HEADER TRANSPORT PROTEIN 24-JUL-12 4GA2 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 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 S.A.KASSUBE,D.H.LIN,T.STUWE,A.HOELZ REVDAT 3 28-FEB-24 4GA2 1 SEQADV REVDAT 2 02-JAN-13 4GA2 1 JRNL REVDAT 1 26-SEP-12 4GA2 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. 0.95 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) : 0.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 91604 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 4588 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 33.9703 - 2.9525 0.98 3108 148 0.2003 0.2261 REMARK 3 2 2.9525 - 2.3437 1.00 3045 153 0.1870 0.2009 REMARK 3 3 2.3437 - 2.0475 1.00 2941 182 0.1565 0.1853 REMARK 3 4 2.0475 - 1.8603 1.00 2933 165 0.1651 0.1863 REMARK 3 5 1.8603 - 1.7269 1.00 2931 166 0.1606 0.1905 REMARK 3 6 1.7269 - 1.6251 1.00 2962 144 0.1497 0.1620 REMARK 3 7 1.6251 - 1.5437 1.00 2900 156 0.1392 0.1593 REMARK 3 8 1.5437 - 1.4765 1.00 2910 164 0.1411 0.1611 REMARK 3 9 1.4765 - 1.4197 1.00 2910 147 0.1507 0.1833 REMARK 3 10 1.4197 - 1.3707 1.00 2929 150 0.1498 0.1882 REMARK 3 11 1.3707 - 1.3278 1.00 2921 147 0.1432 0.1954 REMARK 3 12 1.3278 - 1.2899 1.00 2872 151 0.1493 0.1752 REMARK 3 13 1.2899 - 1.2559 1.00 2924 152 0.1481 0.1708 REMARK 3 14 1.2559 - 1.2253 1.00 2856 143 0.1549 0.1877 REMARK 3 15 1.2253 - 1.1974 1.00 2931 151 0.1597 0.1843 REMARK 3 16 1.1974 - 1.1719 1.00 2859 176 0.1641 0.1944 REMARK 3 17 1.1719 - 1.1485 1.00 2914 134 0.1704 0.1819 REMARK 3 18 1.1485 - 1.1268 1.00 2892 138 0.1776 0.1732 REMARK 3 19 1.1268 - 1.1067 1.00 2868 160 0.1795 0.2044 REMARK 3 20 1.1067 - 1.0879 1.00 2884 144 0.1879 0.1991 REMARK 3 21 1.0879 - 1.0704 1.00 2884 161 0.1972 0.2126 REMARK 3 22 1.0704 - 1.0539 1.00 2828 156 0.2034 0.2668 REMARK 3 23 1.0539 - 1.0384 1.00 2917 146 0.2133 0.2344 REMARK 3 24 1.0384 - 1.0238 1.00 2877 138 0.2273 0.2594 REMARK 3 25 1.0238 - 1.0100 1.00 2851 168 0.2343 0.2337 REMARK 3 26 1.0100 - 0.9968 1.00 2859 157 0.2469 0.2706 REMARK 3 27 0.9968 - 0.9844 0.99 2852 143 0.2731 0.3369 REMARK 3 28 0.9844 - 0.9725 0.99 2879 155 0.2885 0.2841 REMARK 3 29 0.9725 - 0.9612 0.99 2836 153 0.3030 0.2790 REMARK 3 30 0.9612 - 0.9504 0.96 2743 140 0.3342 0.3537 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.009 1541 REMARK 3 ANGLE : 1.311 2096 REMARK 3 CHIRALITY : 0.066 219 REMARK 3 PLANARITY : 0.006 276 REMARK 3 DIHEDRAL : 13.387 629 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 4GA2 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_1000073927. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JAN-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) : 0.7500 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91604 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.950 REMARK 200 RESOLUTION RANGE LOW (A) : 33.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 9.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.79800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 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 29.39400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.58300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.39400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.58300 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 387 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 MET A 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 OE2 GLU A 88 O HOH A 336 2.12 REMARK 500 O HOH A 219 O HOH A 416 2.15 REMARK 500 O HOH A 327 O HOH A 466 2.18 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 ALA A 39 1.10 -66.67 REMARK 500 GLU A 41 78.75 -107.69 REMARK 500 ASP A 108 121.41 -176.54 REMARK 500 VAL A 109 64.58 -108.41 REMARK 500 THR A 110 -23.22 -140.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GA0 RELATED DB: PDB REMARK 900 RELATED ID: 4GA1 RELATED DB: PDB DBREF 4GA2 A 1 145 UNP H2QII6 H2QII6_PANTR 1 145 SEQADV 4GA2 GLY A -4 UNP H2QII6 EXPRESSION TAG SEQADV 4GA2 PRO A -3 UNP H2QII6 EXPRESSION TAG SEQADV 4GA2 LEU A -2 UNP H2QII6 EXPRESSION TAG SEQADV 4GA2 GLY A -1 UNP H2QII6 EXPRESSION TAG SEQADV 4GA2 SER A 0 UNP H2QII6 EXPRESSION TAG SEQRES 1 A 150 GLY PRO LEU GLY SER MET 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 ILE LYS GLY PHE TYR PHE ALA LYS SEQRES 4 A 150 LEU TYR TYR 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 THR 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 FORMUL 2 HOH *267(H2 O) HELIX 1 1 SER A 4 THR A 19 1 16 HELIX 2 2 SER A 21 ILE A 27 1 7 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 ASP A 108 1 16 HELIX 8 8 GLY A 112 PHE A 125 1 14 HELIX 9 9 SER A 128 CYS A 141 1 14 CRYST1 58.788 83.166 29.559 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 0.017010 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012024 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033831 0.00000