HEADER PROTEIN TRANSPORT 01-JUN-01 1JB5 TITLE CRYSTAL STRUCTURE OF NTF2 M118E MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR TRANSPORT FACTOR 2; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NTF2, TRANSPORT, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR C.CHAILLAN-HUNTINGTON,P.J.BUTLER,J.A.HUNTINGTON,D.AKIN,C.FELDHERR, AUTHOR 2 M.STEWART REVDAT 5 25-OCT-23 1JB5 1 REMARK REVDAT 4 10-NOV-21 1JB5 1 SEQADV REVDAT 3 24-FEB-09 1JB5 1 VERSN REVDAT 2 25-DEC-02 1JB5 1 REMARK REVDAT 1 13-MAR-02 1JB5 0 JRNL AUTH C.CHAILLAN-HUNTINGTON,P.J.BUTLER,J.A.HUNTINGTON,D.AKIN, JRNL AUTH 2 C.FELDHERR,M.STEWART JRNL TITL NTF2 MONOMER-DIMER EQUILIBRIUM. JRNL REF J.MOL.BIOL. V. 314 465 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11846560 JRNL DOI 10.1006/JMBI.2001.5136 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : ERGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 9197 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 475 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1986 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 112 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.00 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 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.500 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 : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JB5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013576. 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 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX7.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.488 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9197 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.27200 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: AMORE REMARK 200 STARTING MODEL: 1JB4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, PH 4.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K 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 39.10500 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 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 465 GLY B 127 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 GLN A 45 CD OE1 NE2 REMARK 480 ASN A 109 CG OD1 ND2 REMARK 480 GLN B 20 CD OE1 NE2 REMARK 480 GLN B 44 CD OE1 NE2 REMARK 480 LYS B 49 CE NZ REMARK 480 LYS B 63 CD CE NZ REMARK 480 ASN B 109 CB CG OD1 ND2 REMARK 480 HIS B 124 CG ND1 CD2 CE1 NE2 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 118 O HOH A 180 2.06 REMARK 500 NE2 HIS A 100 O HOH A 180 2.11 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 ASP A 25 63.67 -154.89 REMARK 500 PHE A 61 37.61 14.77 REMARK 500 GLN A 62 37.14 -77.48 REMARK 500 LYS A 63 -10.80 174.32 REMARK 500 ASP A 92 -116.02 62.05 REMARK 500 ILE A 96 -139.96 -101.41 REMARK 500 PRO B 60 61.39 -69.60 REMARK 500 ASP B 92 -118.00 53.64 REMARK 500 ASN B 109 52.19 70.76 REMARK 500 HIS B 124 81.67 -50.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JB2 RELATED DB: PDB REMARK 900 1JB2 CONTAINS THE SAME PROTEIN M84E MUTANT REMARK 900 RELATED ID: 1JB4 RELATED DB: PDB REMARK 900 1JB4 CONTAINS THE SAME PROTEIN M102E MUTANT DBREF 1JB5 A 1 127 UNP P61972 NTF2_RAT 1 127 DBREF 1JB5 B 1 127 UNP P61972 NTF2_RAT 1 127 SEQADV 1JB5 ASN A 16 UNP P61972 GLN 16 CONFLICT SEQADV 1JB5 GLU A 118 UNP P61972 MET 118 ENGINEERED MUTATION SEQADV 1JB5 ASN B 16 UNP P61972 GLN 16 CONFLICT SEQADV 1JB5 GLU B 118 UNP P61972 MET 118 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 ASN 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 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 GLU 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 ASN 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 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 GLU PHE ARG LEU ALA LEU HIS ASN PHE GLY FORMUL 3 HOH *112(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 57 1 10 HELIX 4 4 PRO B 5 ASP B 25 1 21 HELIX 5 5 ARG B 26 ALA B 31 5 6 HELIX 6 6 GLY B 48 LEU B 59 1 12 SHEET 1 A 6 GLN A 44 GLN A 47 0 SHEET 2 A 6 TYR A 33 TRP A 41 -1 O LEU A 39 N PHE A 46 SHEET 3 A 6 ALA A 111 ALA A 122 1 O CYS A 114 N ILE A 34 SHEET 4 A 6 ASP A 94 ILE A 108 -1 O GLY A 98 N ALA A 122 SHEET 5 A 6 ILE A 81 ALA A 91 -1 O ILE A 81 N LEU A 105 SHEET 6 A 6 ILE A 64 PRO A 75 -1 O GLN A 65 N LYS A 90 SHEET 1 B 6 GLN B 44 GLN B 47 0 SHEET 2 B 6 TYR B 33 TRP B 41 -1 N LEU B 39 O PHE B 46 SHEET 3 B 6 TRP B 112 LEU B 121 1 O CYS B 114 N ILE B 34 SHEET 4 B 6 MET B 97 ASN B 107 -1 N HIS B 100 O ARG B 120 SHEET 5 B 6 ILE B 81 ALA B 91 -1 O ILE B 81 N LEU B 105 SHEET 6 B 6 ILE B 64 PRO B 75 -1 N GLN B 65 O LYS B 90 CRYST1 34.680 78.210 41.430 90.00 104.55 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 0.028835 0.000000 0.007484 0.00000 SCALE2 0.000000 0.012786 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024937 0.00000