HEADER PROTEIN TRANSPORT 28-JUL-04 1U5O TITLE STRUCTURE OF THE D23A MUTANT OF THE NUCLEAR TRANSPORT CARRIER NTF2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR TRANSPORT FACTOR 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NTF-2; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: NUTF2, NTF2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSPORT, NUCLEAR TRANSPORT PROTEIN, NTF2 MUTANT D23A, PROTEIN KEYWDS 2 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR I.CUSHMAN,B.R.BOWMAN,M.E.SOWA,O.LICHTARGE,F.A.QUIOCHO,M.S.MOORE REVDAT 5 14-FEB-24 1U5O 1 REMARK REVDAT 4 20-OCT-21 1U5O 1 SEQADV REVDAT 3 10-SEP-14 1U5O 1 JRNL VERSN REVDAT 2 24-FEB-09 1U5O 1 VERSN REVDAT 1 07-DEC-04 1U5O 0 JRNL AUTH I.CUSHMAN,B.R.BOWMAN,M.E.SOWA,O.LICHTARGE,F.A.QUIOCHO, JRNL AUTH 2 M.S.MOORE JRNL TITL COMPUTATIONAL AND BIOCHEMICAL IDENTIFICATION OF A NUCLEAR JRNL TITL 2 PORE COMPLEX BINDING SITE ON THE NUCLEAR TRANSPORT CARRIER JRNL TITL 3 NTF2. JRNL REF J.MOL.BIOL. V. 344 303 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15522285 JRNL DOI 10.1016/J.JMB.2004.09.043 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 405929.860 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.7 REMARK 3 NUMBER OF REFLECTIONS : 8715 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.600 REMARK 3 FREE R VALUE TEST SET COUNT : 924 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1189 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE : 0.3620 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 151 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1973 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.96000 REMARK 3 B22 (A**2) : 3.34000 REMARK 3 B33 (A**2) : -2.39000 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) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.29 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.44 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 19.03 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1U5O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1000023276. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : MACSCIENCE REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : DOUBLE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8715 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 34.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, MAGNESIUM ACETATE, SODIUM REMARK 280 ACETATE, PH 4.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 27.92350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.97450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.45850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.97450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.92350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.45850 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 1 REMARK 465 GLY A 127 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 ASP B 3 REMARK 465 ASN B 125 REMARK 465 PHE B 126 REMARK 465 GLY B 127 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 3 -119.09 155.49 REMARK 500 ASP A 25 82.79 -173.82 REMARK 500 THR A 27 6.51 -68.82 REMARK 500 ALA A 36 41.53 -89.90 REMARK 500 PRO A 60 19.31 -58.04 REMARK 500 ASP A 92 -125.02 59.47 REMARK 500 ASN B 24 -72.56 -86.13 REMARK 500 PRO B 60 63.80 -62.47 REMARK 500 ALA B 70 145.44 -171.30 REMARK 500 ASP B 78 40.18 -94.93 REMARK 500 ASP B 92 -118.14 41.58 REMARK 500 ALA B 111 140.72 -175.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OUN RELATED DB: PDB REMARK 900 RELATED ID: 1AR0 RELATED DB: PDB REMARK 900 RELATED ID: 1ASK RELATED DB: PDB DBREF 1U5O A 1 127 UNP P61972 NTF2_RAT 1 127 DBREF 1U5O B 1 127 UNP P61972 NTF2_RAT 1 127 SEQADV 1U5O ALA A 23 UNP P61972 ASP 23 ENGINEERED MUTATION SEQADV 1U5O ALA B 23 UNP P61972 ASP 23 ENGINEERED MUTATION SEQRES 1 A 127 MET GLY ASP LYS PRO ILE TRP GLU GLN ILE GLY SER SER SEQRES 2 A 127 PHE ILE GLN HIS TYR TYR GLN LEU PHE ALA ASN ASP ARG SEQRES 3 A 127 THR GLN LEU GLY ALA ILE TYR ILE ASP ALA SER CYS LEU SEQRES 4 A 127 THR TRP GLU GLY GLN GLN PHE GLN GLY LYS ALA ALA ILE SEQRES 5 A 127 VAL GLU LYS LEU SER SER LEU PRO PHE GLN LYS ILE GLN SEQRES 6 A 127 HIS SER ILE THR ALA GLN ASP HIS GLN PRO THR PRO ASP SEQRES 7 A 127 SER CYS ILE ILE SER MET VAL VAL GLY GLN LEU LYS ALA SEQRES 8 A 127 ASP GLU ASP PRO ILE MET GLY PHE HIS GLN MET PHE LEU SEQRES 9 A 127 LEU LYS ASN ILE ASN ASP ALA TRP VAL CYS THR ASN ASP SEQRES 10 A 127 MET PHE ARG LEU ALA LEU HIS ASN PHE GLY SEQRES 1 B 127 MET GLY ASP LYS PRO ILE TRP GLU GLN ILE GLY SER SER SEQRES 2 B 127 PHE ILE GLN HIS TYR TYR GLN LEU PHE ALA ASN ASP ARG SEQRES 3 B 127 THR GLN LEU GLY ALA ILE TYR ILE ASP ALA SER CYS LEU SEQRES 4 B 127 THR TRP GLU GLY GLN GLN PHE GLN GLY LYS ALA ALA ILE SEQRES 5 B 127 VAL GLU LYS LEU SER SER LEU PRO PHE GLN LYS ILE GLN SEQRES 6 B 127 HIS SER ILE THR ALA GLN ASP HIS GLN PRO THR PRO ASP SEQRES 7 B 127 SER CYS ILE ILE SER MET VAL VAL GLY GLN LEU LYS ALA SEQRES 8 B 127 ASP GLU ASP PRO ILE MET GLY PHE HIS GLN MET PHE LEU SEQRES 9 B 127 LEU LYS ASN ILE ASN ASP ALA TRP VAL CYS THR ASN ASP SEQRES 10 B 127 MET PHE ARG LEU ALA LEU HIS ASN PHE GLY FORMUL 3 HOH *96(H2 O) HELIX 1 1 PRO A 5 ASP A 25 1 21 HELIX 2 2 ARG A 26 ALA A 31 5 6 HELIX 3 3 GLY A 48 SER A 58 1 11 HELIX 4 4 PRO B 5 ASN B 24 1 20 HELIX 5 5 ASP B 25 ALA B 31 5 7 HELIX 6 6 GLY B 48 SER B 58 1 11 SHEET 1 A 6 GLN A 44 GLN A 47 0 SHEET 2 A 6 TYR A 33 TRP A 41 -1 N LEU A 39 O PHE A 46 SHEET 3 A 6 ALA A 111 ALA A 122 1 O PHE A 119 N THR A 40 SHEET 4 A 6 MET A 97 ILE A 108 -1 N ILE A 108 O ALA A 111 SHEET 5 A 6 ILE A 81 ALA A 91 -1 N ILE A 81 O LEU A 105 SHEET 6 A 6 ILE A 64 PRO A 75 -1 N GLN A 74 O ILE A 82 SHEET 1 B 6 GLN B 44 GLN B 47 0 SHEET 2 B 6 TYR B 33 TRP B 41 -1 N TRP B 41 O GLN B 44 SHEET 3 B 6 TRP B 112 LEU B 121 1 O PHE B 119 N THR B 40 SHEET 4 B 6 MET B 97 ASN B 107 -1 N LYS B 106 O VAL B 113 SHEET 5 B 6 ILE B 81 ALA B 91 -1 N ILE B 81 O LEU B 105 SHEET 6 B 6 ILE B 64 PRO B 75 -1 N SER B 67 O GLN B 88 CRYST1 55.847 56.917 85.949 90.00 90.00 90.00 P 21 21 21 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 0.017906 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017569 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011635 0.00000