HEADER TRANSPORT PROTEIN 24-JUL-12 4GA0 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: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RANBP2, NUP358; 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: GGEX-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 4 13-SEP-23 4GA0 1 SEQADV REVDAT 3 15-NOV-17 4GA0 1 REMARK REVDAT 2 02-JAN-13 4GA0 1 JRNL REVDAT 1 26-SEP-12 4GA0 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) : 48.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 50201 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 2565 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 48.2035 - 3.0137 0.99 2954 175 0.2133 0.2356 REMARK 3 2 3.0137 - 2.3920 1.00 2860 151 0.2048 0.2068 REMARK 3 3 2.3920 - 2.0897 1.00 2805 137 0.1848 0.2171 REMARK 3 4 2.0897 - 1.8986 0.99 2782 148 0.2024 0.2381 REMARK 3 5 1.8986 - 1.7625 1.00 2785 139 0.1947 0.2403 REMARK 3 6 1.7625 - 1.6586 1.00 2740 161 0.1900 0.2293 REMARK 3 7 1.6586 - 1.5755 1.00 2765 147 0.1774 0.2087 REMARK 3 8 1.5755 - 1.5069 0.99 2748 153 0.2105 0.2319 REMARK 3 9 1.5069 - 1.4489 0.99 2731 135 0.2485 0.2948 REMARK 3 10 1.4489 - 1.3989 1.00 2726 160 0.2434 0.3170 REMARK 3 11 1.3989 - 1.3552 0.97 2647 138 0.2907 0.3186 REMARK 3 12 1.3552 - 1.3164 1.00 2758 151 0.2408 0.3002 REMARK 3 13 1.3164 - 1.2818 0.97 2633 145 0.3293 0.3273 REMARK 3 14 1.2818 - 1.2505 0.90 2431 144 0.4046 0.4118 REMARK 3 15 1.2505 - 1.2221 0.96 2594 153 0.3677 0.4012 REMARK 3 16 1.2221 - 1.1961 0.90 2457 125 0.3092 0.3204 REMARK 3 17 1.1961 - 1.1721 0.82 2237 125 0.3184 0.3476 REMARK 3 18 1.1721 - 1.1500 0.72 1983 78 0.4130 0.4247 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 42.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.18 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 : 0.006 1418 REMARK 3 ANGLE : 1.123 1918 REMARK 3 CHIRALITY : 0.057 201 REMARK 3 PLANARITY : 0.005 250 REMARK 3 DIHEDRAL : 15.238 557 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 4GA0 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_1000073925. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-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) : 1.0332 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50246 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 48.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.4000 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 (%) : 76.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.78700 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4GA2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.03 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 29.60950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.38400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.60950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.38400 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 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 -6 REMARK 465 PRO A -5 REMARK 465 LEU A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 MET A -1 REMARK 465 ARG A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 79 NH1 ARG A 111 2655 1.96 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 37 1.37 -69.95 REMARK 500 GLU A 39 72.34 -106.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GA1 RELATED DB: PDB REMARK 900 RELATED ID: 4GA2 RELATED DB: PDB DBREF 4GA0 A -1 143 UNP P49792 RBP2_HUMAN 1 145 SEQADV 4GA0 GLY A -6 UNP P49792 EXPRESSION TAG SEQADV 4GA0 PRO A -5 UNP P49792 EXPRESSION TAG SEQADV 4GA0 LEU A -4 UNP P49792 EXPRESSION TAG SEQADV 4GA0 GLY A -3 UNP P49792 EXPRESSION TAG SEQADV 4GA0 SER A -2 UNP P49792 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 MET 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 LEU GLU ARG ALA ALA LYS LEU PHE SEQRES 11 A 150 PRO GLY SER PRO ALA ILE TYR LYS LEU LYS GLU GLN LEU SEQRES 12 A 150 LEU ASP CYS GLU GLY GLU ASP FORMUL 2 HOH *85(H2 O) HELIX 1 1 SER A 2 THR A 17 1 16 HELIX 2 2 SER A 19 MET A 25 1 7 HELIX 3 3 LYS A 26 ALA A 37 1 12 HELIX 4 4 GLU A 39 GLN A 54 1 16 HELIX 5 5 ASP A 57 GLU A 71 1 15 HELIX 6 6 ASN A 73 ASN A 88 1 16 HELIX 7 7 GLN A 91 ASP A 106 1 16 HELIX 8 8 ASP A 109 PHE A 123 1 15 HELIX 9 9 SER A 126 GLU A 140 1 15 CRYST1 59.219 82.768 29.543 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 0.016886 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012082 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033849 0.00000