HEADER NUCLEAR TRANSPORT 21-APR-02 1GY5 TITLE D92N,D94N DOUBLE POINT MUTANT OF HUMAN NUCLEAR TRANSPORT FACTOR 2 TITLE 2 (NTF2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR TRANSPORT FACTOR 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NTF-2, PLACENTAL PROTEIN 15, PP15; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS NUCLEAR TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR R.BAYLISS,M.STEWART REVDAT 4 08-MAY-24 1GY5 1 REMARK REVDAT 3 22-MAY-19 1GY5 1 REMARK ATOM REVDAT 2 24-FEB-09 1GY5 1 VERSN REVDAT 1 20-JUN-02 1GY5 0 JRNL AUTH R.BAYLISS,S.LEUNG,R.BAKER,B.QUIMBY,A.CORBETT,M.STEWART JRNL TITL STRUCTURAL BASIS FOR THE INTERACTION BETWEEN NTF2 AND JRNL TITL 2 NUCLEOPORIN FXFG REPEATS JRNL REF EMBO J. V. 21 2843 2002 JRNL REFN ISSN 0261-4189 JRNL PMID 12065398 JRNL DOI 10.1093/EMBOJ/CDF305 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 7519 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1979 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 65 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: FIRST USED REFMAC, THEN CNS REMARK 4 REMARK 4 1GY5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-APR-02. REMARK 100 THE DEPOSITION ID IS D_1290009388. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.50 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 : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7519 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 18.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.45000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 39.51000 REMARK 290 SMTRY3 2 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: PQS 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 2 REMARK 465 ASP A 3 REMARK 465 GLY A 127 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 ASP B 3 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 125 CB CG OD1 ND2 REMARK 470 HIS B 124 CG ND1 CD2 CE1 NE2 REMARK 470 ASN B 125 CG OD1 ND2 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 25 72.93 -165.61 REMARK 500 PRO A 60 40.18 -76.87 REMARK 500 ASN A 92 -127.53 46.28 REMARK 500 ASN A 94 147.26 -36.47 REMARK 500 ARG B 26 1.22 -66.09 REMARK 500 ASN B 92 -133.73 52.27 REMARK 500 ALA B 122 -144.88 -95.14 REMARK 500 ASN B 125 -10.61 59.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A2K RELATED DB: PDB REMARK 900 GDPRAN-NTF2 COMPLEX REMARK 900 RELATED ID: 1AR0 RELATED DB: PDB REMARK 900 NUCLEAR TRANSPORT FACTOR 2 (NTF2) E42K MUTANT REMARK 900 RELATED ID: 1ASK RELATED DB: PDB REMARK 900 NUCLEAR TRANSPORT FACTOR 2 (NTF2) H66A MUTANT REMARK 900 RELATED ID: 1GY6 RELATED DB: PDB REMARK 900 NTF2 FROM RAT, AMMONIUM SULPHATE CONDITIONS REMARK 900 RELATED ID: 1GY7 RELATED DB: PDB REMARK 900 N77Y POINT MUTANT OF S.CEREVISIAE NTF2 REMARK 900 RELATED ID: 1GYB RELATED DB: PDB REMARK 900 N77Y POINT MUTANT OF YNTF2 BOUND TO FXFG NUCLEOPORIN REPEAT REMARK 900 RELATED ID: 1JB2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NTF2 M84E MUTANT REMARK 900 RELATED ID: 1JB4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NTF2 M102E MUTANT REMARK 900 RELATED ID: 1JB5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NTF2 M118E MUTANT REMARK 900 RELATED ID: 1OUN RELATED DB: PDB REMARK 900 THE 1.6 A RESOLUTION CRYSTAL STRUCTURE OF NUCLEAR TRANSPORT FACTOR REMARK 900 2 (NTF2) REMARK 900 RELATED ID: 1QMA RELATED DB: PDB REMARK 900 NUCLEAR TRANSPORT FACTOR 2 (NTF2) W7A MUTANT DBREF 1GY5 A 1 127 UNP P13662 NTF2_HUMAN 1 127 DBREF 1GY5 B 1 127 UNP P13662 NTF2_HUMAN 1 127 SEQADV 1GY5 ASN A 92 UNP P13662 ASP 92 ENGINEERED MUTATION SEQADV 1GY5 ASN A 94 UNP P13662 ASP 94 ENGINEERED MUTATION SEQADV 1GY5 ASN B 92 UNP P13662 ASP 92 ENGINEERED MUTATION SEQADV 1GY5 ASN B 94 UNP P13662 ASP 94 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 ASP 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 ASN GLU ASN 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 ASP 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 ASN GLU ASN 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 *65(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 ARG B 26 1 22 HELIX 5 5 THR B 27 ALA B 31 5 5 HELIX 6 6 GLY B 48 LEU B 59 1 12 SHEET 1 AA 6 GLN A 44 GLN A 47 0 SHEET 2 AA 6 TYR A 33 TRP A 41 -1 O LEU A 39 N PHE A 46 SHEET 3 AA 6 ALA A 111 ALA A 122 1 O CYS A 114 N ILE A 34 SHEET 4 AA 6 MET A 97 ILE A 108 -1 O GLY A 98 N ALA A 122 SHEET 5 AA 6 ILE A 81 ALA A 91 -1 O ILE A 81 N LEU A 105 SHEET 6 AA 6 ILE A 64 PRO A 75 -1 O GLN A 65 N LYS A 90 SHEET 1 BA 6 GLN B 44 GLN B 47 0 SHEET 2 BA 6 TYR B 33 TRP B 41 -1 O LEU B 39 N PHE B 46 SHEET 3 BA 6 TRP B 112 LEU B 121 1 O CYS B 114 N ILE B 34 SHEET 4 BA 6 MET B 97 ASN B 107 -1 O HIS B 100 N ARG B 120 SHEET 5 BA 6 ILE B 81 ALA B 91 -1 O ILE B 81 N LEU B 105 SHEET 6 BA 6 ILE B 64 PRO B 75 -1 O GLN B 65 N LYS B 90 CRYST1 35.040 79.020 42.140 90.00 104.36 90.00 P 1 21 1 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 0.028539 0.000000 0.007306 0.00000 SCALE2 0.000000 0.012655 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024496 0.00000