10 20 30 40 50 60 70 80 2Q5X - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER PROTEIN TRANSPORT 03-JUN-07 2Q5X
TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF HNUP98
COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR PORE COMPLEX PROTEIN NUP98; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 733-887; COMPND 5 SYNONYM: NUCLEOPORIN NUP98, 98 KDA NUCLEOPORIN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 GENE: NUP98; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-21A
KEYWDS NUP98, NUCLEOPORIN, AUTOPROTEOLYSIS, PRECURSOR, PROTEIN KEYWDS 2 TRANSPORT
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.SUN,H.C.GUO
REVDAT 2 24-FEB-09 2Q5X 1 VERSN REVDAT 1 14-OCT-08 2Q5X 0
JRNL AUTH Y.SUN,H.C.GUO JRNL TITL STRUCTURAL CONSTRAINTS ON AUTOPROCESSING OF THE JRNL TITL 2 HUMAN NUCLEOPORIN NUP98. JRNL REF PROTEIN SCI. V. 17 494 2008 JRNL REFN ISSN 0961-8368 JRNL PMID 18287282 JRNL DOI 10.1110/PS.073311808
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 17523 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1728 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 34 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.92 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 459 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE : 0.3670 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 48 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1203 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 97 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.33400 REMARK 3 B22 (A**2) : -2.33400 REMARK 3 B33 (A**2) : 4.66800 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 90.02 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : CIS_PEPTIDE.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2Q5X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-07. REMARK 100 THE RCSB ID CODE IS RCSB043189.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-03; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : NSLS; NSLS REMARK 200 BEAMLINE : X12C; X12C REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.10005; 0.94789, 0.9778, REMARK 200 0.97814 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210; ADSC REMARK 200 QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18307 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.28500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.5M SODIUM FORMATE, PH 4.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 296K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 45.48200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.83700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.83700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.74100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.83700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.83700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 68.22300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.83700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.83700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.74100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.83700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.83700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 68.22300 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 45.48200 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 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 ASP A 787 REMARK 465 ASP A 788 REMARK 465 ASN A 789 REMARK 465 GLN A 790
REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 796 CG CD OE1 OE2 REMARK 480 LYS A 814 CG CD CE NZ REMARK 480 GLN A 869 CG CD OE1 NE2
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 ASP A 747 124.51 78.82 REMARK 500 ASN A 768 17.14 59.67 REMARK 500 TYR A 785 99.06 78.91 REMARK 500 ALA A 864 131.04 72.54 REMARK 500 REMARK 500 REMARK: NULL
DBREF 2Q5X A 716 870 UNP P52948 NUP98_HUMAN 733 887
SEQADV 2Q5X ALA A 864 UNP P52948 SER 881 ENGINEERED
SEQRES 1 A 155 GLY ILE ILE LEU THR LYS VAL GLY TYR TYR THR ILE PRO SEQRES 2 A 155 SER MET ASP ASP LEU ALA LYS ILE THR ASN GLU LYS GLY SEQRES 3 A 155 GLU CYS ILE VAL SER ASP PHE THR ILE GLY ARG LYS GLY SEQRES 4 A 155 TYR GLY SER ILE TYR PHE GLU GLY ASP VAL ASN LEU THR SEQRES 5 A 155 ASN LEU ASN LEU ASP ASP ILE VAL HIS ILE ARG ARG LYS SEQRES 6 A 155 GLU VAL VAL VAL TYR LEU ASP ASP ASN GLN LYS PRO PRO SEQRES 7 A 155 VAL GLY GLU GLY LEU ASN ARG LYS ALA GLU VAL THR LEU SEQRES 8 A 155 ASP GLY VAL TRP PRO THR ASP LYS THR SER ARG CYS LEU SEQRES 9 A 155 ILE LYS SER PRO ASP ARG LEU ALA ASP ILE ASN TYR GLU SEQRES 10 A 155 GLY ARG LEU GLU ALA VAL SER ARG LYS GLN GLY ALA GLN SEQRES 11 A 155 PHE LYS GLU TYR ARG PRO GLU THR GLY SER TRP VAL PHE SEQRES 12 A 155 LYS VAL SER HIS PHE ALA LYS TYR GLY LEU GLN ASP
FORMUL 2 HOH *97(H2 O)
HELIX 1 1 SER A 729 THR A 737 1 9 HELIX 2 2 ASN A 770 ILE A 774 1 5 HELIX 3 3 SER A 822 ILE A 829 1 8 HELIX 4 4 ASN A 830 GLN A 842 1 13
SHEET 1 A 6 TYR A 724 ILE A 727 0 SHEET 2 A 6 ILE A 744 ARG A 752 -1 O GLY A 751 N TYR A 725 SHEET 3 A 6 GLY A 756 ASN A 765 -1 O PHE A 760 N PHE A 748 SHEET 4 A 6 ALA A 802 LEU A 806 -1 O THR A 805 N SER A 757 SHEET 5 A 6 SER A 855 VAL A 860 -1 O VAL A 860 N ALA A 802 SHEET 6 A 6 GLN A 845 ARG A 850 -1 N GLN A 845 O LYS A 859 SHEET 1 B 3 VAL A 775 ARG A 778 0 SHEET 2 B 3 GLU A 781 VAL A 784 -1 O VAL A 783 N HIS A 776 SHEET 3 B 3 TYR A 866 GLY A 867 -1 O TYR A 866 N VAL A 782
CISPEP 1 ILE A 727 PRO A 728 0 -0.71 CISPEP 2 PHE A 863 ALA A 864 0 -0.91
CRYST1 69.674 69.674 90.964 90.00 90.00 90.00 P 41 21 2 8
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 0.014353 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014353 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010993 0.00000