 27 MET SELENOMETHIONINE MODRES 4GA1 MSE A 37 MET SELENOMETHIONINE MODRES 4GA1 MSE A 92 MET SELENOMETHIONINE HET MSE A 27 17 HET MSE A 37 17 HET MSE A 92 17 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *231(H2 O) HELIX 1 1 SER A 4 THR A 19 1 16 HELIX 2 2 SER A 21 LYS A 28 1 8 HELIX 3 3 LYS A 28 ALA A 39 1 12 HELIX 4 4 GLU A 41 GLN A 56 1 16 HELIX 5 5 ASP A 59 GLU A 73 1 15 HELIX 6 6 ASN A 75 ASN A 90 1 16 HELIX 7 7 GLN A 93 VAL A 109 1 17 HELIX 8 8 GLY A 112 PHE A 125 1 14 HELIX 9 9 SER A 128 GLU A 142 1 15 LINK C SER A 26 N MSE A 27 1555 1555 1.34 LINK C MSE A 27 N LYS A 28 1555 1555 1.33 LINK C TYR A 36 N MSE A 37 1555 1555 1.33 LINK C MSE A 37 N GLU A 38 1555 1555 1.34 LINK C PRO A 91 N MSE A 92 1555 1555 1.33 LINK C MSE A 92 N GLN A 93 1555 1555 1.33 CRYST1 58.387 83.641 29.984 90.00 90.00 90.00 P 21 21 2 4 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 0.017127 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011956 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033351 0.00000